HomeMy WebLinkAboutRI04 Shellfish_USFWS_BiOp_2016_08_26United States Department of the Interior
FISH AND WILDLIFE SERVICE
Washington Fish and Wildlife Office
510 Desmond Dr. SE, Suite 102
Lacey, Washington 98503
In Reply Refer To:
OlEWFW00-2016-F-0121
Michelle Walker
U.S. Army Corps of Engineers, Seattle District
ATTN: Regulatory Branch (Bennett)
P.O. Box 3755
Seattle, Washington 98124-3755
Dear Ms. Walker:
AUG 26 2016
This letter transmits the U. S. Fish and Wildlife Service's Biological Opinion (Opinion)
addressing the proposed Programmatic Consultation for Shellfish Activities in Washington State
Inland Marine Waters, located in portions of fourteen counties (Clallam, Grays Harbor, Island,
Jefferson, King, Kitsap, Mason, Pacific, Pierce, San Juan, Skagit, Snohomish, Thurston, and
Whatcom Counties, Washington), and its potential effects on the bull trout (Salvelinus
confluentus), designated critical habitat for the bull trout, and the marbled murrelet
Brachyramphus marmoratus). Formal consultation on the proposed action was conducted in
accordance with section 7 of the Endangered Species Act of 1973, as amended (16 U.S.C. 1531
et seq.).
Your October 30, 2015, request for formal consultation was received on November 5, 2015.
The enclosed Opinion is based on information provided in your Biological Assessment and other
sources of information cited in the Opinion. The enclosed Opinion analyzes the effects of
shellfish operations and activities in coastal bays and the inland marine waters of Washington
State over the next 20 years (2016 to 2036). A complete record of this consultation is on file at
the Washington Fish and Wildlife Office in Lacey, Washington.
Your Biological Assessment included a request for our concurrence with "not likely to adversely
affect" determination(s) for certain listed resources (western snowy plover, Charadrius nivosus
nivosus; and, designated critical habitat for the western snowy plover). The enclosed document
includes a section separate from the Opinion that addresses your concurrence request(s). The
rationale for this concurrence is included in the concurrence section.
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Michelle Walker 2
If you have any questions regarding the enclosed Opinion, our response to your concurrence
request(s), or our shared responsibilities under the Endangered Species Act, please contact Ryan
McReynolds at 360-753-6047, or Martha Jensen at 360- 753-9000.
Eric V. Rickerson, State Supervisor
Washington Fish and Wildlife Office
Enclosure( s)
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Endangered Species Act -Section 7 Consultation
BIOLOGICAL OPINION
U.S. Fish and Wildlife Service Reference:
OlEWFW00-2016-F-0121
Programmatic Consultation for Shellfish Activities in
Washington State Inland Marine Waters
Clallam, Grays Harbor, Island, Jefferson, King, Kitsap, Mason, Pacific, Pierce,
San Juan, Skagit, Snohomish, Thurston, and Whatcom Counties, Washington
Federal Action Agency:
U.S. Army Corps of Engineers -Seattle District
Consultation Conducted By:
U.S. Fish and Wildlife Service
Washington Fish and Wildlife Office
Lacey, Washington
2 ... R~~
Eric V. Rickerson, State Supervisor
Washington Fish and Wildlife Office
Date
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TABLE OF CONTENTS
INTRODUCTION ...........................................................................................................................1
CONSULTATION HISTORY ........................................................................................................1
CONCURRENCE ............................................................................................................................2
Western Snowy Plover and Western Snowy Plover Critical Habitat ......................................2
Effects of the Proposed Action ............................................................................................5
BIOLOGICAL OPINION ................................................................................................................8
DESCRIPTION OF THE PROPOSED ACTION ...........................................................................8
Ground-Based Bottom Culturing of Geoduck .......................................................................10
Ground-Based Culturing of Clams (Bottom, Bag) ................................................................16
Ground-Based Culturing of Oysters (Bottom, Rack-and-Bag, Stake, Longline) ..................21
Suspended (or Floating) Culturing of Oysters and Mussels ..................................................27
Other Related Activities .........................................................................................................29
Activities Excluded from Programmatic Coverage ...............................................................31
Conservation Measures ..........................................................................................................33
Action Area ............................................................................................................................38
ANALYTICAL FRAMEWORK FOR THE JEOPARDY AND ADVERSE
MODIFICATION DETERMINATIONS ..........................................................................42
Jeopardy Determination .........................................................................................................42
Adverse Modification Determination ....................................................................................43
STATUS OF THE SPECIES .........................................................................................................43
Bull Trout ...............................................................................................................................43
Marbled Murrelet ...................................................................................................................43
STATUS OF CRITICAL HABITAT (BULL TROUT) ................................................................44
ENVIRONMENTAL BASELINE.................................................................................................44
Active and Fallow Lands .......................................................................................................44
Willapa Bay ...........................................................................................................................45
Grays Harbor ..........................................................................................................................52
Puget Sound and Hood Canal ................................................................................................56
Current Condition in the Action Area (Bull Trout and Critical Habitat) ...............................73
Conservation Role of the Action Area (Bull Trout) ..............................................................78
Current Condition in the Action Area (Marbled Murrelet) ...................................................88
Conservation Role of the Action Area (Marbled Murrelet) ...................................................92
Climate Change ......................................................................................................................94
EFFECTS OF THE ACTION ........................................................................................................99
Introduction ............................................................................................................................99
Temporary Stressors, Resulting Exposures, and Effects .....................................................100
Physical Disturbance ........................................................................................................101
Exposures and Responses to Physical Disturbance (Bull Trout and Marbled
Murrelet) ....................................................................................................................107
Water Quality ...................................................................................................................107
Exposures and Responses to Water Quality (Bull Trout and Marbled Murrelet)......110
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Sound and Visual Disturbance .........................................................................................112
Exposures and Responses to Sound and Visual Disturbance (Bull Trout and
Murrelet) ....................................................................................................................113
Intentional Hazing of Wildlife .........................................................................................116
Exposures and Responses to Intentional Hazing (Bull Trout and Marbled
Murrelet) ....................................................................................................................118
Physical Entrapment and Stranding .................................................................................119
Risk of Exposure to Physical Entrapment and Stranding (Bull Trout and
Murrelet) ....................................................................................................................129
Persistent Stressors, Long Duration or Long-Term Exposures, and Effects .......................131
Effects to Ecosystem Services, including Water Quality ................................................132
Effects to Substrates and Sediment ............................................................................141
Effects to Eelgrass, Kelp, and Submerged Aquatic Vegetation .................................146
Effects to Benthic/Epibenthic Community Structure and Composition ....................157
Effects to Predator-Prey Dynamics and Productivity (Prey-Mediated Effects) ........168
Exposures and Responses to Persistent Stressors (Bull Trout and Murrelet) ............183
Effects of Interrelated and Interdependent Actions .............................................................189
Effects to the PCEs of Designated Bull Trout Critical Habitat ...........................................189
CUMULATIVE EFFECTS .........................................................................................................197
INTEGRATION AND SYNTHESIS OF EFFECTS (BULL TROUT) ......................................199
INTEGRATION AND SYNTHESIS OF EFFECTS (MARBLED MURRELET) .....................202
CONCLUSION (BULL TROUT AND DESIGNATED CRITICAL HABITAT) .....................204
CONCLUSION (MARBLED MURRELET) ..............................................................................204
INCIDENTAL TAKE STATEMENT .........................................................................................205
AMOUNT OR EXTENT OF TAKE ...........................................................................................205
EFFECT OF THE TAKE.............................................................................................................206
REASONABLE AND PRUDENT MEASURES ........................................................................206
TERMS AND CONDITIONS .....................................................................................................207
CONSERVATION RECOMMENDATIONS .............................................................................207
REINITIATION NOTICE ...........................................................................................................209
LITERATURE CITED ................................................................................................................210
APPENDICES
Appendix A Status of the Species: Bull Trout
Appendix B Status of the Species: Marbled Murrelet
Appendix C Status of Designated Critical Habitat for the Bull Trout
Appendix D Excerpts from Cited Literature
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FIGURES
Figure 1. Washington tidelands, coastal bays, and inland marine waters.......................................9
Figure 2. A Floating Upwelling System, or FLUPSY. .................................................................12
Figure 3. Geoduck tubes. ..............................................................................................................13
Figure 4. Anti-predator cover nets placed over a field of geoduck tubes .....................................13
Figure 5. Common clam aquaculture net mesh sizes ....................................................................14
Figure 6. Geoduck net tunnels over rebar frames (Corps 2015, p. 32). ........................................15
Figure 7. Graveling (frosting) over a clam bed.............................................................................18
Figure 8. Manila clam bags placed on an exposed intertidal bed .................................................18
Figure 9. Mechanical clam harvester ............................................................................................20
Figure 10. Hydraulic escalator ......................................................................................................20
Figure 11. Bundled oyster cultch stacked on pallets.....................................................................22
Figure 12. Oyster tumble bags ......................................................................................................24
Figure 13. Oyster longlines ...........................................................................................................24
Figure 14. Hand harvest of bottom cultured oysters .....................................................................26
Figure 15. Oyster dredge with boom cranes and bags ..................................................................26
Figure 16. A typical mussel raft ....................................................................................................28
Figure 17. Annual spawning biomass for Grays Harbor herring stocks .......................................48
Figure 18. Annual spawning biomass for Willapa Bay herring stocks.........................................49
Figure 19. Shellfish operations and eelgrass in Willapa Bay .......................................................50
Figure 20. Shellfish operations and forage fish in Willapa Bay ...................................................51
Figure 21. Shellfish operations and eelgrass in Grays Harbor......................................................54
Figure 22. Shellfish operations and forage fish in Grays Harbor .................................................55
Figure 23. Increases and decreases in native seagrass area based on all available data for
each site (2003-2013) ............................................................................................................58
Figure 24. Increases and decreases in native seagrass area based on all available data for
each site (2010-2013) ............................................................................................................59
Figure 25. Documented Pacific herring spawning areas in Puget Sound .....................................61
Figure 26. Shellfish operations and eelgrass in north Puget Sound ..............................................66
Figure 27. Shellfish operations and eelgrass in north Puget Sound ..............................................67
Figure 28. Shellfish operations and forage fish in north Puget Sound .........................................67
Figure 29. Shellfish operations and forage fish in north Puget Sound .........................................68
Figure 30. Shellfish operations and eelgrass in south Puget Sound .............................................69
Figure 31. Shellfish operations and forage fish in south Puget Sound .........................................70
Figure 32. Shellfish operations and eelgrass in Hood Canal ........................................................71
Figure 33. Shellfish operations and forage fish in Hood Canal ....................................................72
Figure 34. Bull trout recovery units ..............................................................................................80
Figure 35. Map of the Coastal Recovery Unit and core areas ......................................................82
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Figure 36. Climate-dependent changes in the California Current ................................................98
Figure 37. Development of organism-sediment relationships over time following
disturbance ..........................................................................................................................105
Figure 38. Unsecured culturing equipment; Squamish Harbor, Hood Canal .............................121
Figure 39. Image of a “Clam Net Hotline” newspaper ...............................................................121
Figure 40. Juvenile bald eagle caught in anti-predator net on Harstene Island, Washington .....124
Figure 41. Marine forage fish entrapped in anti-predator netting ...............................................125
Figure 42. Incremental increase in phytoplankton depletion predicted for the proposed
north Totten Inlet mussel rafts ............................................................................................140
Figure 43. Diagrammatic representation of the interim or temporal loss of ecosystem
services (Fonseca et al. 1998, p. 68) ...................................................................................151
Figure 44. The eelgrass meadow; a world of microhabitats .......................................................170
Figure 45. Functional groups with the greatest change in relative biomass ...............................183
TABLES
Table 1. Activities excluded from programmatic coverage ..........................................................32
Table 2. Summary information describing the geographic distribution and spatial extent of
shellfish activities in Washington State. ...............................................................................41
Table 3. Summary information describing subtidal wild geoduck harvest in Washington
State.......................................................................................................................................42
Table 4. Designated bull trout critical habitat within the action area; co-location with
mapped eelgrass and marine forage fish habitat. ..................................................................77
Table 5. Shared FMO habitat in the Coastal Recovery Unit (USFWS 2015a, p. 79)...................83
Table 6. Marbled murrelet population estimates and densities in Conservation Zone 2 from
2001 to 2015 .........................................................................................................................89
Table 7. Marbled murrelet population estimates and densities in Conservation Zone 1 from
2001 to 2015. ........................................................................................................................91
Table 8. Likely physical extent of potential impacts to submerged aquatic vegetation .............156
Table 9. Likely physical extent of potential impacts to marine forage fish spawning areas. .....177
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ACRONYMS AND ABBREVIATIONS
APN anti-predator netting
ATV All-terrian vehicle
BA Biological Assessment
BOD biochemical oxygen demand
CFR Code of Federal Regulations
Corps U.S. Army Corps of Engineers
dB Decibel
DNR Washington State Department of Natural Resources
DO dissolved oxygen
Ecology Washington State Department of Ecology
ESA Endangered Species Act of 1973, as amended (16 U.S.C. l531 et seq.)
FLUPSY Floating Upwelling System
FMO Foraging, Migrating and Overwintering
FR Federal Register
GIS Geographic Information System
HCP Habitat Conservation Plan
km2 square kilometers
MBTA Migratory Bird Treaty Act
MHHW Mean Higher High Water
MLLW Mean Lower Low Water
NMFS National Marine Fisheries Service
NWFPEM Northwest Forest Plan Effectiveness Monitoring Plan
Opinion Biological Opinion
PAHs Polycyclic Aromatic Hydrocarbons
PCBs Polychlorinated Biphenyls
PCE Primary Constituent Element
PCSGA Pacific Coast Shellfish Growers Association
PSAMP Puget Sound Ambient Monitoring Program
PVC polyvinyl chloride
RUIP Recovery Unit Implementation Plan
Service U.S. Fish and Wildlife Service
Services U.S. Fish and Wildlife Service and National Marine Fisheries Service
SLOPES Standard Local Operating Procedures
SPM solid particulate matter
TMDL Total Maximum Daily Load
TS Threshold Shift
TSS total suspended solids
WDFW Washington State Department of Fish and Wildlife
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INTRODUCTION
This document represents the U. S. Fish and Wildlife Service’s (Service) Biological Opinion
Opinion) based on our review of the proposed Programmatic Consultation for Shellfish
Activities in Washington State Inland Marine Waters, located in portions of fourteen counties
Clallam, Grays Harbor, Island, Jefferson, King, Kitsap, Mason, Pacific, Pierce, San Juan,
Skagit, Snohomish, Thurston, and Whatcom Counties, Washington), and its potential effects on
the bull trout (Salvelinus confluentus), designated bull trout critical habitat, and the marbled
murrelet (Brachyramphus marmoratus), in accordance with section 7 of the Endangered Species
Act of 1973, as amended (16 U.S.C. 1531 et seq.)(ESA).
The U.S. Army Corps of Engineers, Seattle District (Corps) submitted a September 12, 2014,
request for formal consultation, which was received on September 15, 2014. A revised
Biological Assessment (BA), dated December 29, 2014, was received on December 30, 2014.
On April 27, 2015, the Service met with the Corps and National Marine Fisheries Service
NMFS) to discuss unresolved questions about the proposed action, including implementation of
the proposed conservation measures, and several related issues and concerns voiced by Tribal
and Native American Indian Nations, representatives of the shellfish industry in Washington, and
the general public. On June 8, 2015, the Corps provided notice to the U.S. Fish and Wildlife
Service and National Marine Fisheries Service (collectively, the Services) that it intended to
review and revise the previously submitted BA.
On November 5, 2015, the Corps submitted a final revised BA and new request for formal
consultation (dated October 30, 2015). The enclosed Opinion is based on information provided
in the final revised BA (dated October 30, 2015), and other sources of information cited in the
Opinion. A complete record of this consultation is on file at the Washington Fish and Wildlife
Office in Lacey, Washington.
The Corps made “no effect” determinations for additional species and critical habitat that are
known to occur in Clallam, Grays Harbor, Island, Jefferson, King, Kitsap, Mason, Pacific,
Pierce, San Juan, Skagit, Snohomish, Thurston, and Whatcom Counties. Your determinations
that the action will have no effect on these listed species and critical habitat rest with the federal
action agency. The Service has no regulatory or statutory authority for concurring with “no
effect” determinations, and no consultation with the Service is required. We recommend that the
Corps document their analyses and maintain that documentation as part of their files.
CONSULTATION HISTORY
The following is a summary of important events associated with this consultation:
The Corps submitted a BA and initial request for consultation on September 15, 2014.
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On October 27, 2014, the Services received a letter from the Pacific Coast Shellfish
Growers Association providing written comments and suggestions regarding the Corps’
regional, special permit conditions for shellfish activities (Plauche’ and Carr 2014).
The Corps submitted a revised BA on December 30, 2014.
During March 2015, the Service received copies of two letters sent to the Corps by the
Pacific Coast Shellfish Growers Association (PCSGA 2015) and Washington State’s
Congressional Delegation (U.S. Congress, House of Representatives, 6th District,
Washington 2015).
On June 8, 2015, the Corps provided notice to the Services that it intended to review and
revise the previously submitted BA; the consultation was put on hold.
The Corps submitted a final revised BA and new request for formal consultation on
November 5, 2015. Formal consultation on the proposed action was initiated on
November 5, 2015.
A copy of the draft Opinion was provided to the Corps on May 13, 2016.
Comments for the draft Opinion were received from the Corps on June 20, 2016.
The Corps and Service corresponded via email (on July 28 and August 17, 2016)
regarding implementation of the programmatic.
CONCURRENCE
Western Snowy Plover and Western Snowy Plover Critical Habitat
The western snowy plover (Charadrius nivosus nivosus) is a small shorebird, about 6 inches
long, with a thin dark bill, pale brown to gray upper parts, white or light belly, darker patches on
its shoulders and head, white forehead and supercilium (eyebrow line). Their dark gray or black
legs are useful characteristics when comparing them to other plover species (Page et al. 1995a).
The Pacific Coast population of the western snowy plover is defined as those individuals that
nest adjacent to tidal waters of the Pacific Ocean, and includes all nesting birds on the mainland
coast, peninsulas, offshore islands, adjacent bays, estuaries, and coastal rivers (USFWS 2004a,b).
The breeding range of this population extends from the south-central Washington coast to Bahia
Magdalena, Baja California, Mexico (USFWS 2004a,b). Western snowy plovers that nest at
inland sites are not considered part of the Pacific Coast population, although a few individuals
may migrate to coastal areas during the winter months.
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The Pacific Coast population of the western snowy plover was listed as threatened on March 5,
1993. Primary threats that warranted listing include loss and modification of habitat resulting
from European beach grass (Ammophila arenaria) encroachment, shoreline stabilization and
development, human disturbance (including recreational activities), and predation exacerbated
by development and human activities. On September 24, 2007, the Service published a final
recovery plan for the Pacific Coast population of the western snowy plover.
The Service has also published a final rule designating critical habitat for the western snowy
plover (77 FR 36727; June 19, 2012). The designation includes 60 units totaling 24,526 acres
along the coasts of California, Oregon, and Washington. Recovery Unit 1 includes four units in
Washington and nine units in Oregon. The four units in Washington are: WA 1 Copalis Spit
407 acres), WA 2 Damon Point (673 acres), WA 3 Midway Beach (697 acres) and
Shoalwater/Graveyard Spit (696 acres), and WA 4 Leadbetter Spit (2,700 acres) and Gunpowder
Sands Island (904 acres).
The Corps issues permits and permit verifications authorizing shellfish activities on the tidelands
and in the inland marine waters of the State of Washington. While they may be issued for a
variety of purposes (i.e., commercial aquaculture, tribal and commercial wildstock harvest,
recreational enhancement, and restoration), the majority of these permits and permit verifications
both by number and acreage) are issued to parties engaged in commercial aquaculture (i.e.,
farming and production of shellfish for human consumption)(Corps 2015, pp. 40-49). Issuance
of permits and permit verifications establishes a nexus requiring consultation under section
7(a)(2) of the ESA.
Shellfish culturing activities and practices are diverse (Corps 2015, pp. 11-38):
The culturing of mussels and oysters suspended from floating rafts or longlines.
Ground-based bottom culturing of oysters and clams, including geoduck clams (Panopea
generosa).
Ground-based rack-and-bag, stake, and longline culturing of oysters. And,
Ground-based bag culturing of clams.
Most shellfish culturing and harvest methods, practices, and techniques are used to some extent
across portions of each geographic sub-area (Willapa Bay, Grays Harbor, Hood Canal, south and
north Puget Sound), and many farm operators culture multiple species using a variety of
practices and techniques. Although shellfish activities are not always conducted for the purposes
of commercial aquaculture, the industry’s methods, practices, and techniques are also fairly
typical of those used in support of wildstock harvest, recreational enhancement, and restoration.
When viewed from a landscape perspective, shellfish activities are variable in density and
spatially discontinuous. At some locations, cultured tidelands extend with only occasional
interruption along extended lengths of the nearshore. At other locations, cultured tidelands are
interspersed along shorelines that support a range of other uses (residential, recreational, etc.).
Where cultured tidelands extend with only occasional interruption, interspersed uncultured areas
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may experience direct or indirect effects, and are therefore considered part of the action area.
Regulated shellfish activities in Washington State, specifically those for which this Opinion
provides programmatic coverage, are likely to directly or indirectly affect more than 45,000
acres of nearshore marine habitat (45,000 to 50,000 acres in total; Willapa Bay: approx. 30,000
acres; Grays Harbor: approx. 4,000 acres; north Puget Sound: approx. 5,000 acres; south Puget
Sound: approx. 5,000 acres; and, Hood Canal: approx. 3,000 acres). Regulated shellfish
activities in Washington State also include subtidal wild geoduck harvest (a maximum of 6,050
acres per year in Hood Canal and Puget Sound).
The action area includes approximately 34,000 acres of tidelands located in Willapa Bay and
Grays Harbor. As working tidelands, where shellfish activities have for many years and will
continue to affect habitat conditions, most of the action area cannot be regarded as pristine in its
current state. Also, at some locations this habitat exhibits the effects of shoreline development
and alteration. Armored and hardened shorelines, marine and estuarine fill, and navigational
features are characteristic of the action area. At some locations these features impair important
natural processes that create and maintain functional western snowy plover habitat.
Shellfish culturing and harvesting activities have direct and indirect effects to nearshore marine
habitat structure, function, and productivity. These effects may have significance for how well
these habitats support the essential behaviors and needs of listed species, including the western
snowy plover.
Shellfish activities result in temporary elevated sound levels and visual disturbance. Most
shellfish activities associated with ground-based culturing are conducted as bouts of intermittent
activity, with each bout lasting a few hours. While some activities (e.g., frosting or graveling,
mechanical harrowing, mechanical harvest, dive-harvest, and suspended culturing techniques)
may be relieved or partially relieved of strict timing constraints, many still target specific tidal
elevations and therefore proceed as bouts of intermittent activity. Effects to the sound and visual
environment are temporal and limited in both physical extent and duration.
Shellfish culturing and harvesting activities result in measurable, temporary impacts to water
quality. Where these temporary impacts to water quality are concerned, our primary focus is on
four biologically and behaviorally relevant water quality parameters: turbidity, dissolved oxygen
DO), biological oxygen demand (BOD), and nutrients (e.g., nitrogen and ammonium).
ENVIRON International Corp. (2011, p. 41) has observed that water quality conditions typically
reflect the pervasive influence of oceanic conditions, residence time, and other human activities
in these same nearshore environments and watersheds. Forrest et al. (2009, p. 5) have observed,
the potential for adverse water quality-related effects … is low, which is perhaps not
surprising considering that intertidal farm sites are substantially or completely flushed on every
tidal cycle.” Temporary impacts to water quality are localized, limited in physical extent, and
low intensity.
Bivalves and other filter-feeding shellfish, whether occurring naturally or in farmed/cultured
settings, provide important benefits in the form of ecosystem services. The Service expects that
shellfish activities will generally, and in the majority of cases, provide long-term benefits in the
form of improved water quality and sequestration of carbon and nutrients. These ecosystem
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services may be important as a means to control and prevent the effects of excess nutrient
additions occurring elsewhere in the contributing watersheds and may lessen or counteract the
potential for climate-induced ocean acidification and hypoxia.
Interactions between benthic/epibenthic communities and shellfish activities are complex and not
easily characterized with simple generalizations. Culturing equipment and materials placed on
and over the bed (including nets, bags, racks, stakes, longlines, and tubes), and the intensively
cultured shellfish (many of which are non-native species), modify habitat and may create new
habitat types (or habitat variants). The benthic community interacts with, and is influenced by,
equipment and materials placed on and over the bed, currents, wave action, patterns of sediment
transport, and the intensively cultured shellfish. Over the long-term (i.e., “grow-out” and cycles
of production), benthic community structure and composition may be strongly influenced by
these interactions.
Interactions between submerged aquatic vegetation, such as native eelgrass (Zostera marina) or
rooted kelp (attached brown algae in the order Laminariales), and shellfish activities are complex
and not easily characterized with simple generalizations. These interactions include competition
for space, competition for light (or shading), and physical damage that results from some
activities, practices, and techniques. However, not all of these interactions are detrimental to the
health of native eelgrass and rooted kelp. For instance, shellfish culturing provides a source of
nutrient enhancement, which supports plant growth and vigor, and frequently improves water
quality. The variety of factors influencing eelgrass recovery suggests the potential for significant
site-by-site and temporal variability. Culturing methods and techniques have variable effects to
patterns of eelgrass disturbance, recovery, and persistence, but the majority of these temporal
impacts are not likely to be persistent at the estuarine landscape scale.
Regulated shellfish activities occur in the vicinity of designated western snowy plover critical
habitat, but are generally located at a distance of at least one mile. The Corps has stated that
no activity would occur within 0.25 mile of … critical habitat” (Corps 2015, p. 120). The
Corps has included a total of 28 conservation measures as elements of their proposed action
Corps 2015, pp. 49-53). Permits and permit verifications issued by the Corps will incorporate
these measures as enforceable terms and conditions.
Effects of the Proposed Action
Willapa Bay is protected from the Pacific Ocean by Long Beach Peninsula, a long barrier spit.
Shellfish activities are located within the bay (east of the Long Beach Peninsula), while known
western snowy plover nesting areas and designated critical habitat are located west (i.e., on the
ocean side) of the spit. In Grays Harbor, known western snowy plover nesting areas and
designated critical habitat are located on protected state-owned lands (i.e., designated wildlife
areas and natural area preserves). The exposed intertidal zones (sand and mudflat) and
ephemeral sand spits present in both Willapa Bay and Grays Harbor provide suitable foraging
habitats. Therefore, there is a limited potential for foraging western snowy plovers to be exposed
to shellfish culturing and harvesting activities.
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Although the Corps has included a number of conservation measures addressing the security of
culturing equipment (Corps 2015, pp. 49-53) and many growers and farm operators invest
significant time and resources to prevent the loss of culturing equipment, equipment such as nets
and tubes occasionally become dislodged and moved from farmed areas by wind and waves.
However, because regulated shellfish activities are located some distance from the beaches, spits,
and islands used intensively by western snowy plovers, and there is little overlap between
shellfish culturing and harvesting activities and suitable western snowy plover nesting and
foraging habitat, the Service expects that few, if any, western snowy plovers will be directly
exposed to shellfish activities. Also, to our knowledge, there have been no reported instances of
western snowy plovers becoming entrapped or entangled in shellfish culturing equipment, and
the foraging behaviors of this species make it extremely unlikely that individuals would become
entrapped or entangled in culturing equipment or gear. The Service concludes that the potential
for western snowy plover injury or mortality is discountable.
The Service concludes that the proposed action, consisting of the issuance of Corps permits and
permit verifications for the operation of existing and proposed new shellfish activities and farms,
will have no measurable adverse effects to the western snowy plover, its habitat, or prey
resources. The distances to suitable nesting habitats (i.e., generally, if not always, a distance of
at least one mile and often separated by land) should preclude any adverse effects to nesting
individuals, their nests, or young. The proposed action will not damage, degrade, or disturb
suitable habitats located above the high tide line, will not degrade or impair the function of
suitable foraging habitats, or measurably reduce the availability of cover or essential sources of
food. The Service concludes that shellfish culturing and harvesting activities will not result in a
significant disruption of normal western snowy plover behaviors (i.e., the ability to successfully
feed, move, and/or shelter). With successful implementation of the proposed conservation
measures, the Service concludes that the foreseeable direct and indirect effects to individual
western snowy plovers, their habitat, and prey resources are insignificant.
The primary constituent elements (PCEs) of designated western snowy plover critical habitat
i.e., the physical and biological features essential for conservation of the species) include:
1. Areas that are below heavily vegetated areas or developed areas and above the daily high
tides;
2. Shoreline habitat areas for feeding, with no or very sparse vegetation, that are between
the annual low tide or low water flow and annual high tide or high water flow, subject to
inundation but not constantly under water, that support small invertebrates, such as crabs,
worms, flies, beetles, spiders, sand hoppers, clams, and ostracods, and other essential
food sources;
3. Surf- or water-deposited organic debris, such as seaweed (including kelp and eelgrass) or
driftwood located on open substrates that supports and attracts small invertebrates
described in PCE #2 for food, and provides cover or shelter from predators and weather,
and assists in avoidance of detection (crypsis) for nests, chicks, and incubating adults;
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4. Minimal disturbance from the presence of humans, pets, vehicles, or human-attracted
predators, which provide relatively undisturbed areas for individual and population
growth and for normal behavior.
Note: New critical habitat regulations (81 FR 7214; February 11, 2016) use physical or
biological features (PBFs) rather than PCEs. The shift in terminology does not change the
approach used in conducting a “destruction or adverse modification” analysis, which is the same
regardless of whether the original designation identified PCEs, PBFs, or essential features.
References here to PCEs should be viewed as synonymous with PBFs.]
None of the continuing shellfish activities and farms are located within designated critical habitat
for the western snowy plover. It is extremely unlikely that proposed new shellfish activities and
farms would be located in designated critical habitat.The proposed action will not damage,
degrade, or disturb suitable habitats located above the high tide line, will not degrade or impair
the function of suitable foraging habitats, or measurably reduce the availability of cover or
essential sources of food. The distances to suitable nesting habitats and designated critical
habitat (i.e., generally, if not always, a distance of at least one mile and often separated by land)
should preclude any measurable effects. With successful implementation of the proposed
conservation measures, the Service concludes that shellfish culturing and harvesting activities
will not measurably degrade or impair the current function of the PCEs. Foreseeable direct and
indirect effects to the PCEs of designated western snowy plover critical habitat are therefore
considered insignificant.
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BIOLOGICAL OPINION
DESCRIPTION OF THE PROPOSED ACTION
A federal action means all activities or programs of any kind authorized, funded, or carried out,
in whole or in part, by federal agencies in the United States or upon the high seas (50 CFR
402.02).
This Biological Opinion (Opinion) addresses permits and permit verifications issued by the U.S.
Army Corps of Engineers, Seattle District (Corps), for shellfish activities conducted on the
tidelands and in the inland marine waters of the State of Washington. The Corps issues permits
and permit verifications, under Section 404 of the Clean Water Act and Section 10 of the Rivers
and Harbors Act, authorizing shellfish activities for the purposes of commercial aquaculture
i.e., farming and production of shellfish for human consumption), wildstock harvest, recreation,
and restoration. This Opinion analyzes the effects of shellfish operations and activities in
coastal bays and the inland marine waters of Washington State over the next 20 years (2016 to
2036).
Issuance of permits and permit verifications establishes a nexus requiring consultation under
section 7(a)(2) of the Endangered Species Act of 1973, as amended (16 U.S.C. 1531 et
seq.)(ESA). This Opinion addresses the Corps’ shellfish permits and permit verifications, and
related or resulting potential effects to ESA-listed species and designated critical habitat that are
under the jurisdiction of the U.S. Fish and Wildlife Service (Service).
The Corps issues permits and permit verifications authorizing shellfish activities on the tidelands
and in the inland marine waters of the State of Washington. While they may be issued for a
variety of purposes (i.e., commercial aquaculture, tribal and commercial wildstock harvest,
recreational enhancement, and restoration), the vast majority of these permits and permit
verifications (both by number and acreage) are issued to parties engaged in commercial
aquaculture (i.e., farming and production of shellfish for human consumption)(Corps 2015, pp.
40-49).
Historically, commercial shellfish aquaculture has been important to both the state and regional
economies. This importance continues today, and the industry is both well established and
diversified. Commercial aquaculture farms operating on the Washington coast (Willapa Bay,
Grays Harbor), in Hood Canal, and the Puget Sound (Figure 1) culture and harvest more than a
dozen commercially viable varieties of clams, oysters, and mussels.
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Figure 1. Washington tidelands, coastal bays, and inland marine waters.
Corps 2015, p. 10)
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Shellfish culturing activities and practices are correspondingly diverse and include (Corps 2015
pp. 11-38):
The culturing of mussels and oysters suspended from floating rafts or longlines.
Ground-based bottom culturing of oysters and clams, including geoduck clams (Panopea
generosa).
Ground-based rack-and-bag, stake, and longline culturing of oysters. And,
Ground-based bag culturing of clams.
Farm operators generally choose to culture those species, and generally choose to select from
those culturing methods or practices, that are best suited to the tidal elevations, substrates, and
other physical and biological conditions or factors found at specific sites (e.g., exposure to
prevailing wind and wave action, predation pressure). Market conditions and the desired
marketable product are also important considerations. Some shellfish culturing activities and
practices are better established, better suited and more profitable, in one or another geographic
locality. For example, across Washington’s marine waters, intertidal geoduck culturing and
harvest is concentrated on the suitable mud- and sand-dominated tidelands of the south Puget
Sound (Corps 2015, p. 45).
However, most shellfish culturing and harvest methods, practices, and techniques are used to
some extent across portions of each geographic locality (Willapa Bay, Grays Harbor, Hood
Canal, south and north Puget Sound), and many farm operators culture multiple species using a
variety of practices and techniques. Although shellfish activities are not always conducted for
the purposes of commercial aquaculture, the industry’s methods, practices, and techniques are
also fairly typical of those used in support of wildstock harvest, recreation, and restoration.
The sub-sections that follow describe sequentially: ground-based bottom culturing of geoduck
clams; ground-based culturing of clams (bottom, bag); ground-based culturing of oysters
bottom, rack-and-bag, stake, longline); and suspended culturing of oysters and mussels. Each
briefly describes hatchery and nursery operations, site/bed preparation, seeding or planting,
maintenance, and harvest. For a fuller description of these methods, practices, and techniques,
the reader is referred to documentation prepared by the Corps (Corps 2015, pp. 11-38).
Ground-Based Bottom Culturing of Geoduck
The Pacific geoduck is a large native clam found in soft intertidal and subtidal substrates from
California to Alaska, to depths of more than 60 meters (Goodwin 1976 in Straus et al. 2013, p.
1). Lucrative commercial geoduck fisheries exist in Washington and Alaska, British Columbia,
and Baja California (Hoffmann et al. 2000 and Aragon-Noriega et al. 2012 in Straus et al. 2013,
p. 1). In Washington, geoduck are typically cultured on intertidal beds, from +5.0 to -4.5 mean
lower low water (MLLW)(Corps 2015, p. 30). For a full description of the life history,
reproduction, distribution, and habitat of this species, the reader is referred to an available
Washington Sea Grant publication (Straus et al. 2013, pp. 1-5).
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Hatchery and Nursery Operations
Hatcheries are typically corporate and off-site, serving many customers. They are often located
in the uplands and their operations do not require a Corps permit. Shellfish seed is grown and
matured in hatcheries to a size where it is less vulnerable to either predation or desiccation,
before being outplanted. Operation of upland hatcheries is not part of the Corps’ proposed
action.
Floating Upwelling Systems, or FLUPSYs as they are commonly called (Figure 2), provide a
means for maturing large quantities of seed (Corps 2015, p. 16). FLUPSYs are typically placed
in the lower intertidal or shallow subtidal zones. Seed is placed in bins with screened bottoms,
lowered into openings in a floating frame, and suspended in the water column. A paddle wheel
or pump continuously draws seawater through the system, feeding the shellfish seed, and
flushing feces and pseudofeces. FLUPSY floating platforms are typically equipped with
overhead hoists and, because they also typically require a source of electrical power, they are
commonly positioned next to a dock or pier (Corps 2015, p. 16).
Once purchased by a grower/farm operator, seed is often allowed to further mature before being
outplanted. Some growers use upland tanks for this purpose, while others use elevated trays or
bins, placed on and above the intertidal substrates of their farm footprint (Corps 2015, p. 15).
These trays, bins, and racks are typically composed of plastic, angle iron, and/or rebar; wood and
plywood materials are less commonly used. “Seed boosting” on the intertidal bed is a
widespread and well-established practice, and is typical of many or most farms that practice
ground-based shellfish culturing.
Site/Bed Preparation
Preparation of a geoduck bed or farm plot typically includes the following activities: pre-harvest
of marketable product; removal or relocation of coarse wood, unrooted algae (e.g., sea lettuce,
Ulva lactuca), and native and non-native shellfish predators; and, hand raking (Corps 2015, p.
30). Some growers/farm operators may use a mechanical harrow, often pulled on the exposed
intertidal bed with a small tractor or all-terrain vehicle (ATV), to remove marketable product
e.g., pre-harvest of clams). Leveling and harrowing of the bed may in some instances result in
measurable impacts to submerged aquatic vegetation, including native eelgrass and/or rooted
kelp.
Native shellfish predators, which are sometimes actively removed from farm plots, include moon
snails (Polinices lewisii), sea stars (Pisaster brevispinus and Pycnopodia helianthoides), and
sand dollars (Clypeasteroida), including the eccentric sand dollar or sea-cake (Dendraster
excentricus). The non-native eastern oyster drill (Urosalpinx cinerea) and Japanese oyster drill
Ocinebrellus inornatus) are not typically a problem for cultured geoduck, but are commonly
removed from oyster beds.
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Figure 2. A Floating Upwelling System, or FLUPSY.
Corps 2015, p. 16)
A mechanical harrow is a skidder with many tines, towed along and through the shallow surface
of the substrate. The harrow’s tines penetrate the substrate a few inches, break up oyster
clusters, and move clams and oysters upward toward the surface (Corps 2015, p. 17).
Mechanical harrowing typically plays a small role in preparing some cultured geoduck beds, but
plays a significant role on many farms that practice ground-based clam and oyster culturing.
Seeding or Planting
Until more fully matured and embedded in the substrate, geoduck seed is vulnerable to both
predation and desiccation. The geoduck culturing practices and techniques that are in widest use
employ tubes and nets placed on the intertidal bed to prevent and minimize losses of seed and
immature clams.
The most common method uses inert (i.e., chemically inactive) 6-inch diameter by 9-inch long
polyvinyl chloride (PVC) pipe; exact dimensions vary (Corps 2015, p. 30). The pipe sections, or
tubes, are typically inserted in the substrate by hand, at low tide. Tubes are typically installed at
a density of approximately 1 tube per square foot, or about 42,000 tubes per acre (Figure 3).
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Two to four geoduck seeds are placed in each tube, and the top of each tube is often covered with
a small, plastic mesh covering, which is secured with a rubber band. Some growers have begun
to use flexible net tubes (composed of Vexar®) instead of PVC pipe (Corps 2015, p. 30). Many,
perhaps most, geoduck growers/farm operators also install large, anti-predator, cover nets over
the field of tubes (Figure 4).
Figure 3. Geoduck tubes.
Corps 2015, p. 31)
Figure 4. Anti-predator cover nets placed over a field of geoduck tubes
Corps 2015, p. 32)
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Anti-predator, cover nets may be composed of either plastic or organic fibers, and are typically
anchored at the periphery with embedded rebar or metal staking. Cover nets minimize predation
losses, but also serve to prevent tubes from becoming dislodged under wind and wave action,
and keep dislodged tubes on the farm plot (Corps 2015, p. 30). Anti-predator, cover and
exclusion nets are available from a variety of commercial sources, in varying mesh size and
dimensions (Washington Sea Grant 2005, pp. 10, 17). Mesh size varies by application and/or
preference, typically ranging from ¼ x ¼ inch to ¾ x ¾ inch or larger (Figure 5).
Figure 5. Common clam aquaculture net mesh sizes
InterNet® Inc., 2004 in Ayers 2006, p. 5)
Another method being used to exclude predators on cultured geoduck beds. “Net tunnels” are
composed of narrow and long polyethylene nets, placed over a rebar frame (Corps 2015, p. 30).
The edges of the tunnels are embedded in the substrate and anchored. The mesh opening is
typically either 1/4-inch or 3/8-inch, and the typically 24-inch to 48-inch wide net is held a few
inches above the substrate by the rebar frame (Figure 6).
Maintenance
Geoduck farm plots are patrolled by crews on a regular basis. Cover nets and net tunnels may
become fouled with algae and other organisms (especially during warmer summer months), and
are therefore typically removed and/or cleaned with some frequency. Nets may be taken to an
upland location for drying and cleaning, or (less commonly) fouling organisms may be removed
from the nets while they remain in place (Corps 2015, p. 33).
Geoduck tubes and nets are typically removed after one or two growing seasons, after the young
clams have buried themselves to a depth sufficient to evade predators (approximately 14 inches).
Used tubes and nets are dried, cleaned, and re-used. Worn-out tubes and nets are handled as
waste, and are disposed of at appropriate upland facilities and locations.
The Corps commonly requires that (Corps 2015, p. 51): “All tubes, mesh bags, and area nets
shall be clearly, indelibly, and permanently marked to identify the permittee name and contact
information (e.g., telephone number, email address, mailing address). On nets, identification
markers shall be placed with a minimum of one identification marker for each 50 ft of net.”
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Figure 6. Geoduck net tunnels over rebar frames (Corps 2015, p. 32).
Harvest
Cultured geoduck clams are typically harvested 4 to 7 years after planting, when individuals
reach approximately 2 pounds in weight. Geoduck clams are harvested from intertidal beds at
low tide (“beach harvest”), or by divers at middle or high tides from intertidal and subtidal beds
dive harvest”)(Corps 2015, p. 33). In either case, the clams are typically harvested using hand-
operated water jet probes. Seawater pumped at a pressure of approximately 40 pounds per
square inch, and 20 gallons per minute, is injected at the vicinity of each harvestable geoduck,
liquefying the substrate and allowing extraction of the clam by hand.
Geoduck harvesting occurs year-round and is not limited by tidal height. However, dive
harvesting tends to be the dominant method during winter months (November through February),
due to the prevalence of high daytime tides and absence of suitable low tides for daytime beach
harvests (Corps 2015, p. 33). Because market conditions for geoduck clams are most favorable
during the winter months, dive harvests probably account for 75 percent or more of the total
geoduck harvest effort. A dive harvest is typically supplemented with a follow-up beach harvest,
and both dive and beach harvests are conducted by most growers. Farm operators typically make
several sweeps of the geoduck bed to ensure that all marketable geoduck clams are removed
before the bed is prepared for a new crop.
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Subtidal Wild Geoduck Harvest
The Corps’ BA also describes subtidal wild geoduck harvest (Corps 2015, pp. 3, 5, 30, 34, 46,
47, 80, 84, 89, 92, 93, 99, 100). The Corps has indicated that they are seeking programmatic
coverage for this activity. The Corps is seeking programmatic coverage for subtidal wild
geoduck harvest on a maximum of 6,050 acres per year, at depths to -70 ft MLLW in Hood
Canal and the Puget Sound.
During 2008, the Service and NMFS approved a low-effect Habitat Conservation Plan (HCP)
developed in coordination with the Washington State Department of Natural Resources (DNR)
for their commercial geoduck fishery. The HCP and corresponding Opinion (USFWS 2009b)
assessed effects of the State’s program for commercial harvest of wild geoduck clams at depths
between -18 and -70 ft MLLW, across approximately 400 harvest tracts and more than 30,000
acres (separate from the Tribal harvest areas) in the Puget Sound, Hood Canal, San Juan Islands,
and eastern Strait of Juan de Fuca. That record of HCP approval indicates minor and small-scale
effects resulting from elevated turbidity and sedimentation during harvest activities (Service Ref.
No. PRT-TE187810-0). The low-effect HCP and corresponding Opinion (USFWS 2009b) found
that deep subtidal harvest of wild geoduck has at most a low potential for any significant effects
on listed species and critical habitat.
While to date the Corps has seldom, if ever, applied its authorities and jurisdiction to regulate
subtidal wild geoduck harvest, it has consistently requested that the Services provide coverage
for the activity (Corps 2015, pp. 3, 5, 30, 34, 46, 47, 80, 84, 89, 92, 93, 99, 100). This Opinion
addresses the potential effects of subtidal wild geoduck harvest because it is included as part of
the Corps’ proposed action.
Ground-Based Culturing of Clams (Bottom, Bag)
Several species of clams are commercially cultured and harvested in Washington State, including
the Pacific littleneck clam (Leukoma staminea), Manila clam (Venerupis philippinarum), butter
clam (Saxidomus gigantea), Eastern soft shell clam (Mya arenaria), horse clam (Tresus nuttallii
and Tresus capax), and cockle (Clinocardium nuttallii)(Corps 2015, p. 23). The most commonly
and widely cultured clam, the Manila clam, is not native to Washington State. Clams are
typically cultured on the intertidal bed, from +7.0 to –4.5 MLLW.
Hatchery and Nursery Operations
An earlier sub-section discussed hatchery and nursery operations typical of geoduck culturing
p. 11). Clam growers and farm operators use all or most of the same methods, practices, and
techniques. However, reliance upon natural set and seeding is also a fairly common practice
among both clam and oyster growers. Where wild populations and natural spawning occur,
viable seed can be acquired by creating substrate conditions that foster larval attachment and
survival.
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Site/Bed Preparation
Where clams are cultured directly on the substrate (bottom culture) graveling or frosting is a very
common practice (Corps 2015, p. 24). Washed gravel, shell, and shell fragments are distributed
over the substrate surface in thin layers. The most common method for graveling or frosting
uses a floatable barge deck, from which piles of gravel and shell are sprayed or sluiced onto a
tidally-inundated bed (Figure 7). Several thin layers of material are typically placed over a
period of days. Some growers/farm operators gravel or frost their clam beds on an annual basis,
while others do so less frequently. These decisions generally reflect site-specific physical
conditions and needs.
An earlier sub-section discussed methods of site/bed preparation typical of geoduck culturing
p. 11). Clam growers and farm operators use all or most of the same methods, practices, and
techniques. Preparation of a ground-based culture clam bed or farm plot typically includes the
following activities: pre-harvest of marketable product; removal or relocation of coarse wood,
unrooted algae (e.g., sea lettuce), and native and non-native shellfish predators; and, hand raking
Corps 2015, p. 24). Some growers/farm operators may use a mechanical harrow to remove
marketable product (pre-harvest). Larger, contiguous clam and oyster tracts are sometimes
leveled mechanically, most commonly by dragging a chain or bag from a vessel traveling at slow
speed (Corps 2015, p. 17). Leveling and harrowing of the bed may in some instances result in
measurable impacts to submerged aquatic vegetation, including native eelgrass and/or rooted
kelp.
Seeding or Planting
Where hatchery-produced clam seed is used, methods for seeding bottom culture clam beds or
farm plots vary depending on site-specific factors (including predation pressure). Methods
include (Corps 2015, p. 24): hand-spreading seed at low tide upon bare, exposed substrate; hand-
spreading seed on an incoming tide at water depths of approximately 4 inches; hand-spreading
seed on an outgoing tide at water depths of approximately 2 to 3 ft; and, spreading seed at high
tide from a boat or barge.
Immediately after planting, anti-predator cover nets are typically placed over the entire seeded
clam bed. These nets may be composed of either plastic or organic fibers, and are typically
anchored at the periphery with embedded rebar or metal staking. Mesh size varies by application
and/or preference, typically ranging from ¼ x ¼ inch to ¾ x ¾ inch or larger (Figure 5, p. 14).
Some growers bury the net edges, or weigh-down the edges with a lead line (Corps 2015, p. 25).
Once placed over a seeded clam bed, anti-predator cover nets typically remain in place until
harvest.
Clams cultured in plastic mesh bags are typically placed directly on the substrate (Figure 8). The
bags contain washed gravel, shell, shell fragments, and clam seed, and are closed with a plastic
or metal fastener (Corps 2015, p. 29). Prior to setting bags on the intertidal bed, shallow
trenches (typically 2 to 4 inches deep) may be dug, typically during low tide and with hand tools,
to establish a secure foundation for the bags. Where tidal, wind, or wave action is strong, bags
may be held in place with metal stakes or rebar.
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Figure 7. Graveling (frosting) over a clam bed
Corps 2015, p. 25)
Figure 8. Manila clam bags placed on an exposed intertidal bed
Corps 2015, p. 29)
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Maintenance
Farm plots are patrolled by crews on a regular basis. Surveys are conducted seasonally, to assess
seed survival and distribution, and to estimate potential yield (Corps 2015, p. 25). Depending
upon survey results, bottom cultured clam beds may be seeded again. Crews also monitor clams
cultured in plastic mesh bags. The bags are commonly turned and de-fouled to optimize growing
conditions.
Cover nets may become fouled with algae and other organisms, and are therefore typically
removed and/or cleaned with some frequency. Nets may be taken to an upland location for
drying and cleaning, or (less commonly) fouling organisms may be removed from the nets while
they remain in place (Corps 2015, p. 25).
Harvest
Bottom cultured clams are typically dug by hand at low tide, using a clam rake and/or shovel. A
given clam bed may contain multiple year classes of clams, and therefore only the market-size
clams (typically corresponding to 3 years of age) are selectively harvested, placed in buckets,
bagged, tagged, and removed from the farm plot (Corps 2015, p. 25). Once sorted, any
undersized clams are typically returned to the beds. Those that are that are retained for sale are
typically bagged and placed in wet storage elsewhere on the farm footprint. Clams are typically
held in wet storage for a period of approximately 24 hours, to facilitate purging of sand and grit,
and thereby improve the marketable product.
Clams cultured in bags are harvested by hand, typically when the bed is covered by one or two ft
of water (Corps 2015, p. 29). Sand and mud is shaken from the bags before they are removed for
sorting.
Bottom cultured clams are sometimes harvested mechanically, most notably in Samish Bay
Corps 2015, p. 26). Mechanical clam harvesters are driven or pulled across the exposed bed at
low tide, and the clams are “swept” onto a conveyor belt (Figure 9). Another type of mechanical
harvesting equipment, the hydraulic escalator (Figure 10), has been mostly or completely phased
out and is no longer used in Washington State. The Corps’ programmatic consultation for
shellfish activities does not provide coverage for harvesting conducted with a hydraulic escalator
and use of this type of machinery is specifically excluded from coverage under the Corps
programmatic consultation (Corps 2015, p. 26). A complete list of the activities, methods, and
practices that are excluded from coverage under the Corps programmatic consultation is
provided in a sub-section that follows.
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Figure 9. Mechanical clam harvester
Pacific Shellfish Institute 2015)
Figure 10. Hydraulic escalator
MacPhail 1961)
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Ground-Based Culturing of Oysters (Bottom, Rack-and-Bag, Stake, Longline)
Several species of oyster are cultured or harvested in Washington State, including the Pacific
oyster (Crassostrea gigas), Kumamoto oyster (Crassostrea sikamea), Eastern or American
oyster (Crassostrea virginica), European flat oyster (Ostrea edulis), and the Olympia oyster
Ostrea conchaphila)(Corps 2015, p. 14). Only the Olympia oyster is native to Washington
State, and the species (because of its small size) is generally cultured for the purposes of
restoration.
Oyster growers and farm operators use a wide variety of culturing methods, practices, and
techniques. Where appropriate, the content that follows describes and differentiates between the
practices common to ground-based bottom culturing, rack-and-bag, stake, and longline culturing.
A final sub-section addresses culturing of oysters and mussels suspended from floating rafts.
Hatchery and Nursery Operations
An earlier sub-section discussed hatchery and nursery operations typical of geoduck culturing
p. 11). Oyster growers and farm operators use all or most of the same methods, practices, and
techniques. However, reliance upon natural set and seeding is also a fairly common practice
among oyster growers. Where wild populations and natural spawning occur, viable seed can be
acquired by creating substrate conditions that foster larval attachment and survival.
Oyster cultch is the basis for both ground-based and suspended culturing of oysters. While the
term “cultch” may refer to the mass of stone, broken shell, and grit that compose an oyster bed,
where used here the term refers to aged oyster shell that has been prepared and placed in the
intertidal or shallow subtidal zone with the specific goal of collecting a natural set of oyster seed
or “spat”)(Corps 2015, p. 14). Cultch is sometimes seeded in a hatchery or in upland tanks, but
the practice of placing bundled cultch on the intertidal bed is more common.
Washed and aged oyster shells are bundled in plastic mesh bags and then placed in the intertidal
or shallow subtidal zone, either directly on the substrate or on pallets (Figure 11). After spat has
settled and firmly attached (or cemented) to the shells, the seeded cultch is ready for out-planting
on the bed or farm plot (Corps 2015, p. 14).
Site/Bed Preparation
An earlier sub-section discussed methods of site/bed preparation typical of geoduck culturing
p. 11). Oyster growers and farm operators use all or most of the same methods, practices, and
techniques. Preparation of a ground-based culture oyster bed or farm plot typically includes the
following activities: pre-harvest of marketable product; removal or relocation of coarse wood,
unrooted algae (e.g., sea lettuce), and native and non-native shellfish predators; and, leveling and
harrowing of the bed (Corps 2015, p. 16). Leveling and harrowing of the bed may in some
instances result in measurable impacts to submerged aquatic vegetation, including native eelgrass
and/or rooted kelp.
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An earlier sub-section discussed graveling or frosting of cultured clam beds (p. 17). This same
practice is used by many oyster growers/farm operators (Corps 2015, p. 17), especially where the
native substrates are unconsolidated and must be “hardened” to prevent oysters from sinking and
smothering. Some growers gravel or frost their oyster beds on an annual basis, while others do
so less frequently. These decisions generally reflect site-specific physical conditions and needs.
Figure 11. Bundled oyster cultch stacked on pallets
Corps 2015, p. 15)
Mechanical methods of preparing and maintaining the cultured beds, and of harvesting, are fairly
common and widespread among Washington State’s oyster growers and farm operators. Larger,
contiguous oyster beds are often leveled mechanically, most commonly by dragging a chain or
bag from a vessel traveling at slow speed (Corps 2015, pp. 15, 17, 19). Growers use mechanical
harrows to pre-harvest and prepare beds, to pull sunken and embedded oysters to the surface, and
to recover oysters that have dislodged and fallen from stakes or longlines (Corps 2015, pp. 17,
20). A sub-section that follows discusses these practices in detail, including their unavoidable
impacts to submerged aquatic vegetation (native eelgrass and rooted kelp). These practices are
used extensively in Willapa Bay, but are far less common in all of other geographic sub-areas
Grays Harbor, Hood Canal, south and north Puget Sound).
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Historically, some oyster growers have used anchored vertical fencing or nets (drift fences or
oyster corrals) to stabilize and prevent oysters and oyster shell from being moved off the cultured
bed. Available information suggests this practice was never widely used in Washington State,
and the Corps’ programmatic consultation does not provide coverage for the practice or activity;
use of drift fences or oyster corrals is specifically excluded from coverage under the Corps
programmatic consultation (Corps 2015, p. 39). A complete list of the activities, methods, and
practices that are excluded from coverage under the Corps programmatic consultation is
provided in a sub-section that follows (see Activities Excluded from Programmatic Coverage).
Seeding/Planting
Where oysters are cultured directly on the intertidal bed (bottom culture) seeded cultch may be
cast by hand and distributed on the beds, or sluiced/sprayed from a barge deck (Corps 2015, p.
16). Oysters cultured in plastic mesh bags may be placed directly on the substrate, or hung from
racks (rack-and-bag culture). Anchored wood or metal racks are used to suspend the bags above
the intertidal bed (Corps 2015, p. 22), prevent smothering, and create optimal growing
conditions. Bags are commonly fixed to the racks with plastic or metal fasteners.
Some oyster growers use a tumble bag system (Figure 12). Tumble bags incorporate small floats
and, as the tides rise and fall, the bags are repeatedly inverted and tumbled (Corps 2015, p. 23).
Tumble bags prevent smothering and harden oysters, sometimes producing a product meant
specifically for the premium, raw-on-shell market.
Ground-based culturing systems that use oyster stakes and longlines are fairly common and
widespread in Washington State. Stakes composed of a hard-surfaced material (e.g., metal or
PVC pipe) are embedded in the substrate, typically with 2-foot spacing (Corps 2015, p. 21).
Seeded cultch is attached to the stakes and suspended above the intertidal bed. Some growers
attach unseeded cultch, or allow a native encrusting community to grow on the stakes, and then
rely upon a natural seed set (Corps 2015, p. 21).
Where longline culturing is practiced, oysters are grown in clusters, attached to rope lines
suspended above the intertidal bed between upright stakes (Corps 2015, pp. 19, 20). The rope
lines are typically composed of either polypropylene or nylon, and are typically held less than
three feet above the intertidal bed (Figure 13). Stakes and longlines prevent oysters from sinking
and smothering, and also serve to control and minimize exposure to predators inhabiting the
intertidal bed.
Maintenance
Where oysters are cultured directly on the intertidal bed (bottom culture) anti-predator cover nets
may be installed and maintained. These nets may be composed of either plastic or organic fibers,
and are typically anchored at the periphery with embedded rebar or metal staking. Mesh size
varies by application and/or preference, typically ranging from ¼ x ¼ inch to ¾ x ¾ inch or
larger (Figure 5, p. 14). Some growers bury the net edges, or weigh-down the edges with a lead
line. Also, where oysters are cultured directly on the intertidal bed, the farm plot may be
reseeded to either augment the natural seed set or address poor hatchery seed survival.
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Farm plots are patrolled by crews on a regular basis. Nets, bags, racks, stakes, and longlines are
all routinely inspected to ensure that they remain secure (Corps 2015, pp. 17-23). Culturing
equipment is de-fouled, repaired, and replaced as necessary, and oysters are periodically thinned
or redistributed to optimize growing conditions.
Figure 12. Oyster tumble bags
Corps 2015, p. 23)
Figure 13. Oyster longlines
Corps 2015, p. 20)
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Farmed oysters are commonly collected and redistributed across multiple farm plots during
grow-out (Corps 2015, p. 17). Some beds and farm plots provide conditions that are best suited
for collecting a natural seed set, some are ideal for maturing young oysters, and others are better
suited for “fattening” mature oysters prior to final harvest. Many, perhaps most, growers/farm
operators transplant their oysters across multiple sites within and between individual farms,
depending upon age, maturity, and rate of growth.
Growers/farm operators commonly use mechanical harrows to pull sunken and embedded
oysters to the surface, and to recover oysters that have dislodged and fallen from stakes or
longlines (Corps 2015, pp. 17, 21).
Harvest
Rack-and-bag, staked, and longline cultured oysters are all typically harvested by hand at low
tide (Corps 2015, pp. 19-21). A given bed may contain multiple year classes of oysters, and
therefore only the market-size oysters are selectively harvested, sorted, bagged, tagged, and
removed from the farm plot.
Oysters cultured on longlines are sometimes harvested mechanically (Corps 2015, p. 21). Buoys
are attached to the lines at low tide. Specialized equipment is used during a middle or high tide
to reel the lines in to a working vessel or barge deck, and cut and remove the market-size oysters.
Where oysters are cultured directly on the intertidal bed (bottom culture) hand harvesting at low
tide (Figure 14), and mechanical dredge harvesting at middle or high tides, are both common and
widespread practices (Corps 2015, p. 17). Mechanical oyster dredges are deployed from one or
both sides of a working vessel or barge. The dredge bag(s) are lowered to an elevation at or just
below the bed surface by boom crane or hydraulic winch, and pulled at slow vessel speeds across
and through the substrate. The dredge bags are emptied onto a barge deck, and then redeployed
Figure 15). A given area may be dredged twice in succession to ensure recovery of the
maximum number of oysters, and the farm plot may be mechanically harrowed between the two
successive dredge harvests in order to increase the recovery of oysters (Corps 2015, p. 17). A
sub-section that follows discusses these practices in detail, including their unavoidable impacts
to submerged aquatic vegetation (native eelgrass and rooted kelp).
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Figure 14. Hand harvest of bottom cultured oysters
Corps 2015, p. 19)
Figure 15. Oyster dredge with boom cranes and bags
Corps 2015, p. 19)
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Oyster Culturing and Native Bed Enhancement for the Purposes of Restoration
Over recent years, native oysters (O. conchaphila) have been cultured, and native and non-native
oyster beds have been enhanced, for purposes of habitat improvement, ecological restoration,
water quality improvement, and/or to increase the size of native shellfish populations (Corps
2015, p. 48). Much of this work serves the dual purpose of testing and monitoring new methods
and protocols, and will provide scientific information to inform future decisions. Examples of
these projects include: Puget Sound Restoration Fund - Native Oyster Enhancement Projects
Service Ref. No. 01EWFW00-2013-I-0414); Eelgrass Pilot Study - Custom Plywood Interim
Remedial Action (Service Ref. No. 13410-2011-I-0435); and, Hood Canal Mariculture and Puget
Sound Restoration Fund - Algae Mariculture Demonstration Facility (Service Ref. No.
01EWFW00-2016-I-0147). These activities include site/bed preparation, seeding or planting,
maintenance, monitoring, and limited harvest (i.e., for the purpose of biological sampling).
Suspended (or Floating) Culturing of Oysters and Mussels
In addition to the previously mentioned oyster species, two species of mussel are cultured in
Washington State: the native Pacific blue mussel (Mytilus trossulus), and the non-native
Mediterranean or Gallo mussel (Mytilus galloprovincialis)(Corps 2015, p. 11). Oysters and
mussels are both grown in Washington State using methods that suspend nets, screens, socks,
ropes, wires, and/or longlines from floating rafts and buoys.
Hatchery and Nursery Operations
An earlier sub-section discussed hatchery and nursery operations (p. 11). Farm operators
growing oysters and mussels use all or most of the same methods, practices, and techniques.
Oyster cultch is the basis for both ground-based and suspended culturing of oysters.
Site/Bed Preparation
Suspended culturing of oysters and mussels is practiced over subtidal waters and there is little or
no direct engagement with the bed and substrate (Corps 2015, pp. 11, 16). Floating rafts and
buoyed longlines do require an anchoring system, and waste produced by the growing shellfish
feces, pseudofeces) settles on the sea bed below. However, other than the setting of secure
anchors, suspended culturing does not generally require site or bed preparation.
Floating rafts are composed of lumber, aluminum, galvanized steel, and/or plywood, with some
form of encapsulated flotation (Corps 2015, p. 11). Longlines are typically composed of heavy
polypropylene or nylon rope, suspended from a float or series of buoys.
Seeding or Planting
Mature seed is scraped or sluiced into “socks”, with discs placed every few feet to support the
weight of growing shellfish (Corps 2015, p. 12). The socks are then lashed to frames within a
floating raft (Figure 16), or to longlines.
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Figure 16. A typical mussel raft
Corps 2015, p. 13)
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Maintenance
Anti-predator exclusion nets are typically hung around the perimeter of the rafts (Figure 16).
Depending on the farm location, these nets may only be necessary on a seasonal basis. When
nets become excessively fouled (e.g., with barnacles, algae or other biological growth) they are
removed and cleaned (Corps 2015, p. 12). Farm operators also de-foul other structural elements
of their floating rafts. Rafts and suspended longlines are patrolled by crews on a regular basis.
Anchors, nets, screens, socks, ropes, wires, and longlines are all routinely inspected to ensure
that they remain secure.
Some growers/farm operators regularly sort and grade their oysters throughout the growth cycle.
Every three or four months, oysters growing on suspended trays are put through a hand or
mechanical grading process, trays are restocked, de-fouled, and returned to the water column
Corps 2015, p. 16). Oysters grown as clusters on suspended ropes, lines, or wires are given less
attention between seeding and harvest.
Harvest
Harvest is conducted from the rafts and attending work boats or barges. Winches retrieve nets,
socks, ropes, lines, wires, and bags. Sorting is conducted either on-deck or off-site (Corps 2015,
p. 16).
When cultured mussels reach market-size, corresponding to approximately 12 to14 months of
age, they are stripped from the suspended socks and lines, and bulk-bagged and tagged for
transport to shore. Additional, more thorough cleaning and grading is typically conducted on
shore. Weights are reclaimed for re-use, and used socks and lines are either recycled or disposed
of at appropriate upland facilities and locations (Corps 2015, p. 14). Harvest is conducted year-
round, as mussels mature.
After oysters are grown using a suspended culturing system, they are typically transplanted to an
intertidal bed before final harvest. The practice, referred to as “hardening,” extends the shelf-life
of oysters (Corps 2015, p. 16). The hardened oysters are subsequently re-harvested (after 2 to 4
weeks) using bottom culture harvest methods. Some growers/farm operators simply bag and
hang oysters from their docks or piers, allowing tide cycles to expose and harden the oysters.
Other Related Activities
Vessel operations, farm site access, and onshore facilities are all inherent to shellfish activities
conducted on the tidelands and the inland marine waters. These activities do not have
independent utility, but may result in additional effects.
Vessel Operations
Shellfish activities generally require the operation of small- and medium-sized vessels. Small
vessels provide the means for transporting crews, equipment, and materials, by-water, to and
from cultured areas. Typical small vessels include open work boats and skiffs powered by two-
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or four-stroke outboard motors. Larger, medium-sized vessels are used to mechanically prepare
sites, frost or gravel beds, and to mechanically harrow and harvest ground-based cultured areas.
Typical larger vessels include work boats and barges with a flat fore or rear deck, an enclosed or
partially enclosed cabin or deckhouse, above- and/or below-deck stowage, and mechanical
equipment (including booms and winches). Larger, medium-sized vessels are typically powered
by larger and stronger diesel inboard motors.
Small vessels are commonly anchored or grounded, on a temporary basis, while crews conduct
their work. Farm operators and their crews typically avoid eelgrass (Zostera sp.) meadows,
vegetated shallows, and actively cultured beds, when temporarily grounding or anchoring their
small vessels. A typical pattern of site access from the water includes: temporarily grounding on
exposed sand- or mudflats; off-loading of crew, equipment, and materials; and, off-shore
motoring, at a short distance from the ongoing work, to temporarily anchor the vessel in deeper
intertidal or subtidal waters. Larger vessels are not typically grounded (even temporarily), with
the exception of flat-bottomed work barges used by some farm operators.
Fueling, maintenance, and repair of vessels are not commonly conducted at the cultured area or
over the open waters. Instead, these activities are typically conducted at commercial facilities, or
at designated locations where the farm operator has purpose-specific equipment, materials, and
protective measures in place.
Farm Site Access
Crews must access and traverse over the cultured intertidal beds, and adjacent areas, when
performing their work. Some cultured areas can be easily accessed, and are therefore routinely
accessed from the adjacent uplands. Crews typically carry equipment and materials on-foot, or
with the assistance of an ATV(s).
Where access to cultured areas is from the adjacent uplands, most farm operators and crews
establish and use well-defined routes of access through the nearshore riparian buffer and high,
upper-intertidal beach. Where ATVs, small tractors, or mechanical harvesters are used on the
exposed intertidal bed, this equipment may be refueled on-site (subject to permit conditions and
other restrictions). Equipment maintenance and repair is generally, if not always, conducted in
the uplands and away from the water.
Onshore Facilities
Hatcheries are typically corporate and off-site, serving many customers. They are often located
in the uplands and their operations do not require a Corps permit. Operation of upland hatcheries
is not part of the Corps’ proposed action.
Once purchased by a grower/farm operator, seed is often allowed to further mature before being
outplanted. Some growers use tanks located in the uplands, a practice that may include
withdrawals from and discharges to the adjacent marine waters. Discharges are sometimes, but
not always, regulated under a permit(s) issued by the Washington State Department of Ecology
Ecology).
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Many, perhaps most, farm operators maintain an onshore facility where they store, stage, dry,
clean/de-foul, repair, and maintain their culturing equipment and materials (nets, bags, tubes,
racks, stakes, longlines, etc.). Most operators accomplish these tasks with no direct discharge to
the adjacent waters.
Wet storage” refers to temporary storage of harvested shellfish, typically prior to onshore
cleaning, grading, and processing. Some farm operators hold their shellstock in wet storage
located on the farm footprint, some float their product in subtidal waters, and others use upland
tanks for the purpose of wet storage. Tanks may be prepared synthetically, with the addition of
salts to potable water, or may be filled with withdrawals from the adjacent marine waters.
Whether used to mature seed or to store harvested shellfish, tanks are regularly cleaned,
disinfected, and buffered. Some operate with recirculation, minimizing the total volumes of
withdrawal and/or discharge. Return water discharges generally deviate minimally from ambient
marine water, with only trace and negligible additional amounts of nutrients, phytoplankton,
and/or feces/pseudofeces (Corps and Seattle Shellfish 2014; Corps and BWH Seafood 2015).
Wastewaters, both fresh and saline, are byproducts of storing, cleaning, grading, and processing
harvested shellfish. However, most or all of these facilities are located in the uplands, and their
operations do not require a Corps permit. Resulting wastewaters are typically collected and
reused or recycled. Processing operations, and State regulations and requirements, dictate
methods of wastewater disposal at each facility.
Shell and shell fragments are the main byproducts of processing harvested shellfish. Whole
oyster shell is valuable and commonly reclaimed for use as cultch. Shell may also be crushed
and sold or marketed for other purposes (e.g., landscape surfacing and aggregate).
Activities Excluded from Programmatic Coverage
The Corps and Service have determined that some shellfish activities and practices are not
appropriate for programmatic coverage, either because: a) The activity or practice results in
potential effects, of a kind, extent, or severity, that warrant case-by-case consideration (and
individual section 7 ESA consultation); or, b) The activity or practice extends sufficiently
beyond the jurisdiction of the Corps’ regulatory program, or is regulated under the authorities
and jurisdiction of another Federal agency (Corps 2015, p. 38, 39). Table 1, below, represents
the Corps’ list of shellfish activities, methods, and practices (or other, interrelated activities) that
are specifically and intentionally excluded from coverage under the programmatic consultation.
The Service expects that the Corps will actively solicit information from their applicants about
all of the excluded activities prior to approving coverage under the programmatic consultation,
and before issuing each permit or permit verification. Growers and farm operators who seek
coverage under the programmatic consultation, but who also engage in an excluded activity (or
activities), will not satisfy the requirements of their Corps permit and are potentially liable under
the provisions of the ESA.
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Table 1. Activities excluded from programmatic coverage
1) Vertical fencing/vertical nets or drift fences (includes oyster corrals).
2) New berms or dikes or the expansion or maintenance of current, authorized berms or
dikes.
3) Use of a hopper-type barge or other method that results in material (i.e. gravel or shell)
placed during graveling or frosting activities that is thicker than 1 inch in depth even for
short periods of time.
4) Pile driving.
5) Installation and maintenance of mooring buoys.
6) Construction, maintenance, and operation of upland hatcheries.
7) Cultivation of shellfish species not previously cultivated in the action area.
8) Construction, maintenance, and operation of attendant features, such as docks, piers,
boat ramps, stockpiles, or staging areas.
9) Deposition of shell material back into waters of the United States as waste.
10) Dredging or creating channels so as to redirect fresh water flow.
11) Installation of new rafts, floats, or FLUPSYs, or the relocation or expansion of
continuing rafts, floats, or FLUPSYs.
12) Any form of chemical application to control undesired species (e.g., non-native
eelgrass, Zostera japonica; ghost shrimp, Neotrypaea californiensis; mud shrimp,
Upogebia pugettensis).
13) Use of materials that lack structural integrity in the marine environment (e.g. plastic
children’s wading pools, unencapsulated Styrofoam®).
14) Unauthorized activities.
Corps 2015, p. 39)
On April 2, 2014, and April 16, 2015, Ecology issued National Pollutant Discharge Elimination
System permits allowing the application of a selective aquatic herbicide for the control of non-
native Japanese eelgrass (Zostera japonica; multiple Permit No.s), and allowing the application
of imidacloprid, a neonicotinoid pesticide, for the control of burrowing shrimp (Permit No.
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WA0039781) on commercial oyster and clam beds in Willapa Bay and Gray Harbor. On
May 3, 2015, the Willapa-Grays Harbor Oyster Growers Association and Ecology announced an
agreement to withdraw and cancel the permit issued for use of imidacloprid.
These practices (i.e., the application of herbicides or pesticides to the bed or waters) do not have
coverage under the Corps’ programmatic consultation (Corps 2015, pp. 39, 54). The Service
assumes and expects that the Corps will actively solicit information about chemical applications
prior to approving coverage under the programmatic consultation, and before issuing each permit
or permit verification. Growers and farm operators who seek coverage under the programmatic
consultation, but who also engage in chemical application to control undesired species, will not
satisfy the requirements of their Corps permit and are potentially liable under the provisions of
the ESA. In the event that a Corps applicant or group of applicants has been issued a valid State
permit(s) to engage in application of herbicides or pesticides to the bed or waters, the Service
expects that the Corps will confirm compliance with the procedural requirments of the ESA
before issuing a permit or permit verification.
Conservation Measures
The Corps and Services developed the following conservation measures through a Standard
Local Operating Procedures (SLOPES) process, and the Corps has included the following
conservation measures as elements of their proposed action (Corps 2015, pp. 49-53). Permits
and permit verifications issued by the Corps will incorporate these measures as enforceable
terms and conditions. If a Corps permit applicant or group of applicants cannot or will not
commit to fully implementing the following measures, the issuance of that permit or permit
verification cannot be covered under the programmatic consultation, and case-by-case
consideration and individual section 7 ESA consultation will be required. Corps permit
applicants who seek coverage under the programmatic consultation, but who also fail to fully
comply with these conservation measures (where applicable), will not satisfy the requirements of
their Corps permit and are potentially liable under provisions of the ESA.
Shellfish activities will be conducted in a manner consistent with the following conservation
measures (Corps 2015, pp. 49-53):
1. Gravel and shell shall be washed prior to use for substrate enhancement (e.g., frosting,
shellfish bed restoration) and applied in minimal amounts using methods which result in
less than 1 inch depth on the substrate annually. Shell material shall be procured from
clean sources that do not deplete the exiting supply of shell bottom. Shells shall be
cleaned or left on dry land for a minimum of one month, or both, before placement in the
marine environment. Shells from the local area shall be used whenever possible. Shell
or gravel material shall not be placed so that it creates piles on the substrate. Use of a
split-hull (e.g., hopper-type) barge to place material is prohibited.
2. The placement of gravel or shell directly into the water column (i.e., graveling or
frosting) shall not be conducted between February 1 and March 15 in designated critical
habitat for Hood Canal summer chum salmon.
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3. For ‘new’ activities only, gravel or shell material shall not be applied to enhance
substrate for shellfish activities where native eelgrass (Zostera marina)* or kelp
rooted/attached brown algae in the order Laminariales) is present.
Note: Where the conservation measures refer to native eelgrass, they refer to and use
the definition, description, and methods of delineation that have been endorsed and
adopted by the Corps’ Seattle District (Corps 2016).]
4. Turbidity resulting from oyster dredge harvest shall be minimized by adjusting dredge
bags to “skim” the surface of the substrate during harvest.
5. Unsuitable material (e.g., trash, debris, car bodies, asphalt, tires) shall not be discharged
or used as fill (e.g., used to secure nets, create nurseries, etc.).
6. For ‘new’ activities only, shellfish activities (e.g., racks, stakes, tubes, nets, bags, long-
lines, on-bottom cultivation) shall not occur within 16 horizontal ft of native eelgrass
Zostera marina) or kelp (rooted/attached brown algae in the order Laminariales). If
eelgrass is present in the vicinity of an area new to shellfish activities, the eelgrass shall
be delineated and a map or sketch prepared and submitted to the Corps. Surveys to
determine presence and location of eelgrass shall be done during times of peak above-
ground biomass (June 1 to September 30). The following information must be included
to scale: parcel boundaries, eelgrass locations and on-site dimensions, shellfish activity
locations and dimensions.
7. For ‘new’ activities only, activities shall not occur above the tidal elevation of +7 ft
MLLW if the area is listed as documented surf smelt (Hypomesus pretiosus) spawning
habitat by the Washington State Department of Fish and Wildlife (WDFW). A map
showing the location of documented surf smelt spawning habitat is available at the
WDFW website.
8. For ‘new’ activities only, activities shall not occur above the tidal elevation of +5 ft
MLLW if the area is listed as documented Pacific sand lance (Ammodytes hexapterus)
spawning habitat by WDFW. A map showing the location of documented Pacific sand
lance spawning habitat is available at the WDFW website.
9. If conducting 1) mechanical dredge harvesting, 2) raking, 3) harrowing, 4) tilling,
leveling or other bed preparation activities, 5) frosting or applying gravel or shell on
beds, or 6) removing equipment or material (nets, tubes, bags) within a documented or
potential spawning area for Pacific herring (Clupea pallasi) outside the approved work
window (see Seattle District Corps website), the work area shall be surveyed for the
presence of herring spawn prior to the activity occurring. Vegetation, substrate, and
materials (nets, tubes, etc.) shall be inspected. If herring spawn is present, these activities
are prohibited in the areas where spawning has occurred until such time as the eggs have
hatched and herring spawn is no longer present. A record shall be maintained of spawn
surveys including the date and time of surveys; the area, materials, and equipment
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surveyed; results of the survey, etc. The Corps and the Services shall be notified if spawn
is detected during a survey. The record of spawn surveys shall be made available upon
request to the Corps and the Services.
10. For ‘new’ activities only, activities occurring in or adjacent to potential spawning habitat
for sand lance, or surf smelt shall have a spawn survey completed in the work area by an
approved biologist* prior to undertaking bed preparation, maintenance, and harvest
activities if work will occur outside approved work windows for these species. If eggs
are present, these activities are prohibited in the areas where spawning has occurred until
such time as the eggs have hatched and spawn is no longer present. A record shall be
maintained of spawn surveys including the date and time of surveys; the area, materials,
and equipment surveyed; results of the survey, etc. The Corps and the Services shall be
notified if spawn is detected during a survey. The record of spawn surveys shall be made
available upon request to the Corps and the Services.
Note: For information on how to become an “approved biologist” for the purpose of
conducting forage fish surveys parties should contact WDFW.]
11. All shellfish gear (e.g., socks, bags, racks, marker stakes, rebar, nets, and tubes) that is
not immediately needed, or is not firmly secured to the substrate, will be moved to a
storage area landward of mean higher high water (MHHW) prior to the next high tide.
Gear that is firmly secured to the substrate may remain on the tidelands for a consecutive
period of time up to 7 days. [Note: This conservation measure does not apply to the wet
storage of harvested shellfish.]
12. All pump intakes (e.g., for washing down gear) that use seawater shall be screened in
accordance with NMFS and WDFW criteria. [Note: This conservation measure does not
apply to work boat motor intakes (jet pumps) or through-hull intakes.]
13. Land vehicles (e.g., all-terrain, trucks) shall be washed in an upland area such that wash
water is not allowed to enter any stream, waterbody, or wetland. Wash water shall be
disposed of upland in a location where all water is infiltrated into the ground (i.e., no
flow into a waterbody or wetland).
14. Land vehicles shall be stored, fueled, and maintained in a vehicle staging area located
150 ft or more from any stream, waterbody, or wetland. Where this is not possible,
documentation must be provided to the Corps as to why compliance is not possible,
written approval from the Corps must be obtained, and the operators shall have a spill
prevention plan and maintain a readily-available spill prevention and clean-up kit.
15. For boats and other gas-powered vehicles or power equipment that cannot be fueled in a
staging area 150 ft away from a waterbody or at a fuel dock, fuels shall be transferred in
Environmental Protection Agency (EPA)-compliant portable fuel containers 5 gallons or
smaller at a time during refilling. A polypropylene pad or other appropriate spill
protection and a funnel or spill-proof spout shall be used when refueling to prevent
possible contamination of waters. A spill kit shall be available and used in the event of a
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spill. All spills shall be reported to the Washington Emergency Management Office at
800) 258-5990. All waste oil or other clean-up materials contaminated with petroleum
products will be properly disposed of off-site.
16. All vehicles operated within 150 ft of any stream, waterbody, or wetland shall be
inspected daily for fluid leaks before leaving the vehicle staging area. Any leaks detected
shall be repaired in the vehicle staging area before the vehicle resumes operation and
documented in a record that is available for review on request by the Corps and Services.
17. The direct or indirect contact of toxic compounds including creosote, wood preservatives,
paint, etc. with the marine environment shall be prevented.
18. All tubes, mesh bags, and area nets shall be clearly, indelibly, and permanently marked to
identify the permittee name and contact information (e.g., telephone number, email
address, mailing address). On the nets, identification markers shall be placed with a
minimum of one identification marker for each 50 ft of net.
19. All equipment and gear including anti-predator nets, stakes, and tubes shall be tightly
secured to prevent them from breaking free.
20. All foam material (whether used for floatation of for any other purpose) must be
encapsulated within a shell that prevents breakup or loss of foam material into the water
and is not readily subject to damage by ultraviolet radiation or abrasion. Un-encapsulated
foam material used for current, on-going activities shall be removed or replaced with the
encapsulated type.
21. Tires shall not be used as part of above and below structures or where tires could
potentially come in contact with the water (e.g., floatation, fenders, hinges). Tires
currently being used for floatation shall be replaced with inert or encapsulated materials,
such as plastic or encased foam, during maintenance or repair of the structure.
22. At least once every three months, beaches in the project vicinity will be patrolled by
crews who will retrieve debris (e.g., anti-predator nets, bags, stakes, disks, tubes) that
escapes from the project area. Within the project vicinity, locations will be identified
where debris tends to accumulate due to wave, current, or wind action, and after weather
events these locations shall be patrolled by crews who will remove and dispose of
shellfish related debris appropriately. A record shall be maintained with the following
information and the record will be made available upon request to the Corps and
Services: date of patrol, location of areas patrolled, description of the type and amount of
retrieved debris, other pertinent information.
23. When performing other activities on-site, the grower shall routinely inspect for and
document any fish or wildlife found entangled in nets or other shellfish equipment. In the
event that a fish, bird, or mammal is found entangled, the grower shall: 1) provide
immediate notice (within 24 hours) to WDFW (all species), the Services (ESA listed
species), or the Marine Mammal Stranding Network (marine mammals), 2) attempt to
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release the individual(s) without harm, and 3) provide a written and photographic record
of the event, including dates, species identification, number of individuals, and final
disposition, to the Corps and Services. Contact the U.S. Fish and Wildlife Service Law
Enforcement Office at (425) 883-8122 with any questions about the preservation of
specimens.
24. Vehicles (e.g., ATVs, tractors) shall not be used within native eelgrass (Zostera marina).
If there is no other alternative for site access, a plan will be developed describing specific
measures and/or best management practices that will be undertaken to minimize negative
effects to eelgrass from vehicle operation. The access plan shall include the following
components: (a) frequency of access at each location, (b) use of only the minimum
vehicles needed to conduct the work and a description of the minimum number of
vehicles needed at each visit, and (c) consistency in anchoring/grounding in the same
location and/or traveling on the same path to restrict eelgrass disturbance to a very small
footprint.
25. Vessels shall not ground or anchor in native eelgrass (Zostera marina) or kelp
rooted/attached brown algae in the order Laminariales) and paths through native eelgrass
or kelp shall not be established. If there is no other access to the site or the special
condition cannot be met due to human safety considerations, a site-specific plan shall be
developed describing specific measures and/or best management practices that will be
undertaken to minimize negative effects to eelgrass and kelp from vessel operation and
accessing the shellfish areas. The access plan shall include the following components: (a)
frequency of access at each location, (b) use of only the minimum number of boats and/or
crew members needed to conduct the work and a description of the minimum number of
boats and crewmembers needed at each visit, and (c) consistency in anchoring/grounding
in the same location and/or walking on the same path to restrict eelgrass disturbance to a
very small footprint.
26. Unless prohibited by substrate or other specific site conditions, floats and rafts shall use
embedded anchors and midline floats to prevent dragging of anchors or lines. Floats and
rafts that are not in compliance with this standard shall be updated to meet this standard
during scheduled maintenance, repair, or replacement, or before the end of the term of the
next renewed authorization. [Note: Any alternative to using an embedded anchor must be
approved by the NMFS.]
27. Activities that are directly associated with shellfish activities (e.g., access roads, wet
storage) shall not result in removal of native riparian vegetation extending landward 150
ft horizontally from MHHW (includes both wetland and upland vegetation), and
disturbance shall be limited to the minimum necessary to access or engage in shellfish
activities.
28. Native salt marsh vegetation shall not be removed and disturbance shall be limited to the
minimum necessary to access or engage in shellfish activities.
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Action Area
The action area is defined as all areas to be affected directly or indirectly by the federal action
and not merely the immediate area involved in the action (50 CFR 402.02). In delineating the
action area, we evaluated the farthest reaching physical, chemical, and biotic effects of the
action on the environment.
Geographic Distribution and Spatial Extent of Covered Activities
The Corps has compiled information from permit applications, and has obtained estimates from
the DNR, WDFW, and shellfish industry representatives, to document the geographic
distribution and spatial extent of continuing shellfish activities (footprints, acres, fallow acres),
and “new” shellfish activities (acres)(Corps 2015, pp. 40-49, 77-82). Table 2 below,
summarizes this information. All values are estimates based on the best available information.
While the Corps may issue permits and permit verifications authorizing shellfish activities for a
variety of purposes (i.e., commercial aquaculture, tribal and commercial wildstock harvest,
recreational enhancement, and restoration), the majority of these permits and permit
verifications (both by number and acreage) are issued to parties engaged in commercial
aquaculture (i.e., farming and production of shellfish for human consumption)(Corps 2015, pp.
40-45).
Applicants wishing to continue regulated shellfish activities must obtain reauthorization from the
Corps every five to ten years. The majority of the Corps’ shellfish permit actions (permits and
permit verifications) involve reauthorization of continuing activities and farms; specifically,
reauthorizations of continuing commercial, intertidal farms producing shellfish for human
consumption (Corps 2015, p. 5). Over the expected 20-year timeframe of the programmatic,
activities located within the same farm footprint could be reauthorized by the Corps as many as
three or four times.
Under the Corps’ regulatory program in Washington State, continuing shellfish activities are
those activities that were granted a permit, license, or lease from a state or local agency,
authorizing shellfish activities within a defined footprint prior to March 18, 2007 (Corps 2015, p.
6). “New” shellfish activities are those activities that were undertaken after March 18, 2007.
This programmatic consultation provides coverage for most culturing activities and practices on
continuing farms and operations (except excluded activities; Table 1, pp. 32). This
programmatic consultation extends this same coverage to most culturing activities and practices
on “new” farms and operations, but does not provide coverage for some specific suspended
culturing practices (i.e., initial installation of new rafts, floats, or FLUPSYs; relocation and/or
expansion of continuing rafts, floats, or FLUPSYs)(Corps 2015, p. 39).
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Some continuing shellfish activities include a fallowed farm footprint, or a portion of the defined
farm footprint that is currently fallow (i.e., left un-farmed or un-cultured). For the purpose of
defining and documenting the geographic distribution and spatial extent of fallowed farm
footprints, the Corps assessed status as of March 18, 2007, and again during 2012-2013 when
most continuing shellfish activities were last reauthorized (Corps 2015, p. 6).
Commercial intertidal aquaculture accounts for most of the continuing shellfish activities (99
percent), on a total of more than 36,000 acres (Table 2). Suspended commercial aquaculture,
defined here to include FLUPSYs, is very limited (less than 130 acres in total). “New” shellfish
activities conducted as restoration, or to enhance recreation opportunities, are also very limited
approximately 315 acres in total; Table 2).
Fallow acreage is greatest in Willapa Bay, where the Corps reports that more than 9,000 acres
have been fallow (approximately 37 percent of the continuing acreage) since 2007 or earlier
Corps 2015, pp. 40-49, 77-82). However, when expressed as a percentage of the continuing
acreage, fallowed farm footprints are more prevalent in Grays Harbor (approximately 61 percent)
and the north Puget Sound (approximately 63 percent)(Table 2).
The Corps has compiled information from permit applications, and has obtained estimates from
the DNR, WDFW, and shellfish industry representatives, to project or estimate future growth of
the industry over the next 20 years (Corps 2015, pp. 40-49, 77-82). These estimates suggest
future increases of approximately 32 percent in Hood Canal, 14 percent in south Puget Sound,
and 9 percent in north Puget Sound; they also suggest future growth of 3 percent and less than 1
percent in Grays Harbor and Willapa Bay, respectively.
This Opinion addresses permits and permit verifications issued by the Corps for shellfish
activities conducted on the tidelands and in the inland marine waters of the State of Washington
Figure 1, p. 9). The action area includes significant portions of fourteen counties: Clallam,
Grays Harbor, Island, Jefferson, King, Kitsap, Mason, Pacific, Pierce, San Juan, Skagit,
Snohomish, Thurston, and Whatcom Counties, Washington. Shellfish activities are conducted
across a wide range of tidal elevations, from +7 MLLW, to depths of -70 MLLW or greater. The
action area includes all of the tidelands and nearshore marine waters associated with continuing
and “new” shellfish activities (including projected future activities), encompassing an area of
approximately 38,716 acres (Corps 2015, pp. 40-49, 77-82).
When viewed from a landscape perspective, or even from the perspective of a single waterbody
e.g., Willapa Bay) or portion thereof (e.g., Totten Inlet or Samish Bay), shellfish activities are
variable in density and spatially discontinuous. At some locations, cultured tidelands extend
with only occasional interruption along extended lengths of the nearshore. At other locations,
cultured tidelands are interspersed along shorelines that support a range of other uses (residential,
recreational, etc.).
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Where cultured tidelands extend with only occasional interruption, interspersed uncultured areas
may experience direct or indirect effects, and are therefore considered part of the action area.
However, where cultured tidelands occur sporadically, and lengths of intervening shore are not
cultured but instead managed for other uses, these nearshore areas are unlikely to experience
measurable direct or indirect effects, and are therefore not considered part of the action area.
At all locations, the action area extends a minimum of 2,000 ft from the farm footprint (active
and fallow). This distance encompasses those areas of the nearshore that may experience
temporary effects (e.g., temporary effects to water quality, temporary effects to the sound
environment, etc.). Factoring and incorporating these other considerations, we estimate
conservatively that regulated shellfish activities in Washington State, specifically those for which
this Opinion provides programmatic coverage, are likely to directly or indirectly affect more than
45,000 acres of nearshore marine habitat (45,000 to 50,000 acres in total; Willapa Bay: approx.
30,000 acres; Grays Harbor: approx. 4,000 acres; north Puget Sound: approx. 5,000 acres; south
Puget Sound: approx. 5,000 acres; and, Hood Canal: approx. 3,000 acres).
The Corps’ BA describes subtidal wild geoduck harvest (Corps 2015, pp. 3, 5, 30, 34, 46, 47, 80,
84, 89, 92, 93, 99, 100). The Corps has indicated that they are seeking programmatic coverage
for subtidal wild geoduck harvest on a maximum of 6,050 acres per year, at depths to -70 ft
MLLW in Hood Canal and Puget Sound. While harvests might be conducted across a maximum
of 6,050 acres per year, available information suggests that harvest schedules are typically far
more limited (less than 300 acres per year) (Table 3).
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Table 2. Summary information describing the geographic distribution and spatial extent of shellfish activities in Washington State.
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Table 3. Summary information describing subtidal wild geoduck harvest in Washington State.
GEOGRAPHY Hood Canal South Puget
Sound
North Puget
Sound Total
Harvestable Acreage
State Lands 6,503 22,176 18,454 47,133
Non-State Lands 200 500 300 1,000
Sub-Total 6,703 22,676 18,754 48,133
DNR HCP
Annual Acreage
Typical Year (State Lands) 62 137 54 253
Maximum 1,500 3,000 3,000 6,000
Corps Programmatic
Annual Acreage
Typical Year (State Lands) 62 137 54 253
Maximum State Lands 1,500 3,000 3,000 6,000
Typical Non-State Lands 10 25 15 50
ANALYTICAL FRAMEWORK FOR THE JEOPARDY AND ADVERSE
MODIFICATION DETERMINATIONS
Jeopardy Determination
The following analysis relies on the following four components: (1) the Status of the Species,
which evaluates the rangewide condition of the listed species addressed, the factors responsible
for that condition, and the species’ survival and recovery needs; (2) the Environmental Baseline,
which evaluates the condition of the species in the action area, the factors responsible for that
condition, and the relationship of the action area to the survival and recovery of the species; (3)
the Effects of the Action, which determines the direct and indirect impacts of the proposed federal
action and the effects of any interrelated or interdependent activities on the species; and (4)
Cumulative Effects, which evaluates the effects of future, non-federal activities in the action area
on the species.
In accordance with policy and regulation, the jeopardy determination is made by evaluating the
effects of the proposed federal action in the context of the species’ current status, taking into
account any cumulative effects, to determine if implementation of the proposed action is likely to
cause an appreciable reduction in the likelihood of both the survival and recovery of listed
species in the wild.
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The jeopardy analysis in this Opinion emphasizes the rangewide survival and recovery needs of
the listed species and the role of the action area in providing for those needs. It is within this
context that we evaluate the significance of the proposed federal action, taken together with
cumulative effects, for purposes of making the jeopardy determination.
Adverse Modification Determination
The designation of critical habitat for bull trout uses the term primary constituent element (PCEs)
or essential features. The new critical habitat regulations (81 FR 7214) replace this term with
physical or biological features (PBFs). The shift in terminology does not change the approach
used in conducting a “destruction or adverse modification” analysis, which is the same regardless
of whether the original designation identified PCEs, PBFs, or essential features. Please note that
references to PCEs in the following analysis should be viewed as synonymous with PBFs.
Our analysis of effects to critical habitat relies on the following four components: (1) the Status
of Critical Habitat, which evaluates the range-wide condition of designated critical habitat for
the bull trout in terms of PCEs or PBFs, the factors responsible for that condition, and the
intended recovery function of the critical habitat overall; (2) the Environmental Baseline, which
evaluates the condition of the critical habitat in the action area, the factors responsible for that
condition, and the recovery role of the critical habitat in the action area; (3) the Effects of the
Action, which determines the direct and indirect impacts of the proposed federal action and the
effects of any interrelated or interdependent activities on the PCEs or PBFs, and how that will
influence the recovery role of affected critical habitat units; and (4) Cumulative Effects, which
evaluates the effects of future, non-federal activities in the action area on the PCEs or PBFs and
how that will influence the recovery role of affected critical habitat units.
The proposed federal action is evaluated to determine if it would likely result in a direct or
indirect alteration that appreciably diminishes the value of critical habitat for the conservation of
species). Such alterations may include, but are not limited to, those that alter the physical or
biological features essential to the conservation of a species or that preclude or significantly
delay development of such features.
STATUS OF THE SPECIES
Bull Trout
For a detailed account of bull trout biology, life history, threats, demography, and conservation
needs, refer to Appendix A: Status of the Species Bull Trout.
Marbled Murrelet
For a detailed account of marbled murrelet biology, life history, threats, demography, and
conservation needs, refer to Appendix B: Status of the Species Marbled Murrelet.
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STATUS OF CRITICAL HABITAT (BULL TROUT)
For a description of the rangewide status of designated bull trout critical habitat, refer to
Appendix C: Status of the Designated Critical Habitat for Bull Trout.
ENVIRONMENTAL BASELINE
Regulations implementing the ESA (50 CFR 402.02) define the environmental baseline as the
past and present impacts of all Federal, State, or private actions and other human activities in the
action area. Also included in the environmental baseline are the anticipated impacts of all
proposed federal projects in the action area that have undergone section 7 consultation, and the
impacts of state and private actions which are contemporaneous with the consultation in
progress.
There is a long history of culturing shellfish and other shellfish activities in every part of the
action area. Conditions prevailing in the action area exhibit the influence of these activities.
However, prevailing conditions also reflect broader patterns of land use and development, in the
nearshore environment, along shorelines, and in the larger watersheds that drain to these marine
waters.
Active and Fallow Lands
Some continuing shellfish activities include a fallowed farm footprint, or a portion of the defined
farm footprint that is currently fallow (i.e., left un-farmed or un-cultured). For the purpose of
defining and documenting the geographic distribution and spatial extent of fallowed farm
footprints, the Corps assessed status as of March 18, 2007, and again during 2012-2013 when
most continuing shellfish activities were last reauthorized (Corps 2015, p. 6).
Acreage classified as continuing active has by definition been engaged in shellfish
activity since at least 2007 and likely for much longer” (Corps 2015, p. 79).
Acreage identified as continuing fallow may also have been engaged in shellfish activity
at some point in the past … but is not engaged in shellfish activity presently … No
shellfish activity has occurred on fallow lands since at least 2007 and most for a much
longer time period (e.g., decades)” (Corps 2015, p. 79).
The aquatic habitat has … been modified by shellfish cultivation and harvest activities
that have been occurring for many years on the continuing active acreage. [However,]
the status of the aquatic habitat on fallow acreage is unknown since shellfish activities on
these lands have not occurred for many years. Based on the permit application record
which indicates the fallow areas have not had active cultivation since at least 2007, it is
assumed … that the fallow lands exist currently in an unmodified or ‘recovered’ state. A
resumption of shellfish activity in these areas may therefore result in impacts to the
aquatic habitat similar to the impacts that might result from aquaculture initiated in areas
classified as new” (Corps 2015, p. 79).
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Since no activity has occurred on the fallow lands for at least five years [since 2007], the
habitat conditions … [are] likely different than if [they] had been engaged in aquaculture
or some regular rotation of aquaculture. [The habitat] has likely ‘recovered’ from any
prior aquaculture impact” (Corps 2015, p. 81).
We divide the action area into five geographically distinct sub-areas: 1) Willapa Bay; 2) Grays
Harbor; 3) north Puget Sound; 4) south Puget Sound; and, 6) Hood Canal. We use these sub-
areas to structure our discussion of the environmental baseline; we describe, in summary form,
the variety of physical and biological settings where shellfish activities are conducted. Some
biologically relevant characteristics of the environmental baseline are similar, while others are
variable and may be very different, across the five sub-areas and individual farm sites.
Willapa Bay
Six watersheds drain to Willapa Bay: the North, Willapa, Palix, Nemah, Naselle, and Bear
watersheds. The largest river systems are the North, Willapa, and Naselle drainages. In total,
there are approximately 745 streams encompassing over 1,470 linear stream miles in the greater
Willapa watershed (Phinney and Bucknell 1975). Approximately two-thirds of the watershed’s
uplands are managed as commercial forest land. Cranberry farms comprise an additional seven
percent, including 1,400 acres of bogs.
Willapa Bay is relatively shallow. Approximately one-half of the estuary lies in the intertidal
zone (Andrews 1965 in Banas et al. 2004, p. 2414). At low tide, expansive subtidal areas are
covered by less than 10 ft of water. Three pronounced channels in the bay run to depths of 30 or
60 ft deeper than the surrounding tidelands. Tidal elevations vary by 14 to 16 ft over the course
of each tidal cycle, and approximately 50 percent of the bay’s volume is exchanged with the
Pacific Ocean on a daily basis. Willapa Bay opens to the Pacific Ocean at its northwest corner,
through a broad shallow pass extending approximately six miles between Cape Shoalwater and
Leadbetter Point at the tip of the Long Beach Peninsula. There are numerous sand bars, spits,
and islands, and large areas of exposed sand- and mudflat.
Major tributaries that support anadromous fish include the South Fork Willapa River, Trap
Creek, Mill Creek, Wilson Creek, Fork Creek, and Ellis Creek. The greater Willapa watershed
supports fall Chinook salmon (Oncorhynchus tshawytscha), coho salmon (O. kisutch), fall chum
salmon (O. keta), winter steelhead trout (O. mykiss), and coastal cutthroat trout (O. clarki clarki).
The Willapa Bay estuary is vital to the health of these populations, as it provides important
migratory and transitional habitat for outmigrating juvenile and returning adult salmonids. These
salmonid populations are not listed under the ESA, and current information indicates that the
greater Willapa watershed does not support the spawning and rearing of any ESA-listed
anadromous fish species, including bull trout.
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According to the Washington State Conservation Commission (Smith and Wenger 2001,
pp. 7-9), primary limiting factors for salmonid productivity in each of the major sub-watersheds
North, Willapa, Palix, Nemah, Naselle, and Bear) include lack of large wood, poor riparian
conditions, excess sediment inputs from landslides and the roads network, and significant loss of
lower floodplain and estuary habitat due to diking and tidegates; also, the Willapa and Naselle
watersheds experience seasonal high water temperatures and low dissolved oxygen levels.
The Washington State Conservation Commission reports the following regarding conditions in
the estuary (Smith and Wenger 2001, pp. 83-90):
More than 850 acres of wetland have been lost from the lower North River and estuary,
approximately 30 percent of the historic total.
More than 580 acres of wetland have been lost from the lower Willapa River and estuary,
approximately 20 percent of the historic total.
More than 810 acres of wetland have been lost from the lower Palix River and estuary,
approximately 30 percent of the historic total.
More than 500 acres of wetland have been lost from the lower Bear River and estuary,
approximately 30 percent of the historic total.
The Nemah and Naselle River estuaries are relatively intact and healthy, exhibiting
wetland losses of less than 2 percent of the historic total.
Invasive cordgrass (Spartina spp.) was introduced from the East Coast more than 100 years ago,
grows as dense meadows, displaces native eelgrass, and raises the elevation of tide and mudflats
Smith and Wenger 2001, p. 83). However, according to the U.S. Fish and Wildlife Service
USFWS 2011, p. 4-2), efforts led by federal, state, and county agencies, and the cooperation of
the oyster industry and private landowners, have eradicated Spartina from nearly all areas of
Willapa Bay.
Vast beds of eelgrass (Zostera spp.) occur at the lower levels of the intertidal zone and are a
staple food for several varieties of waterfowl (USFWS 2011, p. 4-26). Roots and stems of
eelgrass stabilize mudflats, and leaf blades are grazed and support the growth of diatoms and
small invertebrates. Eelgrass beds provide habitat for numerous species of mollusk and
crustacean, and serve as a nursery ground for juvenile, resident, and migrating fish. Non-native
Japanese eelgrass is also present and expanding (USFWS 2011, p. 4-26).
Marine Forage Fish
Forage fish resources include herring, anchovies, and smelt, all of which are important to other
fish and wildlife of the bay (USFWS 2011, p. 4-35). Pacific herring use Willapa Bay as a
spawning and nursery ground. The eggs are adhesive and can be found on rocks, piling,
seaweed, and eelgrass during January and February. Immature herring are found in the bay
during the spring, summer, and fall months. Northern anchovies (Engraulis mordax) are also
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plentiful in the bay during summer months. Longfin smelt (Spirinchus thaleichthys) and
eulachon (Thaleichthys pacificus) use both the deeper channels of the bay and the lower reaches
of tributary rivers and streams (USFWS 2011, p. 4-35).
Stick and Lindquist (2009) prepared the 2008 Washington State Herring Stock Status Report,
and reported the following regarding the condition of coastal stocks (p. 71):
Spawning populations of Pacific herring are documented in the coastal embayments of
Willapa Bay and Grays Harbor. Initial documentation of spawning activity for Grays
Harbor occurred in 1998 and has been observed intermittently since that time. Herring
stock assessment by WDFW has traditionally been focused on presumed larger Puget
Sound stocks and limited assessment of coastal herring stocks currently takes place.”
Herring spawning activity has been observed in February and March in Willapa Bay and
February through March in Grays Harbor. Most of the spawn deposition in Grays Harbor
appears to occur in the South Bay/Elk River estuary area of south Grays Harbor with
some also documented in the Ocean Shores/Point Damon area.”
Little is known about the [current status of the] coastal herring populations. However,
due to the geographical separation of their spawning grounds, the Willapa Bay and Grays
Harbor spawning populations are considered to be discrete. Herring spawned in coastal
locations are likely components of large summer herring aggregations that concentrate in
coastal offshore areas including the western end of the Strait of Juan de Fuca and the west
coast of Vancouver Island.”
The limited information available and current sampling effort for the coastal herring
populations does not provide adequate basis for evaluation of the status of these stocks.
Abundance of these stocks is considered relatively small compared to Puget Sound
herring stocks. The cumulative spawning biomass estimate for these areas has ranged
from 0 to 694 tons annually.”
Reported fishery landings of seven tons or less have occurred since 1999 for bait herring
caught in Grays Harbor, with no reported landings from Willapa Bay in recent years. No
directed herring fishery harvest is allowed in Washington’s coastal waters.”
Limited survey effort suggests a decrease in spawning biomass for the Willapa Bay
herring stock since 2004. Documented spawning grounds are limited to the southern
portion of the bay. Little is known about this stock’s life history, although it is likely that
these fish spend significant time in ocean waters” (Stick and Lindquist 2009, p. 74).
Figures 17 and 18 report all of the available data to describe the annual spawning biomass for
Grays Harbor and Willapa Bay herring stocks (Stick and Lindquist 2009, pp. 73, 75).
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More recently, Stick, Lindquist, and Lowry (2014, Executive Summary) reported: “This is the
fifth edition of the … Pacific herring stock status report. Unlike previous editions, the scope of
this report is limited to Puget Sound due to a lack of assessment of coastal herring stocks since
the last stock status report published in 2009.”
In 2009, the Service reported that surveys are incomplete and there appear to be few or no data to
describe the status of coastal surf smelt and Pacific sand lance stocks (USFWS 2009a, pp. 99,
100). It appears that is still the case in 2015.
Figures 19 and 20 identify shellfish activities located in the Willapa Bay sub-area, and their
proximity to documented eelgrass beds and marine forage fish spawning habitats.
Figure 17. Annual spawning biomass for Grays Harbor herring stocks
Stick and Lindquist 2009, pp. 73, 75)
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Figure 18. Annual spawning biomass for Willapa Bay herring stocks
Stick and Lindquist 2009, pp. 73, 75)
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Figure 19. Shellfish operations and eelgrass in Willapa Bay
Corps 2015, Appendix D)
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Figure 20. Shellfish operations and forage fish in Willapa Bay
Corps 2015, Appendix E)
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Grays Harbor
Grays Harbor is a medium-sized estuarine bay, approximately 17 miles long and 12 miles wide,
covering at high tide approximately 97 square miles (Smith and Wenger 2001, p. 91).
Orientation is roughly east-west, with a 2 mile-wide western channel opening to the Pacific
Ocean. The Chehalis River, which enters at the easternmost extent of Grays Harbor, is the
second largest river basin in Washington State. Grays Harbor’s other major tributary is the
Humptulips River. The Hoquiam River, Johns River, and several other direct tributaries have far
smaller drainage basins (Smith and Wenger 2001, p. 91). All of Grays Harbor’s direct
tributaries, and several additional small- and medium-sized tributaries to the lower Chehalis
River (e.g., the Wishkah and Wynoochee Rivers), are tidally-influenced along their lower
reaches.
The estuarine habitats in Grays Harbor are more intact than many other similar systems in
Washington State. Historical losses (as a result of diking, fill, etc.) are estimated at 30 percent
Smith and Wenger 2001, p. 16). However, while some portions are relatively undeveloped
e.g., North Bay), the inner harbor and vicinity of the Cities of Hoquiam and Aberdeen are
heavily industrialized (Smith and Wenger 2001, p. 91).
The Chehalis River is more than 115 miles in length and drains an area of approximately 2,200
square miles, making it the second largest river basin in Washington State. Along its tidally-
influenced lower 11 miles, side-channel, riparian, and floodplain habitats along the Chehalis
River are in good to excellent condition, and are considered a high priority for conservation
Smith and Wenger 2001, p. 18).
The greater Grays Harbor-Chehalis watershed supports large and comparatively healthy
populations of Chinook, chum, and coho salmon, steelhead and cutthroat trout. The lower
Chehalis River and Grays Harbor estuary are vital to the health of these populations, as they
provide important migratory and transitional habitat for outmigrating juvenile and returning adult
salmonids.
Water and sediment quality are identified as limiting factors in some portions of the basin. The
basin includes more than 100 impaired river segments, for which Ecology has established seven
Total Maximum Daily Loads (TMDLs) (Ecology 2004, p. 1). Historical marine and industrial
uses focused around the inner harbor, including pulp and paper mills, have been the cause for
water quality concerns (and related fish kills) dating as far back as 1928 (Smith and Wenger
2001, p. 92). However, modernized practices and operations appear now to have controlled and
greatly reduced commercial and industrial inputs. Sediment evaluations point to localized metal
and synthetic organic contaminant concentrations, but it appears that an active sediment transport
regime and good flushing prevent widespread chemical contamination (Ecology 1999, p. iii).
Excess sediment delivery is another important limiting factor for the basin (Smith and Wenger
2001, p. 17). The Chehalis River basin delivers immense quantities of sediment to Grays
Harbor, and maintenance of the lower Chehalis River-Grays Harbor navigational channel
requires dredging and in-water disposal of more than 2.5 million cubic yards of sediment
annually (Smith and Wenger 2001, p. 94). While the system exhibits naturally high levels of
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turbidity and sedimentation at some times of year (Ecology 1993; 1994), dredging and channel
maintenance produce turbidity, and the potential for resuspension of contaminated sediments,
with potential consequences for juvenile fish and eelgrass habitat in particular (Smith and
Wenger 2001, p. 94). Sand bars, spits, and islands, beaches, and large areas of exposed sand-
and mudflat may be found throughout large portions of Grays Harbor.
Grays Harbor’s estuarine habitats lack large woody material and, at some locations, have been
further degraded by the introduction of invasive, non-native vegetation such as Spartina (Smith
and Wenger 2001, pp. 92, 98). Both trends have the effect of reducing available cover and
forage habitat for young salmonids, with potential consequences for survival rates and growth.
Marine Forage Fish
The status of marine forage fish is specifically described here because of their importance to the
bull trout and marbled murrelet, and their link to the sensitive habitats that are affected by
shellfish activities. Forage fish play a key role in the food web of the marine environment and
make up a significant proportion of the diets for bull trout and marbled murrelets.
In Grays Harbor … the primary [Pacific] herring spawning habitat is the outer edges of native
salt-marsh beds, where a turf of rockweed (Fucus), sea-lettuce (Ulva), pickleweed (Salicornia)
and salt-grass (Distichlis) in the uppermost intertidal zone serves as spawn deposition substrate
Spawning [Pacific] herring also use salt-marsh vegetation, along with beds of over-wintering
cordgrass (Spartina) stubble and native eelgrass beds, in Willapa Bay (WDFW unpub. data) …
Pacific] herring spawning has been observed on dock pilings in Puget Sound and coastal bays
WDFW unpub. data)” (Penttila 2007, p. 6).
Stick and Lindquist (2009) prepared the 2008 Washington State Herring Stock Status Report,
including a report on the status of coastal stocks (see Environmental Baseline, Willapa Bay).
Figures 17 and 18 (pp. 48, 49) report all of the available data to describe the annual spawning
biomass for Grays Harbor and Willapa Bay herring stocks (Stick and Lindquist 2009, pp. 73,
75).
Figures 21 and 22 identify shellfish activities located in the Grays Harbor sub-area, and their
proximity to documented eelgrass beds and marine forage fish spawning habitats.
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Figure 21. Shellfish operations and eelgrass in Grays Harbor
Corps 2015, Appendix D)
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Figure 22. Shellfish operations and forage fish in Grays Harbor
Corps 2015, Appendix E)
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Puget Sound and Hood Canal
This sub-section discusses the north Puget Sound, south Puget Sound, and Hood Canal sub-areas.
This geography and portion of the action area presents a huge variety of physical, chemical, and
biological conditions. Describing the environmental baseline for the variety of physical and
biological settings where shellfish activities are conducted is not a simple task, and therefore the
Service has used and incorporates here by reference the excellent summary prepared by the DNR
in support of their Aquatic Lands HCP (DNR 2014a). The DNR’s Aquatic Lands HCP planning
document, which was produced in part with funding provided by the Service, includes a lengthy
discussion of physical, chemical, and biological characteristics, existing conditions, and, land
uses and development. Appendix D includes excerpts from the DNR Aquatic Lands HCP
planning document (DNR 2014a); those summaries are incorporated here by reference.
Existing Conditions for Native Eelgrass
The 2009 Puget Sound Ambient Monitoring Program (PSAMP) Submerged Vegetation
Monitoring Project Report reached the following conclusions (Gaeckle et al. 2011, Executive
Summary):
1) The results in 2009 continue to indicate a pattern of Z. marina decline throughout
Puget Sound. This result is supported by three main findings:
a. There have been twice as many sites with long-term declining trends in Z. marina area
than increasing trends since 2004.
b. More year-to-year significant declines than increases in Z. marina area were evident in
eight out of nine sampling intervals since 2000.
c. The multiple parameter assessment identified the Hood Canal, San Juan-Straits, and
the Central Puget Sound Regions with evidence of Z. marina decline and the Hood Canal
Region having the highest level of concern for Z. marina loss. The assessment found no
current concern for Z. marina loss in the Saratoga-Whidbey and North Puget Sound
Region.”
2) The 2009 Z. marina area estimate in Puget Sound is 22,000 ± 3,600 hectares [± 95
percent Confidence Interval (CI)]. The decadal weighted mean over 2000-2009 is 21,500
1,400 ha (± 95 percent CI). The patterns of Z. marina decline observed at the site level
are not reflected in the soundwide areal estimate. A long-term, weighted linear
regression analysis showed a marginally significant increasing trend in Z. marina area at
the soundwide scale.”
Although there is a marginally significant increasing trend in Z. marina area, the pattern
of site level decline throughout Puget Sound suggests losses are prevalent at individual
sites. There is consistently greater prevalence of year-to-year and long-term declines in
Z. marina area and depth distribution throughout the study area. There is also strong
evidence of Z. marina decline in the Hood Canal region. The occurrence and soundwide
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distribution of sites with significant declines is of concern for habitat connectivity and
ecological functions. The effect of loss in areas that are considered critical nursery,
forage, and migration habitat for ecologically and economically important species could
affect ecosystem processes and the overall health of these areas and Puget Sound”
Gaeckle et al. 2011, Executive Summary).
The 2010-2013 PSAMP Submerged Vegetation Monitoring Project Report reached the following
conclusions (Gaeckle et al. 2015, Executive Summary):
1) Soundwide native seagrass area has been stable over the monitoring record [2003-
2013]. There is no significant long-term linear trend in soundwide native seagrass area
permutation test, p=0.63). It is possible that small variations in soundwide native
seagrass area occurred below the detection limits of the program, but seagrass in Puget
Sound has not experienced a major decline.”
2) Current native seagrass conditions have not yet met the Puget Sound Partnership’s
target for a 20 percent increase in area by 2020. Statistical tests show that current
soundwide native seagrass area is less than the target defined by the Puget Sound
Partnership. It is too early to tell if the trend in seagrass area is on a trajectory to meet the
target by 2020. Test results are equivocal on whether current conditions have progressed
from the baseline conditions.”
3) Most of the 347 individual sites that were analyzed for change were stable
throughout the entire monitoring record. Twenty-five sites decreased in native seagrass
area, 17 sites increased in native seagrass area, 209 sites experienced no detectable
change, and 60 sites did not have seagrass beds present. Thirty-six sites had insufficient
data for trend analysis (sampled only 1 year). Many of the sites with long-term decreases
in native seagrass area were located near Hood Canal, Southern Puget Sound, and the San
Juan Islands ([Figure 23]).”
4) Seagrass conditions improved in the recent 2-3 years. Analysis of individual site
data in recent years (n=156) shows that there are more sites with increasing (n=25) than
decreasing (n=5) native seagrass area between 2010 and 2013. The reason is unknown; it
could be a short-term anomaly or part of a longer-term pattern ([Figure 24]).”
5) Native seagrass area increased at two river deltas following major restoration
projects: the Skokomish River delta in lower Hood Canal and the Nisqually River delta in
southern Puget Sound” (Gaeckle et al. 2015, Executive Summary).
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Figure 23. Increases and decreases in native seagrass area based on all available data for each
site (2003-2013)
Gaeckle et al. 2015, Executive Summary)
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Figure 24. Increases and decreases in native seagrass area based on all available data for each
site (2010-2013)
Gaeckle et al. 2015, Executive Summary)
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Existing Conditions for Marine Forage Fish
Forage fishes in general, and [Pacific] herring specifically, are vital components of the marine
ecosystem and are a valuable indicator of the overall health of the marine environment. Many
species of sea birds, marine mammals, and finfish … depend on herring as an important prey
item (DFO 2001, Fresh et al. 1981). Significant predation occurs at each stage of the herring life
cycle, starting with predation on deposited spawn by invertebrates, gulls, and diving ducks.
Reflecting the importance of herring in the Puget Sound ecosystem, the spawning biomass of
Puget Sound herring was selected as a vital sign indicator of the health of Puget Sound by the
Puget Sound Partnership” (Stick, Lindquist, and Lowry 2014, p.1).
Forage fish are loosely defined as small, schooling fishes that form critical links between the
marine zooplankton community and larger predatory fish, seabirds, and marine mammals in the
marine food web (Penttila 2007, Executive Summary; PSAT 2007). The three most common
marine forage fish species in Puget Sound are Pacific herring, surf smelt, and Pacific sand lance.
These species and their spawning habitats all commonly occur on Puget Sound beaches and in
the intertidal zone, and all three use adjacent nearshore habitats as nursery grounds. “Within the
Puget Sound Basin, where their spawning areas have been most completely mapped, each
species appears to use approximately 10 percent of the shoreline spawning habitat during the
year” (Penttila 2007, Executive Summary). Other marine forage fish species include northern
anchovy, eulachon or Columbia River smelt, and longfin smelt. These species do not spawn in
Puget Sound but do contribute to the total biomass of marine forage fish in Puget Sound (Penttila
2007, Executive Summary).
Some months before the onset of spawning activity, ripening Pacific herring begin to assemble
adjacent to spawning sites in pre-spawning holding areas (Penttila 2007, pp. 6-8). They spawn
by depositing their eggs on eelgrass, algae, hard substrates, man-made structures (such as
pilings), and occasionally polychaete tubes. Figure 25 identifies most of the documented
spawning areas in Puget Sound; two spawning locations only recently documented, Elliot Bay
and Purdy (Stick, Lindquist, and Lowry 2014, p. 5), are not depicted. Most egg deposition
occurs from 0 to -10 ft MLLW (Bargmann 1998), but in some areas spawning can occur as deep
as - 32 ft (-10 m)(Penttila 2007, pp. 6-8). The eggs incubate for 10 to 14 days prior to hatching.
Following hatching, the larvae drift in the currents. Following metamorphosis, young herring
spend their first year in Puget Sound; some then spend their entire lives within Puget Sound,
while others migrate to the open ocean to mature. After reaching sexual maturity (2 to 4 years),
Pacific herring migrate back to spawning grounds. Most spawning occurs between mid-January
and March.
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Figure 25. Documented Pacific herring spawning areas in Puget Sound
Penttila 2007, p. 3)
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Pacific herring are visual feeders. They forage on planktonic macro-zooplankton that may be
found anywhere across the width of Puget Sound. They undergo diurnal depth migrations, i.e.,
deep during the day and shallow at night, often concentrating at depths of 180 to 240 ft where
prey are abundant. During the daytime, some (commonly juveniles) may reside at midwater or
surface water depths. Juvenile Pacific herring commonly rear at shallow depths (a few ft), even
in the daytime.
Surf smelt are common, year-round residents in the nearshore areas of Puget Sound. They are a
short-lived fish with most spawning populations comprised of 1- and 2-year old fish. Spawning
occurs on mixed-sand and gravel substrates in the upper intertidal zone, generally higher than +7
ft MLLW (Penttila 2007, pp. 3, 8-10). Eggs incubate for two to six weeks. It appears that surf
smelt spawn year-round in portions of Puget Sound.
Surf smelt feed on macrozooplankton and are closely associated with the shoreline, spending
their entire lives shoreward of the 10-fathom contour (-60 ft). There is no information on
movement patterns and no evidence of seasonal migration out the Strait of Juan de Fuca. Their
home ranges are unknown and there has been no region wide assessment of stock status (Penttila
2007, pp. 3, 8-10). The WDFW has documented spawning habitat on approximately 200 lineal
miles of Puget Sound shoreline. However, the surveys are incomplete (Bargmann 1998).
Pacific sand lance (or candlefish) are common, year-round residents in the nearshore areas of
Puget Sound. They feed on macrozooplankton. During spring and summer months, Pacific sand
lance are considered epibenthic, schooling pelagically during the day to forage, and burrowing in
the benthic substrate at night (Penttila 2007, pp. 3, 4, 10, 11). Their home ranges are unknown
and there has been no region-wide assessment of stock status. Juveniles may be more closely
associated with shorelines and protected bays, often found in mixed schools with Pacific herring
and surf smelt of similar age and size. There is no information on movement patterns and no
evidence of seasonal migration out the Strait of Juan de Fuca.
The WDFW has documented Pacific sand lance spawning habitat on approximately 130 lineal
miles of shoreline; however, the surveys are incomplete (Bargmann 1998). Several spawnings
may occur at any given site during the November to February spawning season. Pacific sand
lance frequently use the same stretches of beach used by surf smelt, and sometimes at the same
time of year (Bargmann 1998). Spawning is confined to the upper intertidal zone, generally
higher than + 5 ft MLLW. Eggs incubate for approximately 30 days (Penttila 2007, pp. 3, 4, 10,
11).
In 2009, the Service reported the following regarding the status of marine forage fish in Puget
Sound (USFWS 2009a, pp. 62, 63, 98, 99):
Many fish populations have been depleted due to overfishing, reduction in the amount or
quality of spawning habitat, and pollution. As of 2004, only 50 percent of the Puget
Sound herring stocks were classified as healthy or moderately healthy, with north Puget
Sound’s stock being considered depressed and the Strait of Juan de Fuca’s stocks being
classified as critical (McShane et al. 2004a).”
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Natural mortality in some of these stocks has increased; e.g., the mean estimated annual
natural mortality rate for sampled stocks from 1987 through 2003 averaged 71 percent,
up from 20 to 40 percent in the late 1970s (WDFW 2005a).”
There is currently only one commercial herring fishery which operates primarily in
south and central Puget Sound (WDFW 2005c) where herring stocks are healthier.”
While there are commercial and recreational fisheries for surf smelt, the amount of
harvest does not appear to be impacting the surf smelt stocks. There are no directed
commercial fisheries for sand lance (Bargmann 1998). Anchovies are taken
commercially within coastal and estuarine waters of Washington. While the current
harvest level doesn’t appear to be impacting anchovy stocks, there is no current
abundance information (Bargmann 1998).”
WDFW recognizes 19 stocks of herring in Puget Sound, based on the timing and
location of spawning activity (Stick 2005; PSAT 2007). The grounds are well defined
and the timing of spawning is very specific, seldom varying more than seven days from
year to year (Bargmann 1998). Puget Sound herring are thought to be a mix of ‘resident’
and ‘migratory’ stocks, with the migratory populations cycling between winter spawning
grounds in the inside waters and summer on the continental shelf off the mouth of the
Strait of Juan de Fuca (Penttila 2007). However, which fish or stocks are migratory and
which are resident is unknown. It appears as though neither post-spawning adult herring
nor pre-recruit herring persist in numbers in the immediate vicinity of any spawning
ground during non-spawning times of year (Penttila 2007).”
For the period of 2003 to 2004 only 50 percent of all Puget Sound herring stocks were
classified as ‘healthy’ or ‘moderately healthy,’ whereas 71 percent and 83 percent of
stocks were considered healthy or moderately healthy in 2000 and 2002, respectively.
One stock was added to the critical list in 2004. South and central Puget Sound stocks
have maintained a healthy stock status since 1994, while north Puget Sound’s combined
stocks have declined from a healthy status in 1994 to [a] depressed [status] since 1998.
The Strait of Juan de Fuca’s status has been consistently classified as ‘critical’ since
1994” (USFWS 2009a, pp. 62, 63, 98, 99).
In 2009, the Service reported that surveys are incomplete and there appear to be few or no data to
describe the status of Puget Sound surf smelt and Pacific sand lance stocks (USFWS 2009a, pp.
99, 100). It appears that is still the case in 2015.
Stick, Lindquist, and Lowry (2014) have reported findings from the 2012 Washington State
Herring Stock Status Report. Important trends and conclusions include the following:
Fewer stocks may be classified as ‘healthy’ or ‘moderately healthy’.
The Cherry Point stock shows no signs of recovery from its critically low level of
abundance, and the Strait of Juan de Fuca regional spawning biomass continues to be at a
low level of abundance.
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Estimated spawning biomass for the Skagit Bay stock has dropped by over 50 percent
since 2009.
The Fidalgo Bay stock has decreased substantially in recent years. Compared to the
previous 25 year mean spawning biomass, the 2012 status is very depressed.
Two stocks, N.W. San Juan Island and Kilisut Harbor, have not had detectable spawning
activity since 2008 and have a ‘disappearance’ classification.
If Puget Sound herring stocks interact as a metapopulation, observed ‘disappearance’
and/or dramatic decreases in abundance of individual stocks may not be cause for major
concern.
Appendix D includes excerpts from Stick, Lindquist, and Lowry (2014); those fuller excerpts are
incorporated here by reference.
Selleck et al. (2015) recently published the first synthesis of historical sand lance capture records
for the inland waters of Washington State. They report the following:
Despite a number of studies characterizing their distribution and habitat use in Alaska
and British Columbia, surprisingly little is known about population attributes in the
Salish Sea [which includes Puget Sound]. We compiled and analyzed 15,192 records
collected from 1,630 sites, primarily by beach seine or tow net in nearshore shallow areas
between 1970 and 2009, to determine sand lance spatial and seasonal distribution in the
inland waters of Washington State” (p. 185).
Studies have shown that at nearshore sites in the region, juvenile Chinook salmon …
feed largely on larval and juvenile sand lance (Duffy and others 2010). Sand Lance also
are the most numerically abundant prey in the diet of lingcod (Ophiodon elongates), a
recreationally important species (Beaudreau and Essington 2007) … Additionally, they
are one of the two most important prey for common murres (Uria aalge) and rhinoceros
auklets (Cerorhinca monocerata; Lance and Thompson 2005), and can comprise up to 67
percent of the diet of marbled murrelets … in regional populations (Norris and others
2007)” (p. 185).
Commercial exploitation of this species is prohibited by the Washington Department of
Fish and Wildlife (Bargmann 1998). Consequently, unlike other forage fishes such as
Pacific herring … and surf smelt … stock structure and population assessments have not
been conducted (Mitchell 2006; Stick and Lindquist 2009)” (p. 186).
Sampling effort was not uniform spatially or temporally … No data were available from
Hood Canal. [The] Whidbey basin had the highest sampling effort … [and] the Strait of
Juan de Fuca basin had the lowest sampling effort … Of Puget Sound’s estimated 3,970
km of shoreline, approximately 13 percent was sampled for sand lance … which were
present along 78 percent of the shoreline sampled” (p. 187).
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The largest catches … occurred between May and August, with peak catches estimated
at 16,000 and 50,000 fish recorded in the San Juan Archipelago in June 1976 and 2005,
respectively. Work conducted in Alaska also showed increased total beach seine catch …
in summer (Johnson and others 2008). Seasonal abundance has important biological
implications … Abundance of sand lance in marbled murrelet diet varies seasonally, with
fewer sand lance in the winter diet (Burkett 1995). Reduced occurrence in winter could
reflect an absolute reduction in … availability in winter, fewer large schools of fish, or an
increase in the relative abundance or distribution of another more preferred prey fish”
pp. 192, 193).
Lacking a better understanding of the basic biology of this species, it is impossible to
gauge the potential anthropogenic or natural impacts on regional food webs. This study
demonstrates that sand lance are present throughout the inland waters of Washington,
which is consistent with the hypothesis that they are important drivers of local marine
food webs … [However,] numerous knowledge gaps exist about this ecologically
important fish in the inland waters of Washington, including basic knowledge about the
status of populations and subpopulations” (Selleck et al. 2015, p. 193).
Figures 26 through 33 identify shellfish activities located in the north Puget Sound, south Puget
Sound, and Hood Canal sub-areas, and their proximity to documented eelgrass beds and marine
forage fish spawning habitats.
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Figure 26. Shellfish operations and eelgrass in north Puget Sound
Corps 2015, Appendix D)
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Figure 27. Shellfish operations and eelgrass in north Puget Sound
Corps 2015, Appendix D)
Figure 28. Shellfish operations and forage fish in north Puget Sound
Corps 2015, Appendix E)
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Figure 29. Shellfish operations and forage fish in north Puget Sound
Corps 2015, Appendix E).
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Figure 30. Shellfish operations and eelgrass in south Puget Sound
Corps 2015, Appendix D)
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Figure 31. Shellfish operations and forage fish in south Puget Sound
Corps 2015, Appendix E)
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Figure 32. Shellfish operations and eelgrass in Hood Canal
Corps 2015, Appendix D)
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Figure 33. Shellfish operations and forage fish in Hood Canal
Corps 2015, Appendix E)
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Current Condition in the Action Area (Bull Trout and Critical Habitat)
The action area includes all of the tidelands and nearshore marine waters associated with
continuing and new (projected future) shellfish activities, encompassing an area of
approximately 38,716 acres (Corps 2015, pp. 40-49, 77-82). Where cultured tidelands extend
with only occasional interruption, interspersed uncultured areas may experience direct or indirect
effects, and are therefore considered part of the action area. At all locations, the action area
extends a minimum of 2,000 ft from the farm footprint (active and fallow). Factoring and
incorporating these other considerations, we estimate conservatively that regulated shellfish
activities in Washington State, specifically those for which this Opinion provides programmatic
coverage, are likely to directly or indirectly affect more than 45,000 acres of nearshore marine
habitat (45,000 to 50,000 acres in total; Willapa Bay: approx. 30,000 acres; Grays Harbor:
approx. 4,000 acres; north Puget Sound: approx. 5,000 acres; south Puget Sound: approx. 5,000
acres; and, Hood Canal: approx. 3,000 acres).
Anadromous bull trout forage and migrate along the nearshore (generally in water less than 10
meters deep) and are opportunistic foragers, often traveling to access and take advantage of
seasonally abundant food resources. Anadromous bull trout feed primarily on marine forage fish
and juvenile salmonids when in the marine environment. Eelgrass meadows and other complex
nearshore marine and estuarine habitats are a focal point for their foraging activities and provide
essential prey resources.
Hayes et al. (2011) used acoustic transmitter tags, habitat class preferences, and compositional
analysis of selection to describe bull trout movements, position, and marine habitat use in and
around the Skagit River delta:
Summaries of fish positions and habitat descriptions were based on our best estimate of
a fish’s position during each ‘event’ … Detections separated by at least 2 hours were
considered separate ‘events’.” (pp. 398, 399)
Habitat descriptions included shoreline, substrate, and vegetation classes (McBride et al.
2006) … These data were available for the majority of bay perimeter and shallow water
habitat, but not for the Swinomish Channel … Substrate and vegetation data were
available only within the intertidal zone.” (p. 399)
We ranked habitat class preferences (Aebischer et al. 1993) by using a compositional
analysis of selection (Leban 1999) to compare habitat use with habitat availability.” (p.
399)
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Habitat class data and compositional analysis … suggested that bull trout use of habitats
was not random … Coastal deposits, low bank, and sediment bluff accounted for nearly
76 percent (by length) of natural shoreline classes … Modified and unmodified shoreline
classes were used in proportion to their availability … common modifications included
concrete bulkhead and riprap … Green algae, eelgrass (Zostera sp.), and unvegetated
were frequent vegetation classes; combined, they made up more than 70 percent of the
area used by bull trout … Use of spit-berm, salt marsh habitats, and green algae
vegetation classes was greater than expected, based on availability, while the unvegetated
class ranked low.” (p. 400)
One behavior that was common among bull trout in marine waters was the use of
shallow, nearshore habitats … In general, fish positions were within 400 m of the
shoreline and shallower than 4 m … Although some bull trout probably crossed sections
of Skagit Bay with water depths greater than 10 m to reach the east shore of Whidbey
Island, our detections never indicated that fish maintained positions in these deeper areas
The general pattern suggested that individual bull trout moved from the river to a
discrete section of bay shoreline or the Swinomish Channel, stayed there for much of
their marine residency, and then returned to the river … We found no evidence of
consistently nomadic behavior for any fish.” (pp. 403, 404)
Our descriptions of substrate, vegetation, and shoreline classes in bull trout habitats are
the first of this type and thus are valuable despite incomplete mapping … However,
habitat preference data should be considered preliminary because the number of
detections of some fish was small, our fish location data were imprecise, and preference
may be related to other factors … More detailed data are required to determine bull trout
selection and intensity of use for specific habitats.” (Hayes et al. 2011, p. 404)
Appendix D includes excerpts from Hayes et al. (2011); those fuller excerpts are incorporated
here by reference.
Willapa Bay and Grays Harbor: Several coastal drainages to the north, including the Quinault,
Queets, and Hoh Rivers, support local populations and spawning of anadromous bull trout. Bull
trout occur regularly in Grays Harbor and its lower tributaries. They have been documented in
Willapa Bay and its tributaries, though infrequently and in low numbers. These represent the
southernmost populations of anadromous bull trout found anywhere in North America.
The action area provides nearshore marine, foraging, migrating, and overwintering (FMO)
habitat for adult and subadult bull trout originating from coastal Washington core areas and local
populations to the north (the Quinault, Queets, and Hoh River bull trout core areas). The best
available, current information indicates that the major tributaries to Grays Harbor and Willapa
Bay do not support bull trout spawning and rearing, or local populations.
The Quinault, Queets, and Hoh River bull trout core areas support small and moderately sized
local bull trout populations. These local populations appear to be relatively stable, with some
year-to-year variation in the measured indices for abundance and reproduction.
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North Puget Sound: All of the north Puget Sound’s larger drainages support local populations
and spawning of anadromous bull trout. The Elwha and Dungeness Rivers, which both drain to
the Strait of Juan de Fuca, also support local populations. Bull trout occur regularly and in
significant numbers throughout the nearshore marine areas of the north Puget Sound.
The action area provides nearshore marine FMO habitat for adult and subadult bull trout
originating from several core areas (e.g., the Nooksack, Skagit, Stillaguamish, and Snohomish-
Skykomish River bull trout core areas), and numerous local populations. These bull trout core
areas support large and moderately sized local bull trout populations, including the largest
anadromous bull trout populations found anywhere in Washington State (and the entire range of
the species). Most of these local populations appear to be relatively stable, with some year-to-
year variation in the measured indices for abundance and reproduction. The best available,
current information indicates that the Dungeness River continues to support a small population
of anadromous bull trout, but few (if any) anadromous bull trout remain in the Elwha River
system (due to prolonged isolation above the dams, which have recently been removed).
South Puget Sound: The Puyallup River bull trout core area supports anadromous, fluvial, and
resident life history forms. The core area is believed to support the Puget Sound’s southernmost
anadromous bull trout populations. Data available for the Puyallup River core area are
incomplete and do not allow for an accurate estimation of adult abundance or reproduction.
However, trap counts at the Buckley Diversion Dam, and other available sources, suggest that
the Puyallup River core area supports only low to very low numbers of anadromous bull trout.
The action area provides nearshore marine FMO habitat for adult and subadult bull trout
originating from the Puyallup River core area. However, the best available, current information
indicates that tributaries to the Puget Sound located south of Tacoma (including the Nisqually
River) do not support bull trout spawning and rearing, or local populations.
The Puyallup River bull trout core area supports moderately sized local bull trout populations,
including a small population of anadromous bull trout. Most of these local populations appear to
be relatively stable or increasing, with some year-to-year variation in the measured indices for
abundance and reproduction. Bull trout populations in the White River have been increasing
since 2009, possibly due to a significant increase in the populations of pink and coho salmon.
Hood Canal: The nearshore marine waters of Hood Canal provide FMO habitat for anadromous
bull trout. Bull trout originating from the Dungeness or other, north Puget Sound core areas may
occasionally occur within northern portions of Hood Canal.
There are at least two local populations of bull trout in the Skokomish River. One is an adfluvial
population that inhabits Lake Cushman and the North Fork Skokomish River above the lake.
Another population, found in the South Fork Skokomish River, is a depressed but stable fluvial
population. Anadromy has not been documented in the Skokomish River populations and no
bull trout have been captured in the nearshore marine areas of the estuary. However, historic
reports of bull trout in rivers such as the Duckabush, Dosewallips, Hamma Hamma, and
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Quilcene Rivers suggest that a few individuals may be present in the nearshore marine waters of
Hood Canal. The local populations of the Skokomish River are depressed but relatively stable,
with some year-to-year variation in the measured indices for abundance and reproduction.
Factors Responsible for the Condition of the Species
The factors responsible for the condition of the species (bull trout) in the action area are
described elsewhere (see Status of the Species, Status of Critical Habitat, and Environmental
Baseline).
Factors Responsible for the Condition of Critical Habitat
In nearshore marine areas, the inshore extent of critical habitat is the MHHW line, including the
uppermost reach of the saltwater wedge within tidally influenced, freshwater heads of estuaries.
Critical habitat extends offshore to a depth of 10 meters (33 ft) relative to the MLLW line (75 FR
63935; October 18, 2010).
The action area includes approximately 12,000 acres of designated bull trout critical habitat,
mostly located in Grays Harbor (approximately 4,000 acres), the north Puget Sound
approximately 5,000 acres), and Hood Canal (approximately 3,000 acres)(Corps 2015 Appendix
H, Figures H-1 through H-8)(Table 4). South of Tacoma, designated bull trout critical habitat
only extends as far as the Nisqually River delta. No portion of Willapa Bay has been designated
as critical habitat for the bull trout.
Within the action area, the current condition of designated bull trout critical habitat varies
considerably. Current conditions reflect natural variability, patterns of disturbance and recovery
from both natural and man-made events, and the effects of earlier and concurrent, unrelated
activities occurring in the same nearshore environments and watersheds.
As working tidelands, where shellfish activities have for many years and will continue to affect
habitat conditions (i.e., water quality, substrate conditions, physical habitat structure and
function, benthic/epibenthic community structure and composition, and predator-prey dynamics),
most of the action area cannot be regarded as pristine in its current state. Also, at many locations
this habitat exhibits the pervasive effects of shoreline development and alteration. Armored and
hardened shorelines, diking and filling of marine and estuarine areas, and overwater structures
are all characteristic of the action area. At many locations these features impair important
natural processes that create and maintain functional nearshore marine habitat.
Water and sediment quality conditions are generally suitable and adequately functioning, though
some sub-basins and embayments fail to consistently maintain the State’s surface water quality
criteria (Ecology 2016). Portions of Sequim Bay, Discovery Bay, and lower Hood Canal are
listed on the State’s 303(d) list of impaired water bodies for failing to meet criteria for dissolved
oxygen. However, most shellfish activities are conducted on intertidal sites, which “…are
substantially or completely flushed on every tidal cycle” (Forrest et al. 2009, p. 5). Water
temperatures are generally suitable and adequately functioning throughout the action area.
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Natural nearshore habitat complexity is either mildly or moderately impaired throughout much of
the action area. The same can be said for the condition of the bull trout prey base. At some
locations either or both of these functions may be severely impaired.
Table 4. Designated bull trout critical habitat within the action area; co-location with mapped
eelgrass and marine forage fish habitat.
GEOGRAPHY Affected Nearshore
Acres in Designated
Critical Habitat
Action Area)
Continuing
Shellfish Activities (Acres)
Total
Co-Located
with Mapped
Eelgrass
Co-Located
with Mapped
Forage Fish
Grays Harbor 4,000 2,965 1,918 (65%) 73 (2%)
Hood Canal 3,000 1,356 685 (51%) 663 (49%)
North Puget
Sound 5,000 3,687 3,370 (91%) 2,865 (78%)
Total Approx. 12,000 Approx.
8,000 Approx. 6,000 Approx. 3,600
The action area includes nearshore marine environments providing five of the nine PCEs of
designated bull trout critical habitat (50 FR 63898; October 18, 2010):
2) Migration habitats with minimal physical, biological, or water quality impediments between
spawning, rearing, overwintering, and freshwater and marine foraging habitats, including but
not limited to permanent, partial, intermittent, or seasonal barriers.
Within the action area this PCE is impaired but still functions. At some locations, where
armored and hardened shorelines, marine and estuarine fill, and overwater structures are more
pervasive, this PCE is moderately or severely impaired. There are currently no barriers to
migration along the marine shorelines in the action area.
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3) An abundant food base, including terrestrial organisms of riparian origin, aquatic
macroinvertebrates, and forage fish.
Within the action area this PCE is either mildly or moderately impaired. Most of the nearshore
marine areas in the action area provide important spawning habitat for forage fish species such as
Pacific herring, Pacific sand lance, and surf smelt. Across most portions of the action area, both
salmonid and marine forage fish prey resources are well below historic, long-term peaks of
production. However, year-to-year and geographic variability is significant and not easy to
generalize with recognizable trends.
4) Complex river, stream, lake, reservoir, and marine shoreline aquatic environments, and
processes that establish and maintain these aquatic environments, with features such as large
wood, side channels, pools, undercut banks and unembedded substrates, to provide a variety of
depths, gradients, velocities, and structure.
Within the action area this PCE is moderately impaired, but still functions. At some locations,
where armored and hardened shorelines, fill, and overwater structures are more pervasive, and
where important natural processes that create and maintain functional nearshore marine habitat
are impeded, this PCE is severely impaired.
5) Water temperatures ranging from 2 to 15 °C (36 to 59 °F), with adequate thermal refugia
available for temperatures that exceed the upper end of this range. Specific temperatures within
this range will depend on bull trout life-history stage and form; geography; elevation; diurnal
and seasonal variation; shading, such as that provided by riparian habitat; stream flow; and
local groundwater influence.
Though some shallow embayments experience seasonally elevated temperatures (i.e., during
summer months), those conditions are usually of limited duration. Water temperatures in the
nearshore marine areas of Puget Sound and the coastal bays are generally not degraded. Within
the action area this PCE is fully functioning, with little or no significant impairment.
8) Sufficient water quality and quantity such that normal reproduction, growth, and survival are
not inhibited.
Water and sediment quality conditions are generally suitable and adequately functioning, though
some portions of the action area exhibit mild or moderate impairment.
Conservation Role of the Action Area (Bull Trout)
On September 28, 2015, the Service announced the availability of a Recovery Plan for the
Coterminous U.S. Population of Bull Trout (USFWS 2015a). The bull trout is listed as
threatened in the lower 48 states, where it occurs in Montana, Idaho, Washington, Oregon, and
Nevada. The Recovery Plan updates the recovery criteria proposed in the 2002 and 2004 draft
recovery plans, to focus on effective management of threats, and de-emphasize the achievement
of targeted population numbers (i.e., numbers of adult bull trout in specific areas)(USFWS
2015b).
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Between 2002 and 2004, three separate bull trout recovery plans were drafted, including a plan
for the Coastal-Puget Sound in western Washington (2004). The previous 2002 and 2004 bull
trout recovery plans required that all recovery criteria be achieved in each of 27 recovery units.
Although these previous draft recovery plans have served to identify recovery actions and
provide the framework for implementing numerous recovery actions, they were never finalized
USFWS 2015c).
The final Recovery Plan is based on new information regarding bull trout life history, ecology,
distribution, and persistence, including the benefits of various conservation actions implemented
on behalf of the bull trout, along with an improved understanding of the various threat factors.
The Recovery Plan is intended to promote and support cooperative work with our partners, and
serves to focus and implement effective conservation actions in those areas that offer the greatest
long-term benefit and where recovery can be achieved (USFWS 2015c).
The previous 2002 and 2004 draft bull trout recovery plans proposed adult abundance levels
demographics) as recovery targets for each identified bull trout core area, considering
theoretical estimates of effective population size, historic census information, and the
professional judgment of recovery unit team members. In developing the final Recovery Plan,
the Service recognizes that bull trout continue to be found in suitable habitats and generally
remain geographically widespread across 110 core areas in five states. The Recovery Plan
identifies conservation needs for bull trout in each of the 110 core areas. However, the Service
acknowledges, that despite the best conservation efforts, it is likely that bull trout will become
locally extirpated from some core areas within the foreseeable future. Factors responsible for
declining populations and/or local extirpations include impacts of stochastic events on existing
small populations, climate change, and isolation (35 of 110 extant core areas comprise a single
local population). Moreover, the availability of survey data for accurate population estimates is
problematic, and in certain core areas the geographic limitations on available habitat may
inherently constrain the ability of bull trout populations to achieve the earlier demographic
targets (USFWS 2015c).
The strategy set forth in the Recovery Plan has five key elements (USFWS 2015c):
Conserve bull trout so that they are geographically widespread across representative
habitats and demographically stable in six recovery units (Figure 34);
Effectively manage and ameliorate the primary threats in each of six recovery units at the
core area scale so that bull trout are not likely to become endangered in the foreseeable
future;
Build upon the numerous and ongoing conservation actions implemented on behalf of
bull trout, and improve our understanding of how various threat factors potentially affect
the species;
Use that information to work with partners to design, fund, prioritize, and implement
effective conservation actions in those areas that offer the greatest long-term benefit to
sustain bull trout, and where recovery can be achieved; and
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Apply adaptive management principles to implementing the bull trout recovery program
to account for new information.
The final Recovery Plan includes individual Recovery Unit Implementation Plans (RUIPs) for
each recovery unit. The RUIPs were developed through collaboration with federal, Tribal, State,
private, and other partners prior to completion of the plan (USFWS 2015b).
Figure 34. Bull trout recovery units
USFWS 2015d)
The Service does not expect, plan, or intend to fully recover all bull trout populations in each of
the currently occupied core areas identified by the final Recovery Plan. We recognize that
accomplishing recovery at the scale of the recovery units will require that we improve the status
of bull trout local populations, and their habitats, in some core areas relative to the time of
listing. However, in other core areas it may only be necessary to maintain bull trout local
populations and their habitats, more or less in their current condition, into the foreseeable future.
If the threats described in the final Recovery Plan are effectively managed, the Service expects
that bull trout populations in each recovery unit will respond accordingly, reflecting the
biodiversity principles of resiliency, redundancy, and representativeness. Specifically, achieving
the proposed recovery criteria in each recovery unit would result in geographically widespread
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and demographically stable local bull trout populations, and would protect their essential cold
water habitats to allow all diverse life history forms to persist into the foreseeable future
USFWS 2015a, p. viii).
Connectivity between spawning and rearing habitat and downstream FMO habitat sufficient for
bull trout to move freely and with minimal risk is necessary for the expression of migratory life
history patterns. In core areas where multiple local populations exist, interaction among local
populations through movement of migratory individuals is critical to maintaining genetic
diversity and recolonizing local populations that become extirpated. Thus, when connectivity
with FMO habitat is impaired or blocked, bull trout populations tend to become restricted to
isolated local populations, which may have low genetic diversity, are vulnerable to extirpation,
and cannot be readily recolonized. Barriers to connectivity may consist of natural physical
features such as waterfalls; river reaches that create mortality risks or prevent movement of adult
fish because of entrainment, excessively warm water, or poor water quality; instream structures
such as culverts or weirs; or dams (USFWS 2015a, p. 27).
Lack of suitable FMO habitat, including shared FMO habitats in mainstem, estuarine, and
nearshore areas, can increase mortality of migratory individuals or discourage movement through
these areas, resulting in reduced connectivity among local populations or core areas. Therefore,
impaired FMO areas should be identified within core areas and in shared FMO habitats, and
habitat improvement measures should be implemented where feasible. In estuarine and
nearshore habitats, projects may include improving nearshore habitat conditions for forage fish;
removing or modifying structures such as shoreline armoring, bulkheads, dikes, and tide gates;
contaminant remediation; or, restoring eelgrass or kelp beds (USFWS 2015a, p. 28).
With our revised designation of bull trout critical habitat (75 FR 63935; October 18, 2010) the
Service identified a number of marine or mainstem river habitats outside of bull trout core areas
that provide primary constituent elements of critical habitat. These areas do not provide
spawning and rearing habitat, but do provide FMO habitat that is typically shared by bull trout
originating from multiple core areas. These shared FMO areas support the viability of bull trout
populations by contributing to successful overwintering survival and dispersal among core areas
USFWS 2015a, p. 35).
Bull trout are opportunistic feeders, with food habits primarily a function of size and life history
strategy (USFWS 2015a). Resident and juvenile migratory bull trout prey on terrestrial and
aquatic insects, macro-zooplankton, and small fish. Adult migratory bull trout feed primarily on
a wide variety of resident and anadromous fish species. In coastal areas of western Washington,
bull trout feed on forage fish species such as Pacific herring, Pacific sand lance, and surf smelt,
in nearshore marine areas and the Pacific Ocean (USFWS 2015a).
The Coastal Recovery Unit is located within western Oregon and Washington. Major drainages
include the Olympic Peninsula, Puget Sound, and Lower Columbia River basins, Upper
Willamette River, Hood River, Lower Deschutes River, Odell Lake, and the Lower Mainstem
Columbia River. In the Coastal Recovery Unit, the Service identified 21 existing bull trout core
areas, including the Clackamas River core area where bull trout had been extirpated and were
recently reintroduced, and 4 historically occupied core areas that could be reestablished (Figure
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35). Core areas within the recovery unit are distributed among three geographic regions: Puget
Sound, Olympic Peninsula, and Lower Columbia River. Ten shared FMO habitats are also
identified outside of core areas (Table 5). The only core areas in the coterminous states that
currently support anadromous local populations of bull trout are located within the Puget Sound
and Olympic Peninsula geographic regions (USFWS 2015a, pp. 38, 79).
Figure 35. Map of the Coastal Recovery Unit and core areas
USFWS 2015a, p. 78).
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Table 5. Shared FMO habitat in the Coastal Recovery Unit (USFWS 2015a, p. 79).
There are five core areas within the Coastal Recovery Unit that have been identified as current
population strongholds. These are the Lower Skagit and Upper Skagit core areas in the Puget
Sound region, the Quinault River core area in the Olympic Peninsula region, and the Lewis River
and Lower Deschutes River core areas in the Lower Columbia River region. These are the most
stable and abundant bull trout populations in the recovery unit (USFWS 2015a, p. 79).
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The Recovery Plan identifies the following recovery actions (USFWS 2015a, pp. 51, 52):
1. Protect, restore, and maintain suitable habitat conditions for bull trout.
2. Minimize demographic threats to bull trout by restoring connectivity or populations
where appropriate to promote diverse life history strategies and conserve genetic
diversity.
3. Prevent and reduce negative effects of non-native fishes and other non-native taxa on bull
trout.
4. Work with partners to conduct research and monitoring to implement and evaluate bull
trout recovery activities, consistent with an adaptive management approach using
feedback from implemented, site-specific recovery actions, and considering the effects of
climate change.
Promoting and restoring connectivity, both within core areas and with riverine or coastal FMO
habitat, should encourage the full expression of known migratory life history strategies (fluvial,
adfluvial, anadromous, amphidromous), and allow appropriate genetic interaction and
demographic exchanges among core areas (USFWS 2015a, p. 51).
Future climate change impacts on bull trout will require development of a decision framework to
help inform where climate change effects are most likely to impact bull trout. The identification
of core areas and watersheds that are most likely to maintain habitats suitable for bull trout over
the foreseeable future, and under probable climate change scenarios, will help guide the
allocation of bull trout conservation resources to improve the likelihood of recovery (USFWS
2015a, p. 53).
The Recovery Plan summarizes our current knowledge of potential future climate change
scenarios, and their significance for bull trout recovery (USFWS 2015a, pp. 17-19, 30, 31). Bull
trout are vulnerable to the effects of warming climates and changing precipitation and hydrologic
regimes. Climate change in the Pacific Northwest will include rising air temperatures, changes
in the timing and volume of streamflow, increases in extreme precipitation events, and other
changes that are likely to degrade bull trout habitat and increase competition with non-native
warmwater fish (Mote et al. 2014).
Several climate change assessments or studies have been published (Rieman et al. 2007; Porter
and Nelitz. 2009; Rieman and Isaak 2010; Isaak et al. 2010, 2011; Wenger et al. 2011; Eby et al.
2014) or are currently underway assessing the possible effects of climate change on bull trout.
The results of these efforts will allow us to better understand how climate change may influence
bull trout, and help to identify suitable conservation actions to improve the status of bull trout
throughout their range. Issues include: the effects of rising air temperatures and lower summer
flows on range contractions; changing stream temperatures, influenced by stream characteristics
e.g., amount of groundwater base flow contribution to the stream, stream geomorphology, etc.)
affecting suitable bull trout spawning and rearing habitat; threats to redds and juvenile habitat
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from stream scouring caused by increased winter precipitation extreme events and increased rain
in lower elevations; and lower summer flows inhibiting movement between populations, and
from spawning and rearing habitat to foraging habitat (USFWS 2015a, p. 18).
A study of changing stream temperatures over a 13-year period in the Boise River basin
estimated an 11 to 20 percent loss of suitable coldwater bull trout spawning and early juvenile
rearing habitats (Isaak et al. 2010). These results suggest that a warming climate is already
affecting suitable bull trout instream habitats. This is consistent with the conclusions of Rieman
et al. (2007) and Wenger et al. (2011) that bull trout distribution is strongly influenced by
climate, and predicted warming effects could result in substantial loss of suitable bull trout
habitats over the next several decades. Wenger et al. (2011) also noted that bull trout already
seem to inhabit the coldest available streams in some study areas, and in several watersheds bull
trout do not have the potential to shift upstream with warming stream temperatures at lower
elevations (USFWS 2015a, p. 18).
Sensitivity of stream temperature to changes in air temperature is complex and is influenced by
geological and vegetational factors such as topography, groundwater recharge, glaciation history,
and riparian vegetation (Isaak et al. 2010; Isaak and Rieman 2013). A new stream temperature
data collection, modeling and mapping project, NorWeST, provides a much improved foundation
for assessing bull trout cold water habitat (USFS 2014). Stream temperature data have been
compiled from dozens of resource agencies at more than 15,000 unique stream sites. These
temperature data are being used with spatial statistical stream network models to develop an
accurate and consistent set of climate scenarios for all streams (USFWS 2015a, p. 19).
Fine-scale assessments of the current and projected future geographic distribution of coldwater
streams and suitable bull trout habitat have been recently developed through the NorWeST
Isaak et al. 2015) and Bull Trout Vulnerability Assessment (Dunham 2015) processes. These
assessments model probability of presence using the NorWeST stream temperature data and
models, and map suitable habitat “patches” using fish presence, local threats, migratory
connectivity, and climate sensitivity. The climate sensitivity parameters and data that will be
linked to patches include flow variability (e.g., percent high frequency of winter floods), thermal
variability (percent very cold), fire history (percent severely burned relative to patch area), and
snowpack (snow cover frequency). Other factors include composite indicators of human impacts
and non-native presence. Connectivity parameters include data among patches (stream/lake/sea
distance to nearest occupied patch), migratory connectivity (distance to lake/sea), local barriers
culverts, diversions), and natural geomorphic features (USFWS 2015a, p. 19).
Climate change is an independent threat to bull trout, but also one that exacerbates many of the
other threats. The Service expects the threat to increase in severity over coming decades.
Increasing air temperatures and other changes to hydrology, modified by local habitat conditions,
will tend to result in increased water temperatures, and reduce the amount of habitat with suitable
cold water conditions. Warm dry conditions are also likely to increase the frequency and extent
of forest fires, with a potential to increase sedimentation and eliminate riparian shading.
Projected lower instream flows and warmer water in FMO habitats will exacerbate the lack of
connectivity within and between bull trout core areas. And, we expect that increased water
temperatures will alter competitive interactions between bull trout and other fish species that are
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better adapted to warm conditions. Climatic warming will change seasonality of streamflow, and
increased spring runoff from rain-on-snow events will increase scouring of spawning gravels.
Glacial retreat and reduction of summer snowpack will reduce cold water flows during summer
months. Sea level rise will result in the loss of, and changes to, nearshore and estuarine habitat.
Although addressing the root causes of greenhouse gas emissions and climate change is not
within our jurisdiction, management planning should account for these increased threats and
proactively protect those habitats that we expect will best maintain cold water conditions suitable
for bull trout (USFWS 2015a, pp. 30, 31).
The RUIP for the Coastal Recovery Unit includes the following specifics regarding bull trout
recovery actions for shared Puget Sound FMO, the coastal Washington core areas, and shared
Olympic Penninsula FMO (USFWS 2015e, pp. A-57 through A-59, A-63 through A-67, A-71,
A-72):
Implement protection activities in nearshore marine and estuarine habitats. Past and
current impacts from residential development and urbanization along shorelines have
significantly degraded nearshore habitats essential to anadromous bull trout and their
marine prey base. Efforts should prioritize the protection of intact shorelines, key
habitats, and natural shoreline processes (eelgrass beds, forage fish spawning and holding
areas, feeder bluffs), particularly those in close proximity to core areas or shared
freshwater FMO habitats. Use project prioritization identified in the Puget Sound
Partnership’s most current near term action agenda.
Implement restoration activities in nearshore marine and estuarine habitats. Past and
current impacts from residential development and urbanization along shorelines have
significantly degraded nearshore habitats essential to anadromous bull trout and their
marine prey base. Efforts should target the restoration or enhancement of natural
shoreline features, shoreline processes, or key habitats that are currently degraded,
particularly those in close proximity to core areas or shared freshwater foraging,
migration, and overwintering habitats. Use project prioritization identified in the Puget
Sound Partnership’s most current near term action agenda.
Assess impacts of contaminants to anadromous bull trout. Increasing residential
development and urbanization exacerbates the ongoing transfer of contaminants into
nearshore habitats of Puget Sound. Additional evaluation of the impacts to anadromous
bull trout and to their key prey base (salmon and marine forage fish) is required to
develop and implement any necessary and appropriate mitigation strategies.
Assess importance of small independent streams to anadromous bull trout. Small
independent streams play an important overwintering role for anadromous bull trout in
the Olympic Peninsula region (Brenkman et al. 2007 In USFWS 2015e), but their role for
Puget Sound populations is less clear due to the environmental setting. Additional
evaluation of the locations and level of use by anadromous bull trout is required to
develop and implement any necessary protection and restoration strategies.
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Ensure fisheries do not impede recovery. Direct and incidental catch of bull trout from
commercial gill net and popular recreational angling fisheries on the coast (Brenkman et
al. 2007; Kerr et al. 2013; E. Harvey, NPS, in litt. 2014 In USFWS 2015e) can have
significant selective pressure on older and larger bull trout (Brenkman et al. 2007 In
USFWS 2015e). Develop and implement strategies to reduce incidental mortality of
larger spawners caught in fisheries.
Monitor and evaluate fisheries impacts. Develop and implement appropriate level of
monitoring to ensure fisheries do not significantly impact bull trout recovery, and
periodically review harvest management and make recommendations for change as
needed.
Implement restoration activities in nearshore marine and estuarine habitats. Efforts
should target the restoration or enhancement of natural shoreline features, processes, or
key habitats that are currently degraded, particularly those in close proximity to
Dungeness River core area or shared freshwater FMO habitats. Use project prioritization
identified in the Puget Sound Partnership’s most current near term action agenda.
Implement restoration actions in small, independent, coastal marine tributaries. Although
these small independent streams have been identified as either medium or low priority
watersheds for salmon compared to larger natal watersheds (QIN 2011 In USFWS
2015e), these are key shared FMO habitats for anadromous bull trout (Brenkman et al.
2007; USFWS 2010 In USFWS 2015e). Many of these small streams, whose estuaries
and lower reaches are used by anadromous bull trout, have been heavily impacted by past
forest practices (QIN 2011 In USFWS 2015e). Implement appropriate protection and
restoration actions.
In the Chehalis River/Grays Harbor watershed, assess potential for “re-establishing” a
natal population of bull trout to the Satsop River.
Summary
The action area includes more than 45,000 acres of nearshore marine habitat, including
approximately 12,000 acres of designated bull trout critical habitat (45,000 to 50,000 acres in
total; Willapa Bay: approx. 30,000 acres; Grays Harbor: approx. 4,000 acres; north Puget Sound:
approx. 5,000 acres; south Puget Sound: approx. 5,000 acres; and, Hood Canal: approx. 3,000
acres). Bull trout occur in these nearshore marine waters, and the anadromous (or
amphidromous) bull trout that these waters support are unique to the Coastal Recovery Unit and
rangewide distribution of the species. These nearshore marine waters support the complex
migratory behaviors and requirements of the anadromous form of bull trout, provide foraging
opportunities, allow for enhanced individual growth, and support the connectivity of bull trout
core areas over time (with genetic exchange). As such, these nearshore marine waters are
essential to the persistence of the anadromous bull trout life history form.
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Data collected in Puget Sound indicate that the majority of anadromous bull trout tend to migrate
into marine waters in the spring, and return to rivers in the summer and fall. Although much less
common, tagged bull trout have been detected in Puget Sound nearshore marine waters during
December and January, which indicates that some fish may remain in or return to marine waters
during the winter.
Marine FMO habitat located in Puget Sound, Hood Canal, the Pacific Coast, and Grays Harbor is
considered essential for maintaining the anadromous life history form of bull trout. Recovery
plans assign no specific conservation role to Willapa Bay, because bull trout are thought to occur
there infrequently and in low or very low numbers.
Current Condition in the Action Area (Marbled Murrelet)
The action area includes all of the tidelands and nearshore marine waters associated with
continuing and new (projected future) shellfish activities, encompassing an area of
approximately 38,716 acres (Corps 2015, pp. 40-49, 77-82). Where cultured tidelands extend
with only occasional interruption, interspersed uncultured areas may experience direct or indirect
effects, and are therefore considered part of the action area. At all locations, the action area
extends a minimum of 2,000 ft from the farm footprint (active and fallow). Factoring and
incorporating these other considerations, we estimate conservatively that regulated shellfish
activities in Washington State, specifically those for which this Opinion provides programmatic
coverage, are likely to directly or indirectly affect more than 45,000 acres of nearshore marine
habitat (45,000 to 50,000 acres in total; Willapa Bay: approx. 30,000 acres; Grays Harbor:
approx. 4,000 acres; north Puget Sound: approx. 5,000 acres; south Puget Sound: approx. 5,000
acres; and, Hood Canal: approx. 3,000 acres).
The Recovery Plan for the Threatened Marbled Murrelet in Washington, Oregon, and California
USFWS 1997, p. 115) identifies six Conservation Zones throughout the listed range of the
species. Conservation Zone 1 (Puget Sound) includes all the waters of Puget Sound and most
waters of the Strait of Juan de Fuca south of the U.S.-Canadian border. Conservation Zone 2
Western Washington Coast Range) includes marine waters within 1.2 miles (2 km) off the
Pacific Ocean shoreline, with the northern terminus immediately south of the U.S.-Canadian
border near Cape Flattery along the midpoint of the Olympic Peninsula, and extending to the
southern border of Washington (the Columbia River)(USFWS 1997, p. 126).
Offshore Area Subunit/Conservation Zone 2
During the breeding season (April through September), marbled murrelet density in the Offshore
Area Subunit is lower than in the nearshore coastal and inland waters. During the summer, it is
assumed that 5 percent of marbled murrelets detected during Northwest Forest Plan
Effectiveness Monitoring Program (NWFPEM) are offshore (the NWFPEM effort detects
approximately 95 percent of the population, and the remaining 5 percent are assumed to be
offshore), but not beyond the continental shelf (37 km, or 20 nm). Table 6 shows the density
estimates for marbled murrelets detected by NWFPEM in Conservation Zone 2.
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Table 6. Marbled murrelet population estimates and densities in Conservation Zone 2 from 2001
to 2015
Lynch et al. 2016, pp. 10-13)
Inland Waters Subunit/Conservation Zone 1
The Inland Water Subunit within Conservation Zone 1 encompasses all of Puget Sound and the
Strait of Juan de Fuca. Within the Inland Water Subunit, marbled murrelets tend to forage in
well-defined areas during the breeding season. They are found in the highest densities in the
nearshore waters of the San Juan Islands, Rosario Strait, the Strait of Juan de Fuca, Admiralty
Inlet, and Hood Canal. They are more sparsely distributed elsewhere in Puget Sound, with
smaller numbers observed during different seasons within the Nisqually Reach, Possession
Sound, Skagit Bay, Bellingham Bay, and along the eastern shores of Georgia Strait. In the most
southern end of Puget Sound, they occur in extremely low numbers. During the non-breeding
season, they typically disperse and are found farther from shore (Strachan et al. 1995).
It appears that marbled murrelets from Vancouver Island, British Columbia move into more
sheltered waters in Puget Sound and the Strait of Georgia, which contributes to increased
numbers of murrelets in Puget Sound in fall and winter (Burger 1995a). Surveys along the
southern shore of the Strait of Juan de Fuca conducted by the Washington Department of Fish
and Wildlife from 1996-1997 (Thompson 1997) showed an increase in the number and group
size of marbled murrelets in August in the eastern Strait of Juan de Fuca, although numbers
declined in the western portion of the Strait of Juan de Fuca. Surveys in the near-shore waters of
the San Juan Islands (Evans and Associates 1999; Ralph et al. 1995) showed a similar increase in
abundance in August and September. Increases in abundance have been detected as well in
September and October during surveys of Admiralty Inlet, Hood Canal, Saratoga Passage, and
Year
Conservation Zone 2 – Stratum
All 1 2
Density
birds/km2)
Population
Estimate
Density
birds/km2)
Population
Estimate
Density
birds/km2)
Population
Estimate
2001 0.90 1,518 1.43 1,040 0.50 478
2002 1.23 2,031 2.45 1,774 0.28 258
2003 2.41 3,972 2.64 1,912 2-23 2,061
2004 1.82 3,009 3.37 2,444 0.61 565
2005 1.56 2,576 2.79 2,018 0.60 558
2006 1.46 2,381 2.26 1,638 0.80 743
2007 1.54 2,535 2.85 2,065 0.51 470
2008 1.17 1,929 2.58 1,872 0.06 57
2009 0.77 1,263 1.61 1,166 0.11 97
2010 0.78 1,286 1.34 968 0.34 318
2011 0.72 1,189 1.31 952 0.26 237
2012 0.72 1,186 1.18 853 0.36 333
2013 0.77 1,271 1.61 1,163 0.12 108
2014 1.32 2,176 2.88 2,086 0.10 90
2015 1.94 3,204 2.85 2,064 1.23 1,140
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Possession Sound (Merizon et al. 1997). A breeding marbled murrelet, banded in Desolation
Sound in summer, was recovered near Orcas Island in September, and then recovered in
Desolation Sound the following year (Beauchamp et al. 1999).
Marbled murrelet presence in the Inland Water Subunit is documented by several sources. The
most accurate information comes from the consistent sampling method used to estimate
population size and trends under the NWFPEM (Raphael et al. 2007). Since 2000, the estimated
population size for Conservation Zone 1 has ranged from a low of 2,822 marbled murrelets in
2014 to a high of 9,758 in 2002 (Table 7) (Lynch et al. 2016, pp. 10-13). The most recent (2015)
estimated population for Conservation Zone 1 is 4,290 marbled murrelets (2,783-6,492, the
upper and lower 95 percent confidence intervals; see Lynch et al. 2016) (Lance and Pearson
2016, p. 4; Lynch et al. 2016, p. 13). Since 2001, the estimated marbled murrelet density in
Conservation Zone 1 has ranged from 0.81 to 2.79 marbled murrelets per km2, with the most
recent (2015) density of 1.23 birds per km2 (Lynch et al. 2016, p. 13).
Food and Habitat Preferences
Burkett (1995) reviewed marbled murrelet food habits and prey ecology, including the works of
Sealy (1975c), Krasnow and Sanger (1982), Sanger (1983, 1987b), Carter (1984), Vermeer
1992), and others. Speich and Wahl (1995) described the marbled murrelet’s habitat
preferences and variability of occurrence in the inland marine waters of Washington State.
Appendix D includes excerpts from Burkett (1995) and Speich and Wahl (1995); those excerpts
are incorporated here by reference.
Factors Responsible for the Condition of the Species
Some of the factors responsible for the condition of the species (marbled murrelet) in the action
area are described elsewhere (see Status of the Species and Environmental Baseline).
As part of the Service’s 5-year review of the current status of the marbled murrelet, we identified
new threats and stressors across the listed range of the species, including several environmental
factors affecting marbled murrelets in the marine environment:
Habitat destruction, modification, or curtailment of the marine environmental conditions
necessary to support marbled murrelets due to: elevated levels of polychlorinated
biphenyls in murrelet prey species; changes in prey abundance and availability; changes
in prey quality; harmful algal blooms that produce biotoxins leading to domoic acid and
paralytic shellfish poisoning; and climate change in the Pacific Northwest.
Manmade factors that affect the continued existence of the species include: derelict
fishing gear leading to mortality from entanglement; energy development projects (wave,
tidal, and on-shore wind energy projects) leading to mortality; and disturbance in the
marine environment (e.g., sound pressures caused by pile-driving and underwater
detonations, vessel traffic).
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Table 7. Marbled murrelet population estimates and densities in Conservation Zone 1 from 2001 to 2015.
Year
Conservation Zone 1 - Stratum
All 1 2 3
Density
birds/km2)
Population
Estimate
Density
birds/km2)
Population
Estimate
Density
birds/km2)
Population
Estimate
Density
birds/km2)
Population
Estimate
2001 2.55 8,936 4.51 3,809 1.76 2,111 2.07 3,016
2002 2.79 9,758 7.21 6,092 1.88 2,248 0.97 1,419
2003 2.43 8,495 6.64 5,617 1.44 1,721 0.79 1,156
2004 1.56 5,465 3.83 3,241 1.51 1,807 0.29 417
2005 2.28 7,956 2.50 2,114 2.43 2,895 2.02 2,947
2006 1.69 5,899 2.76 2,333 1.42 1,693 1.28 1,873
2007 2.00 6,985 3.45 2,912 1.22 1,453 1.80 2,620
2008 1.34 4,699 3.57 3,019 0.90 1,073 0.42 607
2009 1.61 5,623 3.81 3,221 0.69 822 1.08 1,580
2010 1.26 4,393 2.00 1,694 1.78 2,128 0.39 571
2011 2.06 7,187 5.58 4,717 1.24 1,484 0.68 986
2012 2.41 8,442 7.17 6,056 1.51 1,799 0.40 587
2013 1.26 4,395 2.38 2,010 0.66 784 1.10 1,600
2014 0.81 2,822 1.26 1,063 1.27 1,521 0.16 238
2015 1.23 4,290 2.22 1,875 1.95 2,321 0.06 94
Sources: (Lance and Pearson 2016, p. 4; Lynch et al. 2016, pp. 10-13)
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Prey Resources and Foraging Conditions
Therriault, Hay, and Schweigert (2009) have reported recent marine forage fish trends in the
Salish Sea and their potential significance for seabirds. Cury et al. (2011) considered global
trends in seabird response to forage fish depletion. Vilchis et al. (2014) recently published work
using winter count data collected in the Salish Sea over the period 1994 to 2010, and
epidemiological theory and data processing techniques, to evaluate common drivers for declines
witnessed in marine avian predators. Appendix D includes excerpts from Therriault, Hay, and
Schweigert (2009), Cury et al. (2011), and Vilchis et al. (2014); those excerpts are incorporated
here by reference.
Net Entanglement and Bycatch
Rodway et al. (1992, pp. 30, 31) reported, “Mariculture developments have proliferated in recent
years throughout nearshore feeding areas for murrelets in southern British Columbia (Booth and
Rueggeberg 1988) … Entanglement of alcids was reported at one of 68 salmon farms surveyed
Rueggeberg and Booth 1989) … displacement from traditional foraging areas, contamination of
food supplies by antifoulants and antibiotics, and alteration of local food supplies from
decomposition of fish food and fish excretion are potential problems for marbled murrelets
Vermeer and Morgan).” Laist (1997) compiled a comprehensive list of species with marine
debris entanglement and ingestion records. Carter, McAllister, and Isleib (1995) describe
accidental capture and mortality in commercial gill nets as one of the major threats to marbled
murrelet populations. Good et al. (2010) has reported on the progress made removing derelict
gear in Puget Sound and the Northwest Straits, and the pattern of remaining threats. Zydelis,
Small, and French (2013) have considered recent bycatch trends in Washington State and British
Columbia. Appendix D includes excerpts from Laist (1997); Carter, McAllister, and Isleib
1995); Good et al. (2010); and, Zydelis, Small, and French (2013); those excerpts are
incorporated here by reference.
Conservation Role of the Action Area (Marbled Murrelet)
The action area is critically important to the marbled murrelet populations in Conservation Zones
1 and 2 (Puget Sound and Western Washington Coast Range, respectively), and by extension, is
also critically important to the rangewide conservation and recovery of the species. The action
area provides prey resources that are essential to the health and productivity of marbled murrelet
populations in Conservation Zones 1 and 2. However, the action area also supports individuals
from other conservation zones and/or British Columbia that seasonally forage and migrate in
Washington’s inland marine waters or the coastal bays, and therefore supports additional
marbled murrelet populations from both the south and north. Many of the marbled murrelets that
breed on Vancouver Island, British Columbia, appear to move into more sheltered waters (Puget
Sound and the Strait of Georgia) after the breeding season, where numbers increase in fall and
winter (Burger 1995a,b). The Service’s recovery plan identifies all of Puget Sound, including
the waters of the San Juan Islands, the Strait of Juan de Fuca, and the nearshore waters along the
Pacific Coast from Cape Flattery to Willapa Bay (within 1.2 miles of the shore), including rivers
mouths, as essential for marbled murrelet foraging and loafing (USFWS 1997, p. 135).
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The marine environment will play an essential role in the recovery of the marbled murrelet.
Protecting the quality of the marine environment is identified in the recovery plan as an integral
part of the recovery effort (USFWS 1997, p. 120). Marbled murrelets spend the majority of their
lives in marine areas, usually within five kilometers of the shoreline, where forage fish and other
marine prey resources are most abundant (USFWS 1997, p. 120). If marine areas are degraded
and do not provide sufficient prey resources, individual fitness and reproductive success may be
reduced.
There are threats in the action area that must be addressed to reverse rangewide marbled murrelet
population trends, and to maintain self-sustaining and self-regulating populations. A marbled
murrelet Recovery Implementation Team, convened and led by the Service, found that sustained
low recruitment is the most likely cause for the observed, continuing population declines, and
identified five major mechanisms that contribute to this decline (USFWS 2012, cover letter, pp.
10, 11, 22):
Changes in marine forage conditions, affecting the abundance, distribution, and quality of
prey, is identified as one of the five mechanisms. Depletion of the marine forage fish
resource, degraded spawning and rearing habitats for these fish (often attributable to
shoreline development and alteration), and other losses or degradation of estuarine and
nearshore marine habitat functions are emphasized (pp. 10, 13, 19, 22). Also, “…
marine] food webs are sensitive to climate variability … [and] there is uncertainty about
how future changes will impact these [food] webs” (p. 10). For all geographic areas
across the range of the listed species, degraded marine forage conditions, and the
uncertain future effects of climate variability on marine forage conditions, are identified
as one of the top three causes for low recruitment and the observed, continuing
population declines (USFWS 2012, p. 19).
Post-fledging mortality is another of the five mechanisms. Entanglement in nets and
other marine gear” remains one of the significant, identified causes for this mortality
USFWS 2012, pp. 11, 13).
Cumulative and interactive effects are a top five mechanism, including the “…disconnect
between [high] quality marine and terrestrial habitats…”, or the lack of adequate marine
and terrestrial habitat “coupling” (USFWS 2012, pp. 11, 13). “Longer commuting times
between nesting and foraging habitats can increase both the energetic costs of
reproduction and exposure to predators … the cumulative effect of [these] factors … may
limit reproductive success.”
In Puget Sound and the San Juan Islands, most of the remaining, functional nesting
habitat is located far from marine waters. In this portion of the marbled murrelet’s range,
where there is a “…significant distance between marine areas and remaining nesting
habitat … [the] energetic costs of the commute [are] probably highest” (USFWS 2012, p.
13).
In north Puget Sound and the Strait of Juan de Fuca, herring “…stocks are not doing
well” (USFWS 2012, p. 14).
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On the coast, south of Grays Harbor, the “…disconnect between high quality terrestrial
and marine habitats … [is] of more concern … due to very limited terrestrial [nesting]
habitat” (USFWS 2012, p. 16).
Increasing human populations often result in increased shoreline development, and will likely
further degrade nearshore marine habitat and marine prey resources. Urban and suburban
sprawl, logging, and habitat fragmentation in the uplands have already greatly reduced the
available, suitable nesting habitat, and have increased the distances that marbled murrelets must
travel between high quality nesting and foraging habitats. New information regarding the status
of marine forage fish resources in the action area, and regarding seabird responses to reduced
prey availability, suggest that marbled murrelet populations may be experiencing declines that
are at least partially attributable to a lack of adequate forage resources. These threats, combined
with the other unaddressed rangewide threats, could affect the long-term trajectory for survival
and recovery of the marbled murrelet.
Climate Change
Climate change has already begun to affect conditions throughout the action area. This sub-
section discusses three related subjects: ocean acidification; “other” marine and estuarine
impacts associated with or caused by climate change; and, invasive species. The impacts of
ongoing and future climate change are an important aspect of the environmental baseline.
Climate change will have significance for the health and function of the action area’s nearshore
marine habitats, which are essential to the recovery of both anadromous bull trout and the
marbled murrelet.
Ocean Acidification
Over the past two centuries, atmospheric carbon dioxide (CO2) concentrations have increased
from approximately 280 parts per million (ppm), to approximately 380 ppm; and, over the same
period, the Earth’s oceans absorbed an estimated 550 billion tons of CO2 (Le Quere et al. 2009
and Canadell et al. 2007 in Feely et al. 2012, pp. 442). Decades of observations now show that
CO2 absorbed by the oceans is changing the chemistry of seawater, in a process called ocean
acidification. “When anthropogenic CO2 is absorbed by seawater, chemical reactions occur that
reduce seawater pH, concentration of carbonate ion, and the saturation states of the biominerals
aragonite and calcite … When carbonate saturation states … drop below saturation … whether
due to ocean acidification or other natural processes, carbonate biominerals in shells and
skeletons may begin to dissolve, and we describe the water as corrosive” (Feely et al. 2012, pp.
442, 443).
Since pre-industrial times, “…the pH of average open-ocean surface waters has decreased by
about 0.1, equivalent to an overall increase in the hydrogen ion concentration or ‘acidity’ of
about 30 percent” (Feely et al. 2012, p. 443), and “…there has been an overall decrease of about
16 percent in the aragonite saturation state of North and South Pacific surface and intermediate
waters … and a decrease of about 0.34 [percent per year] over the last two decades” (Feely et al.
2012, pp. 11, 12). These changes to the chemistry of seawater have caused “upward migrations
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of the aragonite and calcite saturation horizons” (i.e., the depths at which these biominerals may
be found at sufficient concentration), as well as related regional changes in circulation and
biogeochemical processes (Feely et al. 2012, p. 1).
However, available information suggests that “…large-scale changes in circulation can be as
important as, or in some cases, more important than, the direct effects of anthropogenic CO2 …
More detailed information on the temporal variability of the physical and chemical properties of
the California Current is required before we can accurately predict how these long-term changes
will affect our coastal ecosystems” (Feely et al. 2012, p. 11).
Coastal waters, which are the source for the marine waters in the Puget Sound system, [already]
carry an anthropogenic CO2 burden, and a corresponding pH decrease associated with ocean
acidification … A reasonable estimate of the range of the present-day pH decrease in the Puget
Sound region due to ocean acidification is between 0.05 and 0.15” (Feely et al. 2012, p. 446).
The calculations … suggest that in pre-industrial times the waters flowing into Puget Sound …
were above saturation with respect to aragonite, whereas today they are undersaturated … While
the deep waters of Hood Canal were likely [naturally] undersaturated during the pre-industrial
era, the degree of undersaturation is greater today than it would have been then” (Feely et al.
2012, p. 447).
Laboratory and mesocosm experiments suggest that pH and saturation state values of the
observed magnitude may impair overall calcification rates for many species of marine calcifiers,
including cold water corals, coccolithophorids, foraminifera, sea urchins and pteropods (Spero et
al. 1997; Riebesell et al. 2000; Engel et al. 2005; Orr et al. 2005; Guinotte et al. 2006; Kleypas
et al. 2006; Fabry et al. 2008; Guinotte and Fabry 2008; Doney et al. 2009; Ries et al. 2009) …
Similar decreases in calcification rates would be expected for edible mussels, clams, and oysters
Green et al. 2004; Gazeau et al. 2007; Hettinger et al. 2010)” (Feely et al. 2012, p. 447).
Numerous authors have emphasized the pervasive nature of these changes and their fundamental
importance to the productivity and resiliency of coastal and estuarine ecosystems.
Feely et al. (2012, pp. 446-448) have discussed current and future patterns of ocean acidification,
and how they are likely to interact with and alter the natural chemistry and biology of the Puget
Sound:
Naturally low carbonate saturation and pH levels in the North Pacific predispose the
Pacific Northwest coast in general, and Puget Sound in particular, to the development of
corrosive, hypoxic marine conditions.”
As CO2 continues to rise in the atmosphere, the ... contribution of anthropogenic CO2 to
the development of corrosive conditions in the deep waters of Puget Sound will likely
increase with time.”
Ocean acidification is likely to play a role, “…exacerbating local or regional hotspots of
corrosive conditions where the impacts of multiple stressors converge.”
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Stressful conditions may be exacerbated by [the] combined impacts of global, regional,
and local anthropogenic processes including ocean acidification, land-use change, and
nutrient enrichment. The additional pH, [altered aragonite saturation state], and CO2
decreases associated with these anthropogenic stressors may cross critical thresholds for
organisms living near the edge of their physiological tolerances.”
The rapid decline of the large mussel populations at Tatoosh Island and the mass
mortalities of oyster larvae in Pacific Northwest oyster hatcheries may be early
indications of the kind of ecosystem changes caused by the combined effects of multiple
processes and stressors interacting in a high-CO2 world.”
By the end of this century, ocean acidification may become the dominant process
reducing the pH and saturation state of this large, economically important estuary”
Feely et al. 2012, pp. 446-448).
Greene et al. (2012, p. 16) found that 92 percent of Hood Canal sites (12 of 13) had minimum
DO concentrations surpassing stressful conditions, and depressed DO concentrations were
typically associated with highly stratified water columns. They report, “One striking bivariate
relationship was observed across all temporal and spatial scales … pH and dissolved oxygen
DO). DO concentrations were positively correlated with pH across basins and months at the
surface, at 6 meters deep, and at the maximum depth of the water column profiles … DO and pH
may be tightly linked.”
Other Marine/Estuarine Impacts Associated with Climate Change
As described by the Independent Scientific Advisory Board (ISAB 2007), the effects of climate
change are likely to include increased ocean temperatures, increased stratification of the water
column, and changes in the intensity and timing of coastal upwelling. These effects have already
begun to alter, and are likely to continue altering primary and secondary productivity and the
structure of marine communities.
For some large estuaries, the effects of climate change may have additional consequences (ISAB
2007): higher winter freshwater flows, and higher sea level elevations, may lead to altered
sediment routing and wave damage; lower freshwater flows in late spring and summer may lead
to upstream extension of the salt wedge, possibly influencing the distribution of prey and
predators; and, the increased temperature of freshwater inflows may extend the range of warm-
adapted non-indigenous species. However, in all of these cases, the likely effects of these
changes to the abundance, productivity, spatial distribution, and diversity of native biota are
poorly understood (ISAB 2007).
Growing human pressures, including climate change, are having profound and diverse
consequences for marine ecosystems. Rising atmospheric … CO2 is one of the most critical
problems because its effects are globally pervasive and irreversible on ecological timescales
Natl. Res. Counc. 2011). The primary direct consequences are increasing ocean temperatures
Bindoff et al. 2007) and acidity (Doney et al. 2009) … [But] Direct effects … [to] ocean
temperature and chemistry may … lead to shifts in the size structure, spatial range, and seasonal
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abundance of populations. These shifts, in turn, lead to altered species interactions and trophic
pathways as change cascades from primary producers to upper-trophic-level fish, seabirds, and
marine mammals, with climate signals thereby propagating through ecosystems in both bottom-
up and top-down directions … Investigating the responses of individual species to single forcing
factors, although essential, provides an incomplete story and highlights the need for more
comprehensive, multispecies- to ecosystem-level analyses” (Doney et al. 2012, p. 12).
Mid-latitude upwelling systems, like the California Current, exhibit strong linkages between
climate and species distributions, phenology, and demography… Population-level shifts … [may
be] occurring because of physiological intolerance to new environments, altered dispersal
patterns, and changes in species interactions” (Doney et al. 2012, p. 11). Figure 36 illustrates
some of the observed climate-dependent changes in the California Current ecosystem.
Zooplankton biomass has declined dramatically over the past 60 years in concert with increases
in ocean temperature (Roemmich and McGowan 1995), a trend that continues to this day …
Because a shift toward less abundant, smaller, and lipid-poor subtropical copepods accompanied
the transition into a warm phase of the [Pacific Decadal Oscillation] (Peterson and Schwing
2003), continued warming of the California Current is predicted to translate up the food chain to
reduce juvenile survivorship in salmonid fishes” (Doney et al. 2012, p. 25).
The Earth’s oceans are warming, with considerable interannual and interdecadal variability
superimposed on the long-term trend (Bindoff et al. 2007). Historically, warm periods in the
coastal Pacific Ocean have coincided with relatively low abundances of salmonids and other cold
water-dependent fish species, while cooler ocean periods have coincided with relatively high
abundances (Scheuerell and Williams 2005; Zabel et al. 2006). “Effects … [to native eelgrass]
from global climate change include rising seawater temperatures and changes in depth from
increased sea levels. High temperatures may cause loss of eelgrass in embayments already
experiencing near-lethal temperatures” (Mumford 2007, p. 14).
Invasive Species
Among the key findings from a report published during 2007, the Puget Sound Action Team
PSAT 2007) found that more than 50 non-native species are documented in Puget Sound, a
large number of these probably introduced via ship ballast. The European green crab (Carcinus
maenas), Chinese mitten crab (Eriocheir sinensis), and zebra mussel (Dreissena polymorpha) are
non-native species that could arrive at any time and threaten the Puget Sound.
Another highly invasive kelp species, Undaria pinnatifida … is not yet in Puget Sound, but has
been found in California and many other temperate areas, and will likely invade here in time
Silva et al. 2002)” (Mumford 2007, p. 4).
Introduction of non-native species is an important management issue, particularly when they
become invasive … Aquaculture and other vectors for marine invasions have been reviewed
elsewhere (Gruet et al. 1976; Carlton and Mann 1996; McKindsey et al. 2007; Minchin 2007) …
Regulations and practices have changed to reduce the role of aquaculture imports in
homogenizing biota (e.g. ICES Code of Practice on the Introductions and Transfers of Marine
Organisms, ICES 2005)” (Dumbauld, Ruesink, and Rumrill 2009, p. 201).
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Figure 36. Climate-dependent changes in the California Current
Doney et al. 2012, p. 27)
However, Forrest et al. (2009, p. 10) have argued that “…the role of elevated oyster culture in
the spread of pest organisms … [is] particularly significant … Inadvertent pest introduction is
one of the more significant issues associated with aquaculture in estuaries (DeFur and Rader
1995) … The reason is that, by comparison with all other issues, the spread of pest organisms …
can occur at regional scales (e.g. as a result of seed-stock transfer) potentially leading to
ecologically significant and irreversible changes to coastal ecosystems (Elliot 2003) … Although
management approaches may be developed to minimize any pest risks that are considered
unacceptable (e.g. treatment of seed-stock before regional transfer), there are few examples
where such strategies have been completely effective (Piola et al. 2009).”
Bendell (2014) has reported that “…several lines of evidence suggest that the [cultured non-
native] Manila [clam] is replacing the native littleneck [clam]” on intensively farmed British
Columbia tidelands. “Prior to the introduction of the Manila clam, the native littleneck … and
the butter clam (Saxidomus gigantea) were the dominant species harvested (Whiteley 2005)” (p.
369). “Within Baynes Sound, either seed spillover or natural spawning by the Manila is
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occurring, making it the dominant bivalve within the region” (p. 375). “The Manila, through the
anthropogenic enhancement of its reproductive effort, is able to outcompete the indigenous
species and overcome its predation disadvantage by occurring in greater numbers” (Bendell
2014, p. 379).
There is also a potentially significant ongoing and likely greater future interaction between
marine species invasions and climate change: “Multiple factors beyond climate change influence
changes in marine community composition and trophic structure, and synergistic effects may
arise among climate, exploitation, and the introduction of invasive species. A survey of four
well-studied marine regions found that invasions are shifting food webs toward domination by
suspension and deposit feeders low in the food chain, presumably reflecting the widespread
transport of small fouling organisms and the decline of large fishes caused by human harvesting
Byrnes et al. 2007) … Evidence from the Atlantic (Stachowicz et al. 2002) and Pacific (Sorte
et al. 2010) coasts of North America indicates that nonnative species in fouling invertebrate
communities are favored over native species in warmer waters. In this way, warming may tend
to homogenize the composition of marine communities … Climate-mediated shifts in species
distributions are creating novel or emerging no-analog ecosystems consisting of species with
little or no shared evolutionary history (Hobbs et al. 2006; Williams and Jackson 2007) … There
is growing evidence that the climate-mediated invasions mentioned above are biased
taxonomically or by functional traits such as life history and trophic level (Byrnes et al. 2007) …
Other studies suggest that a warming climate aggravates the prevalence of marine diseases
Harvell et al. 2002) … Climate-driven impacts on keystone and foundation species may be
especially important … Some critical habitat-forming marine benthic species, such as oysters
and corals, appear sensitive to CO2 and climate change both directly and through pathogens”
Doney et al. 2012, pp. 19, 20).
EFFECTS OF THE ACTION
Introduction
The effects of the action refers to the direct and indirect effects of an action on the species or
critical habitat, together with the effects of other activities that are interrelated or interdependent
with that action, that will be added to the environmental baseline (50 CFR 402.02). Indirect
effects are those that are caused by the proposed action and are later in time, but still are
reasonably certain to occur.
While generally it is our practice to describe first those activities which have insignificant or
discountable effects to listed species, their habitats, and prey, we have taken an alternate
approach with this Opinion’s discussion of potential effects. All or nearly all of the shellfish
activities covered under this programmatic Opinion result in measurable and potentially
significant effects to water quality, substrate condition, physical habitat structure and function,
benthic/epibenthic community structure and composition, and predator-prey dynamics.
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As is always our practice, this Opinion includes an analysis and discussion of temporary
episodic or transient) stressors, resulting exposures, and potential effects. However, because
with this Opinion we must consider and describe potential effects on a large scale, corresponding
to hundreds of farms and farm operations, and thousands of affected nearshore marine acres, we
believe that resulting persistent stressors of long duration (months, years) warrant and require
special attention and focus.
Shellfish culturing activities and practices alter physical, chemical, and biological conditions on
temporal scales that correspond to cycles of production and harvest. Resulting conditions also
reflect variable patterns and rates of recovery from disturbance. And, the discernable direct and
indirect effects of shellfish activities are generally also superimposed on, and further influenced
by, natural variability, patterns of disturbance and recovery from natural events, and the
confounding effects of concurrent, unrelated activities occurring in the same nearshore
environments and watersheds.
The Corps has stated the following (Corps 2015, p. 83):
The effects [of individual activities] may be relatively short-term or longer lasting … Of
equal or more relevance to ESA listed species are the effects of the collective activities,
their frequency, duration, timing, geographic location, and general scale across the
landscape.”
We agree with the Corps and believe that the best available scientific information supports this
conclusion. Our Opinion finds that the most significant and biologically relevant effects are
those that result in aggregate to nearshore marine habitat structure, function, and productivity.
We examine potential effects to ecological processes and ecosystem services. We also consider
potential indirect effects that may result from altered patterns of prey availability and
productivity (“prey-mediated effects”). And, we assess potential effects to natural forms of
nearshore marine habitat structure and complexity, both those that result on the scale of an
individual farm, and those that result from groupings of farms on larger scales.
The portions of the Opinion that follow discuss: 1a) temporary stressors resulting from shellfish
activities, and 1b) resulting short-term exposures and effects to bull trout and marbled murrelets;
2a) persistent stressors of long duration resulting from shellfish activities, 2b) aggregate effects
at larger scales (e.g., groupings of farms, embayments or sub-basins), and 2c) resulting long-
term and indirect exposures and effects to bull trout and marbled murrelets; and, 3) effects to
designated bull trout critical habitat.
Temporary Stressors, Resulting Exposures, and Effects
This portion of the Opinion discusses temporary stressors resulting from shellfish activities, and
resulting short-term exposures and effects to bull trout and marbled murrelets.
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Physical Disturbance
The physical disturbance that results temporarily from shellfish activities generally corresponds
to two principle temporal regimes: the cycle of daily high and low tides; and, cycles of shellfish
production (seeding, maintenance, and harvest). Most shellfish activities are conducted on or
over the exposed or partially exposed intertidal bed. These activities, and their resulting
temporary effects, therefore commonly have a temporal duration measured in hours. For
example, activities conducted on intertidal shellfish beds (bed preparation, seeding or planting,
maintenance, and harvest) typically occur during the 3- to 6-hour periods afforded by each low
tide, or each daylight low tide (Corps 2015, p. 14). Consequently, most shellfish activities
associated with ground-based culturing of oysters, clams, and geoduck are conducted as bouts of
intermittent activity, with each bout lasting a few hours.
Other shellfish activities, including frosting or graveling, some methods of seeding and planting,
mechanical harrowing, mechanical harvest, dive-harvest, and suspended culturing techniques,
are conducted during periods of tidal inundation, and/or over the submerged subtidal bed. While
some of these activities may be relieved or partially relieved of strict timing constraints, many
still target specific tidal elevations and therefore proceed as bouts of intermittent activity.
The Corps has reported values, presented as acres per day, describing the typical (or average)
physical extent of various shellfish activities (Corps 2015, p. 91). These values are reported for
some of the more physically-intrusive or disruptive activities, including: frosting or graveling (1
acre/day); mechanical harrowing (5 acres/day); mechanical dredge harvesting (0.5 acre/day);
mechanical, non-dredge harvesting (0.8 acre/day); longline harvest (0.125 acre/day); and,
geoduck harvest (0.01 to 0.06 acre/day).
The Corps has stated the following (Corps 2015, p. 103):
Shellfish] activities result in a pattern of effects on the environment that individually
have varying levels of persistence, ranging from several days (e.g., temporary increases
in suspended sediment) to many years (e.g., degraded eelgrass, leveling of substrate) …
The proposed action [includes] initiation of aquaculture activities, and their pattern of
effects, in the continuing fallow and new [acreages].”
Some shellfish activities clearly result in pronounced and intensive physical disturbance of the
substrate, benthos, and/or submerged aquatic vegetation, including in some instances native
eelgrass and/or rooted kelp. We would place pre-harvest, some methods of bed preparation
including mechanical leveling and frosting or graveling), and most methods of shellfish harvest
in this category. However, many of the other activities associated with seeding or planting and
maintenance are far less intrusive or disruptive. And, importantly, cycles of shellfish production
seeding, maintenance, and harvest) typically dictate that these less intrusive activities span
durations of many months between bed preparation and harvest. The Corps reports (Corps 2015)
that mussels are typically harvested at 12 to 14 months of age (p. 14), oysters at 18 months to 4
years of age (pp. 14, 20), clams at approximately 3 years of age (p. 25), and geoduck clams at 4
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to 7 years of age (p. 33). During these intervening periods (“grow-out”) less physically-intrusive
or disruptive maintenance activities are the norm, with possible exceptions for removal of area or
cover nets and mechanical harrowing.
Disturbance and Recovery from Disturbance in Estuarine Environments
Estuarine communities have evolved to accommodate certain levels of physicochemical stress
and disturbance. Benthic and epibenthic communities, in particular, have co-evolved in highly
variable regimes of salinity, temperature, and substrate” (Simenstad and Fresh 1995, p. 43).
Describing the Ecology of Eelgrass Meadows in the Pacific Northwest, Phillips (1984, pp. 12,
15, 16) observed “Eelgrass colonizes sediments varying from firm sand with moderate wave
action to soft mud in quiet bays (Ostenfeld 1908; Phillips 1974). Plants have been found on
gravel mixed with coarse sand where growth is patchy (Tutin 1938) … Intertidal plants [are]
subjected to wide fluctuations in temperature, salinity, radiation, grazing, erosion, and wave
action … Subtidal plants are relatively undisturbed physically and biologically.”
Sousa (1984 In Simenstad and Fresh 1995, p. 43) defined disturbance as “…a discrete,
punctuated killing, displacement, or damaging of one or more individuals (or colonies) that
directly or indirectly creates an opportunity for new individuals (or colonies) to become
established.” Short and Wyllie-Echeverria (1996, p. 17) defined disturbance, whether natural or
human-induced, as “…any event that measurably alters resources available to … [biota] so that a
response is induced that results in degradation or loss.”
The ability of estuarine communities to accommodate disturbance at low intensities … and to
rapidly recover from occasional disasters, implies that they are … resilient … Although extreme
events … may devastate benthic communities over the short term, the rate of recovery can be
quite rapid (e.g., within 1 year)(Wolff 1973; Boesch et al. 1976; de Vlas 1982) as long as the
perturbing factor does not persist” (Simenstad and Fresh 1995, p. 44). “The extent to which a
particular disturbance alters structure or function and thereby affects recover y time depends on
the frequency and/or duration of the disturbance (den Hartog 1971), the physiological condition
of the plants, and the characteristics of the particular seagrass species involved (McRoy and
Lloyd 1981; Zieman and Zieman 1989; Williams 1990; Alberte et al. 1994) … Additionally,
recovery from disturbance can vary depending on the level of damage sustained” (Short and
Wyllie-Echeverria 1996, p. 18). “The effect of physical disturbance on plant communities
depends on the size, frequency, and intensity of disruption, and on ecological, physiological, and
life history characteristics affecting ecosystem recovery (Pickett & White 1985)” (Neckles et al.
2005, p. 58).
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Simenstad and Fresh (1995) reviewed the scale and intensity of disturbance, and the response of
intertidal communities to aquaculture activities in Pacific Northwest estuaries. “Aquaculture …
may disturb benthic-epibenthic habitats beyond natural intensities or frequencies, perhaps for
years or decades. When scales of human disturbance exceed that of natural regimes … effects
can potentially cascade … to affect production of other estuarine, marine, and anadromous
populations” (Simenstad and Fresh 1995, p. 44). With their summary conclusions the authors
emphasized three related themes:
1) “On a community scale, responses to chronic, low intensity or infrequent, intermediate
intensity disturbances tend to be within the scope of behavioral or ecological adaptability
of the flora and fauna … Dispersal of most epibenthic populations is often continuous
and dynamic as a function of tidal advection and resuspension … [and] meiofaunal
animals tend to have high … turnover rates that facilitate rapid recolonization” (p. 62).
2) “Subtle differences in the intensity of disturbance (e.g., amount of gravel added), the
natural disturbance regime (e.g., tidal or wave resuspension and resorting of sediments),
and other factors important to intertidal community structure (e.g., sedimentation rate)
define [site-specific and] taxon-specific responses” (p. 63).
3) “Complex physicochemical and ecological linkages among estuarine organisms and
communities can be altered over the long-term by persistent disturbances that exceed
natural regimes … Large-scale disturbances, such as those associated with some intensive
oyster practices, may induce chronic shifts in the benthic community by removing or
reducing the influence of community dominants such as eelgrass or … [by] altering the
apparent … relationship between them” (Simenstad and Fresh 1995, pp. 65, 66).
Dumbauld and McCoy (2015) recently reported the findings of a multi-year study evaluating
model-predicted and actual landscape patterns of eelgrass distribution in Willapa Bay. The
authors describe spatial and temporal patterns of fragmentation, loss, and recovery, and
comparatively evaluate how these patterns relate to oyster culturing and harvest methods. “Our
results demonstrate a negative effect of oyster aquaculture on the native seagrass … at the
landscape scale in Willapa Bay … but also show that this impact is small compared to the overall
signature of both Z. marina and oyster aquaculture in this estuary” (p. 37). “Eelgrass … appears
to be resilient over both short and longer temporal periods and resistant to oyster aquaculture as a
disturbance in this ecosystem” (p. 42). “Our research in Willapa Bay suggests that oyster
aquaculture … is generally within the scope of existing ‘natural’ disturbances to the system (e.g.
winter storms), and eelgrass is inherently adapted to this scale of disturbance … Bivalve
aquaculture has not been implicated in shifts to alternate states or reduced adaptive capacity of
the larger ecological system” (Dumbauld and McCoy 2015, p. 42).
Vanblaricom et al. (2015) recently reported the findings of a multi-site study evaluating the
effects of geoduck harvest on benthic infaunal communities in the south Puget Sound. The
authors use a treatment and control experimental design to describe spatial and temporal (i.e.,
seasonal) patterns of abundance and diversity, and to evaluate the effects of harvest both on and
adjacent to cultured farm plots. The study found, “There was scant evidence of effects on the
community structure … [and] no indications of significant ‘spillover’ effects of harvest on
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uncultured habitat adjacent to cultured plots” (p. 171). The authors suggest, “…a principal
reason for the apparent insensitivity of resident infauna … is accommodation of the infaunal
assemblage to a significant natural disturbance regime ... natural disturbances typical of the area
provide a rate of physical intervention … substantially greater than rates of significant
disturbance caused by geoduck aquaculture operations in a given plot” (p. 183). The authors
suggest, “…the prevailing natural disturbance climate in the region has effectively selected the
infaunal assemblage toward tolerance of and resilience to the types of disturbances associated
with geoduck aquaculture operations,” but also warn that “…the data may not provide a
sufficient basis for unequivocal extrapolation to cases when a given plot is exposed to a long
series of successive geoduck aquaculture cycles” (Vanblaricom et al. 2015, pp. 183, 184).
Physical Disturbance Resulting from Shellfish Activities
When discussing potential impacts and effects to vegetation, the benthic community, and habitat,
the Corps has consistently emphasized that the magnitude and duration of effects vary depending
on culture method, individual grower or husbandry practices, and environmental conditions
Corps 2015, p. 85, 87). We agree with the Corps and believe that the best available scientific
information supports this conclusion.
Pre-harvest: Pre-harvest removes marketable product and removes, or more commonly
relocates, undesirable species. For a period following pre-harvest, and until the cultured species
and colonizing species become re-established, most cultured farm plots exhibit a benthic
community that is reduced in abundance, biomass, and diversity (Corps 2015, p. 85; Straus et al.
2013, p. 20; Vanblaricom et al. 2015, pp. 171, 178, 180).
Frosting and graveling: Frosting and graveling are used to coarsen and firm the cultured farm
plot’s surficial substrates, but at the rates/amounts proposed we would not expect to see
wholesale conversion of the substrate type. Simenstad et al. (1991 In Simenstad and Fresh 1995,
p. 52) found that these practices can alter the benthic infaunal community, especially the
dominant or co-dominant taxa, but unless there is total replacement of the natural substrate,
effects to the epibenthic community (crustaceans and decapod crustaceans, mobile and sessile
echinoderms, mobile and sessile gastropods, bottomfish, etc.) are less pronounced and often site-
specific. The authors do acknowledge that (Simenstad and Fresh 1995, p. 50), “…the
Washington Department of Fisheries has investigated differences in benthic infauna composition
and densities at sites that have been graveled to enhance clam production … [and] their results
Washington Department of Fisheries 1988; Thompson and Cooke 1991; Thompson, 1995;
Washington Department of Fisheries and Fisheries Research Institute, University of Washington
unpublished data) indicate a shift away from communities numerically dominated by glycerid,
sabellid, and nereid polychaetes [bloodworms, feather duster tube worms, and rag or clam
worms] to ones dominated by bivalve molluscs and nemerteans [ribbonworms].”
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Mechanical leveling and harrowing: Mechanical leveling and harrowing turn over the surficial
substrates and shallow subsurface. This has measurable effects on the benthic community,
particle size, sediment chemistry, nutrient status, and aspects of benthic-water column dynamics
Rhoads and Germano 1986, Newell 2004, Forchino 2010, Gutierrez et al. 2011). Leveling and
harrowing of the bed may in some instances result in measurable impacts to submerged aquatic
vegetation, including native eelgrass and/or rooted kelp.
Species richness and functional group diversity are inherent to undisturbed benthic systems,
including within seemingly “barren” or “plain” sand and mud flats (Rhoads and Germano 1986,
pp. 293, 294; Forchino 2010, pp. 16, 17; Gutierrez et al. 2011, pp. 39-45). Benthic communities
are not static and the functional groups that dominate at points along the course of infaunal
succession (Figure 37) influence important benthic ecosystem attributes, including secondary
production, nutrient cycling, and hypoxia (Rhoads and Germano 1986, pp. 291, 298-301).
Infaunal ‘ecosystem engineers’ affect three-dimensional structure and thus the diversity of
microhabitats in marine soft sediments … When infaunal organisms recruit into soft sediment
habitats, they seek refuge by entering into the sediments and – in many cases – by producing
shells, tubes, or burrows (Marinelli and Woodin 2002) … All these structures generate a
remarkably more diverse environment within the sediment matrix relative to the originally
smooth soft sediment” (Gutierrez et al. 2011, pp. 44).
Figure 37. Development of organism-sediment relationships over time following disturbance
Rhoads and Germano 1986, p. 294)
Infaunal succession commonly requires years, and therefore benthic species assemblages and
their functional relationships can be disrupted by disturbance. “[Disturbances that cause] long-
term degradation … frequently involve the loss of equilibrium species … high-order seres are
replaced by pioneering seres … [and] changes in organism-sediment relations and population
dynamics accompany this change” (Rhoads and Germano 1986, p. 295).
Appendix D includes excerpts from Rhoads and Germano (1986), Forchino (2010), and
Gutierrez et al. (2011); those fuller excerpts are incorporated here by reference.
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Benthic microalgae, or microphytobenthos, “…are an important food source for both sessile and
mobile benthic herbivorous meiofauna and macrofauna (Miller et al. 1996) … [these are], in
turn, eaten by many carnivorous fish” (Newell 2004, p. 53). “In [the] Pacific Northwest … a
number of economically-important fishes feed preferentially on specific taxa of intertidal soft-
bottom meiofauna and small macrofauna. Of prime interest are juvenile chum, Chinook, and
coho salmon that exhibit a high fidelity for shallow estuarine habitats. These fish feed on a
restricted suite of epibenthic harpacticoid copepods, gammarid amphipods, [and] cumaceans …
When feeding in estuarine habitats, particularly in eelgrass meadows and mud flats, juvenile
chum salmon prey extensively on only a few taxa of harpacticoid copepods such as Harpacticus
uniremis, Tisbe spp., and Zaus sp. (Healey 1979; Simenstad et al. 1982, 1988; D’Amours 1987,
1988) … A number of other species, including smelts ([Family] Osmeridae), sand lances
Family] Ammodytidae), and sticklebacks ([Family] Gasterosteidae) also prey heavily on these
same prey taxa … early in their life histories (Simenstad et al. 1988) … Similarly, amphipods
such as Corophium salmonis and C. spinicorne and cumaceans are preyed upon extensively by
juvenile Chinook salmon (Dunford 1975; Northcote et al. 1979; Levy and Northcote 1982;
Simenstad et al. 1982) and by migratory waterfowl and shorebirds such as sandpipers and dunlin
Caladris alpina) … (Albright and Armstrong 1982; Baldwin and Lovvorn 1994)” (Simenstad
and Fresh 1995, p. 63).
Eelgrass rhizomes are buried from 3-4 cm (1.2-1.6 inches) up to 20 cm (8.0 inches) deep in
sediment, depending on the sediment consistency. In firmer substrates, rhizomes may be only
half as deep as in soft muddy substrates” (Phillips 1984, p. 9). “Significant injury to roots,
rhizomes, and meristems is lethal to seagrass shoots” (Neckles et al. 2005, p. 58). “Eelgrass may
be impacted by dredging, harrowing, and leveling, all of which extensively disrupt surface
sediments … destroy above-ground eelgrass shoots and leaves, and perhaps below-ground roots
and rhizomes as well” (Simenstad and Fresh 1995, p. 54).
Mechanical dredge harvesting: Mechanical dredge harvesting is among the most physically-
intrusive and disruptive of all the shellfish activities discussed in this Opinion. Dredge
harvesting directly impacts submerged aquatic vegetation and its many important physical,
chemical, biological, and habitat functions. These effects to ecological and habitat functions
may persist for durations extending months or years. A later portion of this Opinion will
examine the significance of these effects in greater detail (see Persistent Stressors, Long
Duration or Long-term Exposures and Effects, Effects to Nearshore Habitat Structure and
Function).
Geoduck harvest: Geoduck harvest (both dive and beach harvest) results in disturbance of the
substrate and benthos. Studies conducted in the Pacific Northwest demonstrate that geoduck
cultivation also results in measurable impacts to eelgrass. A 2-year experiment investigating
seasonal effects of geoduck production at a site in the south Puget Sound found that the largest
impacts (70 percent shoot loss) occurred during harvesting of the clams (Ruesink and Rowell
2012, p. 718).
Horwith (2013) investigated changes in eelgrass and infauna over a 5-year crop cycle in Samish
Bay, located in the northern portion of Puget Sound. “Immediately following harvest … eelgrass
remained patchily distributed within the farm (being present in 64 percent of quadrats), but
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where it was present, Z. marina was now 78 percent more dense in the unfarmed area ... Eelgrass
was no longer present on the farm 1 year after harvest … following a period of heavy [algae]
biofouling on the blanket nets” (Horwith 2013, p. 111). However, “…the first signs of recovery
for eelgrass began 1 year after the removal of tubes and nets, and continued evidence for
recovery appeared in the following year … Geoduck aquaculture practices do not appear to have
made this site unsuitable for later recolonization by eelgrass” (Horwith 2013, p. 112). This too is
a subject for a later portion of this Opinion (see Persistent Stressors, Long Duration or Long-
term Exposures and Effects, Effects to Nearshore Habitat Structure and Function).
Exposures and Responses to Physical Disturbance (Bull Trout and Marbled Murrelet)
This sub-section has discussed physical disturbance with a focus on resulting potential effects to
substrates, sediment size and chemistry, benthic biomass and diversity, and submerged aquatic
vegetation. The effects discussed here, to physical, chemical, and biological conditions, are
temporal and limited in both physical extent and duration.
Shellfish culturing and harvesting have direct and indirect effects to nearshore marine habitat
structure, function, and productivity. These effects may have significance for how well these
habitats support the essential behaviors and needs of listed species. However, when we consider
the frequency, duration, and likely physical extent of temporary physical disturbances that result
in temporary impacts on individual farms and cultured beds, it is difficult or impossible to
establish that they alone are a recognizable and measurable cause for adverse effects to bull trout
or marbled murrelets.
We conclude that temporary physical disturbance resulting from shellfish activities causes
insignificant effects to bull trout and marbled murrelets. However, shellfish culturing activities
and practices do have measurable effects to ecological and habitat functions, some of which are
likely to persist for durations extending months or years. A later portion of this Opinion will
examine the significance of these effects in greater detail (see Persistent Stressors, Long
Duration or Long-Term Exposures and Effects, Effects to Nearshore Habitat Structure and
Function).
Water Quality
The effects to water quality that result temporarily from shellfish activities generally correspond
to the same two temporal regimes that were discussed above with reference to physical
disturbance: the cycle of daily high and low tides; and, cycles of shellfish production (seeding,
maintenance, and harvest). And, the preceding discussion of shellfish activities, their typical
durations, and physical extent is the same that should inform our discussion here of effects to
water quality and their significance.
Shellfish activities result in measurable, temporary impacts to water quality. While many,
perhaps most, activities result in temporary effects that are localized, limited in physical extent,
and low intensity, other culturing activities and practices (such as mechanical leveling,
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mechanical harrowing, frosting or graveling, and mechanical dredge harvesting) may have more
pronounced and intensive impacts to water quality. The removal of biofouling in the field, from
culturing equipment and materials, is another shellfish activity discussed here.
Activities that disturb the substrate create localized turbidity. Activities conducted at low tide,
on the exposed or partially exposed intertidal bed, sometimes create turbidity when water re-
floods the recently worked area (Corps 2015, p. 83). Activities conducted during periods of tidal
inundation (e.g., frosting or graveling, mechanical harrowing and harvest, dive harvest) also
create localized turbidity. Activities that disturb the substrate to some depth, that turn over the
surficial substrates and shallow subsurface (e.g., mechanical leveling, harrowing, and harvest),
have the potential to temporarily increase both turbidity and nutrients in the water column (Corps
2015, p. 83; Riemann and Hoffmann 1991, pp. 171, 176).
Where temporary impacts to water quality are concerned, our primary focus is on four
biologically and behaviorally relevant water quality parameters: turbidity, DO, BOD, and
nutrients (e.g., nitrogen and ammonium). Turbidity is an optical measure of water clarity, and an
indirect measure or indicator of the amount of suspended material (clay, silt, sand, algae,
plankton, etc.). Both DO and BOD relate to the availability of oxygen to support aerobic
respiration. BOD is a measure of the dissolved oxygen necessary to break down organic
materials present in a water sample. “Within the estuarine to coastal continuum, multiple
nutrient limitations occur among nitrogen, phosphorus, and silicon along the salinity gradient and
by season, but nitrogen is generally considered the primary limiting nutrient” (Rabalais 2002, p.
102).
Turbidity
Although few studies have specifically examined the issue as it relates to bull trout, increases in
suspended sediment affect salmonids in several recognizable ways. The variety of effects may
be characterized as lethal, sublethal, or behavioral (Bash et al. 2001, p. 10; Newcombe and
MacDonald 1991, pp. 72-73; Waters 1995, pp. 81-82). Lethal effects include gill trauma and
physical damage to the respiratory structures (Curry and MacNeill 2004, p. 140). Sublethal
effects include reduced respiratory function and performance (Waters 1995, p. 84), increased
metabolic oxygen demand (Servizi and Martens 1992), physiological stress reducing the ability
of fish to perform vital functions (Cederholm and Reid 1987, pp. 388, 390), reduced feeding
efficiency (Newcombe and MacDonald 1991, p. 73), and increased susceptibility to disease and
other stressors (Bash et al. 2001, p. 6). Sublethal effects can act individually or cumulatively to
reduce growth rates and survival over time. Behavioral effects include avoidance of preferred
habitats, loss of territoriality, and related secondary effects to feeding rates and efficiency (Bash
et al. 2001, p. 7). Fish may be forced to abandon preferred habitats and refugia, and may be
exposed to additional hazards (including predators) when seeking to avoid elevated suspended
sediment concentrations.
The marbled murrelet relies primarily on its sense of sight to visually identify, locate, and
capture prey. “Marbled murrelets feed in shallow, nearshore waters (Sealy 1975b, Carter 1984),
often opportunistically on locally abundant prey, mainly fish (Carter 1984) … Marbled murrelets
forage within 500 m of shore in waters less than 30 m deep (Sealy 1975b) … mainly on
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Euphausiids (Thysanoessa spinifera) during the [spring] … later Pacific sandlance (Ammodytes
hexapterus) … along with smaller numbers of seaperch (Cymatogaster aggregata)” (Rodway et
al. 1992, pp. 22, 23). “In Barkley Sound … distribution of [marbled] murrelets paralleled
changes in the distribution of the principle prey, Pacific herring (Clupea harengus) and
sandlance (Carter 1984) … Adults carried single fish, primarily sandlance, to nestlings, and less
frequently herring and anchovy (Engraulis mordax)(Carter 1984, Carter and Sealy 1987a) …
Prey selected for nestlings were larger than ingested prey” (Rodway et al. 1992, p. 23). While a
related species, Kittlitz’s murrelet (B. brevirostris), appears to favor and has specialized to take
advantage of turbid, glacially-affected waters when foraging, the marbled murrelet does not
show the same preference and may actively avoid turbid waters (Day, Prichard, and Nigo 2003,
p. 680).
Dissolved Oxygen and Biochemical Oxygen Demand
Low DO levels, or hypoxia, can result in both bottom substrates and the water column when
biological activity is high (including aerobic decomposition of organic litter and wastes). Some
waterbodies exhibit seasonally low DO levels, which are generally attributable to excessive
nutrients loads and enrichment, seasonally elevated temperatures, seasonal die-off and
decomposition of organic materials, poor or incomplete flushing and mixing, or a combination of
these factors. Some shellfish activities are conducted at locations and/or times of year when
waterbodies already present less than ideal conditions.
The BOD created by feces, pseudofeces, and other decomposing organic materials consumes
oxygen in the sediments and water column. And, as with their potential to temporarily increase
turbidity and nutrients in the water column, shellfish activities that turn over the surficial
substrates and shallow subsurface (e.g., mechanical leveling, harrowing, and harvest) may also
expose and hasten the aerobic decomposition of litter and wastes. At least conceptually, this has
the potential to increase BOD and temporarily suppress DO.
The Corps has reported that shellfish activities are noticeably concentrated in some sub-basins
and embayments, including South Bay (Grays Harbor); Samish Bay; Sequim Bay; Discovery
Bay and Kilisut Harbor (near Port Townsend); the Henderson, Eld, and Totten Inlets; Oakland
Bay; upper Case Inlet; lower Hood Canal; Dabob Bay; and, Dyes Inlet. Some of these same sub-
basins and embayments fail to consistently meet the State’s surface water quality criteria
Ecology 2015). Portions of Sequim Bay, Discovery Bay, Henderson Inlet, Little Skookum Inlet
a portion of larger Totten Inlet), upper Case Inlet, Henderson Bay (upper Carr Inlet), and several
portions of lower Hood Canal are listed on the State’s 303(d) list of impaired water bodies for
failing to consistently meet the DO criteria.
It is widely known that low or extremely low DO levels are a common cause for fish kills.
However, there is less appreciation for the significant sub-lethal effects that can result from
exposure to hypoxic conditions. Kramer (1987) has provided a useful summary review of fish
behavioral responses to DO availability. As with exposure to high temperatures, exposure to
hypoxic conditions frequently imposes a metabolic cost that results in less energy being available
for locomotion and other basic functions which are important to growth and survival. DO levels
indicate the “… amount of medium which must be ventilated in order to obtain a given amount
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of oxygen,” and the increased ventilation rates that are required under hypoxic conditions place a
burden on metabolic and energetic reserves (Kramer 1987, pp. 83, 85). Sustained swimming and
effective escape movements also place demands on energy, and therefore predator avoidance and
locomotion may be compromised under conditions of low DO availability (Kramer 1987, p. 85).
Salmonids are considered “metabolic conformers,” they exhibit a metabolic rate that is
dependent upon environmental conditions, and therefore they are commonly understood to be
less tolerant of high temperatures and/or hypoxia (Barnes et al. 2011, p. 397).
Exposures and Responses to Water Quality (Bull Trout and Marbled Murrelet)
This sub-section has discussed temporary impacts to water quality that result from shellfish
activities. The effects discussed here, to physical, chemical, and biological conditions, are
temporal and limited in both physical extent and duration.
The Corps has stated the following (Corps 2015, p. 92):
In the context of temporary impacts that occur with the activities, the relevance of
frequency is dependent on recovery from the impact. Effects that diminish quickly such
as increases in suspended sediment are minor in the context of a once per year frequency.
The collective activities conducted on a particular acreage may increase this [effect or
impact] to 3 or 4 times per year. Collectively the total … is still minor and on the order
of days.”
We agree with the Corps and believe that the best available scientific information supports this
conclusion. But, before interpreting the potential significance of shellfish activities and their
temporary impacts to water quality, we should acknowledge patterns of natural variability, the
scale of natural events and their effects to water quality, and the confounding effects of
concurrent, unrelated activities occurring in the same nearshore environments and watersheds.
It is widely acknowledged that both naturally occurring and cultured shellfish provide significant
water quality improvement functions (Forrest et al. 2009, p. 5; Straus et al. 2013, pp. 16, 17).
High densities of suspension feeding bivalves can dramatically impact water quality in myriad
ways (Newell 2004). Numerous studies have shown that filter-feeding bivalves can locally
decrease phytoplankton abundance in both natural (Asmus and Asmus 1991, Cressman et al.
2003, Grizzle et al. 2006) and cultured settings (Strohmeier et al. 2005, Grizzle et al. 2006) … In
addition to removing phytoplankton, bivalve filter feeding removes inorganic particles from the
water column, reducing turbidity (Newell 2004). The reduced turbidity results in deeper light
penetration, which can improve the condition for submerged aquatic vegetation, including
seagrasses (Newell and Koch 2004, Straus et al. 2013, p. 16).” “Filter feeding also removes
nitrogen and phosphorus from the water column, nutrients that may ultimately be removed from
the ecosystem via the harvest of cultured bivalves … Thanks to this nutrient-removal capacity,
bivalve aquaculture can improve water quality. Several authors have suggested aquaculture …
to mitigate eutrophication pressure in coastal systems (Newell 2004, Lindahl et al. 2005, Zhou et
al. 2006)” (Straus et al. 2013, p. 17).
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Forrest et al. (2009, p. 5) have observed, “…the potential for adverse water quality-related
effects … is low, which is perhaps not surprising considering that intertidal farm sites are
substantially or completely flushed on every tidal cycle. Any water quality effects associated
with … culture can … be minimized by appropriate site selection and farm design (e.g. ensuring
minimal retardation of flushing processes).” “For the most part … [water quality] conditions
depend on interannual variability in oceanic boundary conditions, residence times in the different
inlet and embayments, and the input of nitrogen into the system through [other] human
activities” (ENVIRON International Corp. 2011, p. 41).
Shellfish culturing and harvesting have direct and indirect effects to nearshore marine habitat
structure, function, and productivity. These effects may have significance for how well these
habitats support the essential behaviors and needs of listed species. However, when we consider
the temporary impacts to water quality that result from activities conducted on individual farms
and cultured beds (i.e., their intensity, frequency, duration, and likely physical extent), it is
difficult or impossible to establish that they alone are a recognizable and measurable cause for
adverse effects to bull trout or marbled murrelets.
During 2008, the Service and NMFS approved a low-effect HCP developed in coordination with
the DNR for their commercial geoduck fishery. That record of HCP approval indicates minor
and small-scale effects resulting from elevated turbidity and sedimentation during harvest
activities (Service Ref. No. PRT-TE187810-0). The Service stated, “…we do not expect this
action to typically result in significant disruption of normal behavior patterns … disruption of the
substrate … during geoduck harvest will have a temporary, negative impact on the benthic
community … [but will] result in short-term effects … [and] significant disruptions to foraging
bull trout are not anticipated” (USFWS 2009b, p. 133). The Service stated, “… [marbled]
murrelets are mobile and will most likely avoid the harvest area … the small area of geoduck
harvest [at any one time] … compared to the size of foraging areas [suggests] that murrelets will
not have to move far to find food … the [Service] therefore has determined that the risk of
impacts to murrelets due to harvest activities is likely to be very small or immeasurable”
USFWS 2009b, pp. 144, 145).
Taking into consideration both the geographic setting (i.e., an open water marine environment),
and the intensity and duration of exposures, we conclude that temporary impacts to water quality
resulting from shellfish activities are unlikely to significantly disrupt normal bull trout or
marbled murrelet behaviors (i.e., the ability to successfully feed, move, and/or shelter). We
conclude that temporary impacts to water quality resulting from shellfish culturing and harvest
activities cause insignificant effects to bull trout and marbled murrelets. However, shellfish
activities do have measurable effects to ecological and habitat functions, some of which are
likely to persist for durations extending months or years. A later portion of this Opinion will
examine the significance of these effects in greater detail (see Persistent Stressors, Long
Duration or Long-Term Exposures and Effects).
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Sound and Visual Disturbance
Shellfish culturing and harvest activities result in temporary elevated sound levels and visual
disturbance. This disturbance corresponds to two principle temporal regimes: the cycle of daily
high and low tides; and, cycles of shellfish production (seeding, maintenance, and harvest).
Most shellfish activities are conducted on or over the exposed or partially exposed intertidal bed.
These activities, and their resulting temporary effects, therefore commonly have a temporal
duration measured in hours. For example, activities conducted on intertidal shellfish beds (bed
preparation, seeding or planting, maintenance, and harvest) typically occur during the 3- to 6-
hour periods afforded by each low tide, or each daylight low tide. Most shellfish activities
associated with ground-based culturing of oysters, clams, and geoduck are conducted as bouts of
intermittent activity, with each bout lasting a few hours. While some activities (e.g., frosting or
graveling, mechanical harrowing, mechanical harvest, dive-harvest, and suspended culturing
techniques) may be relieved or partially relieved of strict timing constraints, many still target
specific tidal elevations and therefore proceed as bouts of intermittent activity.
In-Air and Underwater Sound
The Corps has described elevated sound levels that result temporarily from some typical shellfish
activities and equipment (Corps 2015, pp. 86, 87). Small- and medium-sized work vessels and
skiffs are used widely. These are generally powered with outboard motors, and produce in-air
and underwater sound levels that are likely to exceed the ambient condition to a distance of a few
hundred ft. Most of the other equipment used widely and extensively when conducting shellfish
activities has a similar potential to elevate sound levels (e.g., gas-powered air compressors,
hydraulically powered onboard equipment). Mechanical methods of bed preparation,
maintenance, and harvest (e.g., mechanical dredge harvesting) typically use larger vessels and
may produce more intense underwater sound levels. However, all of these sources of measurable
in-air and underwater sound are non-impulsive, and even the loudest and most intense sounds
resulting from shellfish activities are unlikely to exceed the ambient condition to a distance of
more than 500 hundred ft.
Related or Additional Considerations for Marine Birds and Shorebirds
Shellfish aquaculture typically occurs in shallow, nearshore waters, which also tend to harbor
the greatest densities and diversity of marine birds. However, only a relatively small number of
studies have evaluated the effects of shellfish aquaculture on birds” (Zydelis et al. 2009, p. 2).
Much of the literature to date has focused on marine waterfowl depredation of cultured bivalve
stocks, which in turn sometimes leads to active disturbance or exclusion by shellfish farmers
Vermeer and Morgan 1989; Thompson and Gillis 2001; Caldow et al. 2004; Dionne 2004)”
Zydelis et al. 2009, p. 2).
When disturbance does occur, birds compensate by moving elsewhere or by feeding at a greater
rate during undisturbed periods of the day … birds move from adjacent bed … to bed … when
large numbers of people occur there” (Goss-Custard and Verboven 1993, p. 64). “They can …
habituate to people … though this depends critically on the extent to which the people move
about … Anglers and the local … mussel pickers usually move rather little … having found a
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suitable place, they remain there for much of the tidal cycle … After the initial disturbance, the
birds] settle down and even feed nearby … Severe disturbance … usually arises if … pickers …
give the birds little chance to settle down … The effects on most birds might be insignificant
because they can adapt their foraging behavior” (Goss-Custard and Verboven 1993, p. 65).
More recently, and working with the same species (oystercatcher; Haematopus ostralegus),
Stillman and Goss-Custard (2002, abstract, p. 358) observed the following: “We show how the
response of overwintering oystercatchers … to disturbance is related to their starvation risk …
As winter progresses … energy requirements increase and their feeding conditions deteriorate …
they spend longer feeding and so have less time to compensate for disturbance … Their
behavioral response to disturbance is less … These results have implications for studies which
assume that a larger behavioral response means that a species is more vulnerable to disturbance
The opposite may be true … Studies should measure both behavioral responses and the ease
with which animals are meeting their requirements.”
Appendix D includes excerpts from Zydelis et al. (2009) and Goss-Custard and Verboven
1993); those fuller excerpts are incorporated here by reference.
Exposures and Responses to Sound and Visual Disturbance (Bull Trout and Murrelet)
This sub-section has discussed temporary impacts to the sound and visual environment that result
from shellfish activities. The effects discussed here, to physical and biological conditions, are
temporal and limited in both physical extent and duration.
Exposure to elevated non-impulsive sound may interfere with an organism’s ability to perceive
and respond to their environment, communicate, or engage in other important behaviors. For
many years, the Service has used measures of sound intensity and duration to assess, describe,
and interpret the significance of sound exposures and potential effects. However, in the Pacific
Northwest, most of this work has focused on impulsive sound, including the sound produced by
impact pile driving and underwater detonations.
Injury and mortality in fishes has been attributed to impact pile driving (Stotz and Colby 2001;
John H. Stadler, NMFS, pers. comm. 2002; Fordjour 2003; Abbott et al. 2005; Hastings and
Popper 2005). The injuries associated with exposure to these high underwater sound pressure
levels (SPLs) are referred to as barotraumas, and include hemorrhage and rupture of internal
organs, hemorrhaged eyes, and temporary stunning (Yelverton et al. 1973, p. 37; Yelverton et al.
1975, p. 17; Yelverton and Richmond 1981, p. 6; Turnpenny and Nedwell 1994; Hastings and
Popper 2005).
Interpreting the significance of non-injurious sound exposures is more difficult. There is much
uncertainty regarding the behavioral responses of fish to underwater sound. Measures of
underwater sound expressed as “root mean square” (rms; root square of the energy divided by
duration) are commonly used when evaluating behavioral effects. Turnpenny and others (1994)
investigated the behavioral responses of brown trout (Salmo trutta), bass (Micropterus), sole
family Soleidae), and whiting (family Gadidae). An avoidance reaction was documented in
brown trout when exposed to underwater SPLs above 150 dBrms, and other reactions were
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observed at 170 to 175 dBrms (e.g., a momentary startle). Turnpenny et al. (1994) referenced
Hastings’ “safe limit” recommendation of 150 dBrms, and conclude that the safe limit provides a
reasonable margin below the lowest levels where fish injury was observed. Feist et al. (1992)
suggested that SPLs in this range (above 150 dBrms) may disrupt the normal migratory behaviors
of juvenile salmon. In a study conducted by Fewtrell (2003), responses observed in caged fish
included alarm, changes to swimming speeds and group orientation, and movement toward the
lower portions of the cage. Fewtrell (2003) also evaluated physiological stress responses
measures of plasma cortisol and glucose levels), but found no statistically significant changes.
Given the large amount of uncertainty, not only in extrapolating from experimental data to the
field, but also between sound sources and from one species to another, the Service has generally
applied thresholds analogous to the “lowest observed adverse effect level” used frequently in the
field of toxicology.
The Corps has reported the source sound level for a 250-horsepower outboard motor when
operating at full speed (approximately 147 dBrms re 1 microPascal at 1 meter)( Wyatt 2008 In
Corps 2015, p. 87). Wyatt (2008, pp. 59-62) has also reported source sound levels for the
following: a 50-horsepower four-stroke outboard motor operating at 13 knots (approximately
166 dBrms at 1 meter); a 90-horsepower outboard motor operating at idle and full speed
approximately 141 dBrms, and 163 dBrms, at 1 meter respectively); twin 210-horsepower inboard
motors operating at idle and full speed (approximately 148 dBrms, and 162 dBrms, at 1 meter
respectively); and a 450-horsepower motor operating at 12 knots (approximately 139 dBrms at 30
meters).
Vessels and equipment used when conducting shellfish activities produce underwater sound
levels that exceed 150 dBrms, which has at least some potential to disrupt the normal behaviors of
bull trout. However, other factors must also be considered. First, the small- and medium-sized
work vessels and skiffs that are used most widely are unlikely to exceed 150 dBrms when
operating at low or moderate speeds. Second, larger vessels with larger motors, and small- to
medium-sized work vessels operating at full speed, are unlikely to exceed 150 dBrms to a distance
of more than 100 ft. And third, vessels transiting to and from farms produce in-air and
underwater sound levels that are transient and passing, lasting only a very short time at locations
along the path of travel.
Taking into consideration both the geographic setting (i.e., an open water marine environment),
and the intensity and duration of likely exposures, we conclude that underwater sound resulting
from the operation of vessels, motors, and other shellfish equipment (e.g., gas-powered air
compressors, hydraulically powered onboard equipment) is unlikely to significantly disrupt
normal bull trout behaviors (i.e., the ability to successfully feed, move, and/or shelter). Resulting
temporary impacts to the sound and visual environment are low intensity and limited in both
physical extent and duration. We conclude that related exposures and effects to bull trout are
insignificant.
The Service’s work in the Pacific Northwest involving sound exposures and effects to marbled
murrelets has focused on both underwater and in-air sound. Marbled murrelets typically forage
in groups of two or more and are highly vocal on the surface when foraging (Speckman et al.
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2003; Sanborn 2005). Conspecific vocalizations play an important role, and whether they are
audible may influence foraging efficiency (SAIC 2012, p. 13). Based on field observations, it
appears that the social foraging strategy employed by marbled murrelets requires adequate
acoustic communication to distances up to 30 meters (98 ft)( SAIC 2012, p. 16). Hearing and
hearing sensitivity are also important to predator detection and avoidance.
When hearing sensitivity is reduced, the measurable effect is referred to as threshold shift (TS).
There are varying levels or degrees of TS, the amount and duration of which are correlated to the
duration and intensity of sound exposures (SAIC 2012). When associated with actual injury
e.g., physical damage to the hair cells), either permanent TS or temporary TS can result. A TS
40 dB is generally indicative of injury (SAIC 2012). However, TS occurs whenever the
auditory system processes acoustic stimuli, and some amount of TS is inconsequential because it
is effectively truncated by the masking effect of ambient sound. If TS is below the ambient
sound it is inconsequential; the ambient sound itself interferes with signal perception (SAIC
2012).
Masking occurs when a sound interferes with the perception of a signal of interest. Masking is
assessed by considering the critical ratio, the difference (measured in dB) between a hearing
threshold and the masking noise. Critical ratios are documented for a number of bird species
Dooling et al. 2000). In general, a signal at specific frequency must be approximately 25 dB
above the ambient sound level to be detected by a bird.
The keer call of the marbled murrelet is relatively loud; the source level is approximately 95
dBrms, with the majority of the energy centered at 3 kHz. The Service, working with a panel of
experts (SAIC 2012), has estimated ambient in-air sound levels for industrialized and non-
industrialized marine shoreline areas, and has adjusted those estimates downward to arrive at
ambient in-air sound levels centered at 3 kHz. When adjusted downward, the ambient in-air
sound level for non-industrialized marine shoreline areas is approximately 15 dB (SAIC 2012).
Based on this work, the Service has concluded that non-injurious TS (<40 dB) occurring in the
marine environment would not generally have a measurable effect on marbled murrelet
behaviors; the effect of ambient sound levels on signal perception would be greater than that of
TS (SAIC 2012). The Service also concluded that a TS <40 dB will not generally interfere with
predator detection.
Marbled murrelets exposed to elevated underwater and in-air sound levels resulting from the
operation of vessels, motors, and other shellfish equipment (e.g., gas-powered air compressors,
hydraulically powered onboard equipment) will not experience TS 40 dB, and non-injurious TS
40 dB) occurring in the marine environment is unlikely to significantly disrupt normal marbled
murrelet behaviors (i.e., the ability to successfully feed, move, and/or shelter). In-air sound
levels may mask marbled murrelet vocalizations to a distance of 100 to 200 ft. However, these
exposures will be transient and passing; at a given location, they are unlikely to significantly
interfere with conspecific vocalizations and social foraging, and will not interfere with predator
detection and avoidance.
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However, marbled murrelets are also sensitive to visual disturbance, and there is information to
suggest that sound and visual disturbance experienced in the marine environment may have
implications for the energetics of some individuals (Speckman, Piatt, and Springer 2004; Agness
et al. 2008). Appendix D includes excerpts from Speckman, Piatt, and Springer (2004) and
Agness et al. (2008); those excerpts are incorporated here by reference.
Like most other birds that utilize the nearshore marine environment, marbled murrelets are
accustomed to at least low levels of human activity. Many, perhaps most, individuals are
unlikely to leave, or discontinue foraging, in response to the sound and visual disturbance that
results temporarily from shellfish activities. However, it is also possible that some breeding
adults may incur added energetic costs associated with avoidance diving and flights, or as a
result of failed prey deliveries and bouts of repeated foraging. There is information to suggest
that lower vessel speeds could reduce the frequency and/or severity of adverse responses.
On balance, however, when considering the transient and low intensity nature of sound and
visual disturbances resulting temporarily from shellfish activities, and in light of the fact that
most shellfish activities are conducted on or over the exposed or partially exposed intertidal bed,
the Service expects that the majority of foraging marbled murrelets will typically resume their
activity with nothing more than a short delay. Furthermore, those shellfish activities that are
conducted during periods of tidal inundation, and/or over the submerged subtidal bed (e.g.,
frosting or graveling, mechanical harrowing, mechanical harvest, dive-harvest, and suspended
culturing techniques), are all either stationary or proceed at slow or moderately-slow vessel
speeds.
Available information indicates that marbled murrelets will be exposed to temporary sound and
visual disturbances resulting from shellfish activities. However, taking into consideration both
the geographic setting (i.e., an open water marine environment), and the intensity and duration of
likely exposures, we conclude that sound and visual disturbance resulting from shellfish
activities is unlikely to significantly disrupt normal marbled murrelet behaviors (i.e., the ability
to successfully feed, move, and/or shelter). Resulting temporary impacts to the sound and visual
environment are low intensity and limited in both physical extent and duration. We conclude
that related exposures and effects to marbled murrelets are insignificant. Exposures with the
potential to cause direct injury, or measurable adverse effects to energetics, growth, fitness, or
long-term survival, are extremely unlikely and therefore considered discountable.
This general conclusion regarding shellfish activities does not extend to the practice of
intentionally hazing wildlife. When and where farm operators take measures to intentionally
haze wildlife, those practices, resulting potential exposures, and outcomes may be quite different
see the sub-section that follows, Intentional Hazing of Wildlife).
Intentional Hazing of Wildlife
The Corps has not collected or provided information to describe practices that represent
intentional hazing of wildlife. However, the Service is aware of information indicating that some
growers and farm operators engage in such practices.
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Content from the Pacific Coast Shellfish Growers Association’s (PCSGA) Environmental Codes
of Practice states the following (PCSGA 2011, pp. 60-67):
Pest and Predator Controls. Control methods may include benign forms of prevention
such as planting at times when predation is least likely to occur … Netting and other
predator exclusion devices may be used … especially during [the] most vulnerable,
juvenile, stage … In extreme cases, where other methods have failed, pests and predators
may be destroyed … the lowest impact control methods should be used first, graduating
on to higher impact methods only as needed” (p. 60).
Netting and hand removal [or relocation] are the two most common methods utilized for
control [of oyster drills, starfish, and moon snails]” (p. 61).
In some areas, predation by [waterfowl] is significant, especially Scoter ducks
Melanitta sp.)] … Passive measures including … fencing … tubes and netting are the
preferred methods … Hazing is also used with some degree of success” (p. 61).
Marine Mammals. Most marine mammals do not prey on cultured shellfish … The only
known cases … involve sea otters [(Enhydra lutris)] … Interactions with marine
mammals can have serious consequences for shellfish farmers. Harassment of marine
mammals is not allowed by the [Marine Mammal Protection Act], effectively prohibiting
a farmer … from even scaring away [marine mammals]” (p. 64).
Objective: Develop and Use an Integrated Pest Management Program. Suggested
Strategies: … 4) Schedule farm activities to coincide with times when birds are most
likely to be present … 5) Implement “scaring” or hazing techniques on sites prone to bird
predation, prior to production of any shellfish and immediately upon arrival of early
migrating birds” (PCSGA 2011, p. 67).
Gorenzel and Salmon (2008) have reviewed available techniques and strategies for hazing and
dispersing birds. They present information and recommendations on the use of propane cannons,
pyrotechnics, and other sound-making devices; biosonics (e.g., distress or alarm call generators);
visual scaring devices (e.g., mylar tape, lasers); chemical repellants; manned patrols on-foot or
vehicle; and, hunting. Key points of emphasis include the following:
The species present … will in part determine the types of hazing equipment that can be
used. Certain hazing techniques are very effective in deterring certain species, but could
be completely ineffective and sometimes counterproductive with other species” (p. 2).
The key elements in any strategy to haze birds are timing, organization, variation, and
persistence … Variation, the use of a variety of hazing techniques, whether in
combination or in rotation … helps prevent or delay the onset of habituation … To be
successful, the hazing operation must be diligently applied [and] dynamic” (Gorenzel and
Salmon 2008, p. 10).
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Gorenzel, Conte, and Salmon (1994) have prepared guidance for the control of bird damage at
aquaculture facilities. In addition to the auditory and visual hazing and deterrent techniques
mentioned above, they provide additional guidance regarding a potential role for trapping and
shooting (i.e., hunting):
All fish-eating birds that frequent aquaculture facilities are classified legally as
migratory and thus are protected by federal, and in most cases, state laws” (p. E-10).
A permit is not needed to physically or mechanically exclude any fish-eating bird …
Except for … species such as the bald eagle [(Haliaeetus leucocephalus), which is
protected under the Bald and Golden Eagle Protection Act], a permit is not required to
harass or scare fish-eating birds” (p. E-10).
In recent years more incidences of aquaculture-related bird depredation cases have been
reported, and increased legal action has been directed against growers charged with
wildlife violations. Because of the severe legal consequences, it is highly recommended
that a grower have knowledge of all these factors and proceed through the proper permit
process before taking action against depredating species” (Gorenzel, Conte, and Salmon
1994, p. E-10).
Similar guidance and suggestions have been offered more recently (Tucker and Hargreaves eds.
2008, p. 212): “When all measures to disperse birds using nonlethal techniques have been
exhausted, farmers may consider … killing birds to reinforce the fear of nonlethal measures.
Depredation permits are required from the USFWS, and in some states from the state wildlife
agency, to kill almost any species of bird. For currently applicable laws, contact the nearest
USDA Wildlife Services or USFWS office.”
Appendix D includes excerpts from Gorenzel, Conte, and Salmon (1994), Gorenzel and Salmon
2008), and Tucker and Hargreaves (eds. 2008); those fuller excerpts are incorporated here by
reference. Appendix D also includes related information obtained from the Service’s Pacific
Region Migratory Birds and Habitat Program (USFWS 2016).
Exposures and Responses to Intentional Hazing (Bull Trout and Marbled Murrelet)
It is extremely unlikely that bull trout will be exposed to stressors as a result of intentional
hazing of wildlife. Exposures and resulting effects to bull trout are extremely unlikely, and
therefore considered discountable.
Entranco, Inc. and Hamer Environmental (2005) have reported outcomes from a program of
intentional hazing implemented in conjunction with marine construction at the Hood Canal
Bridge. A program of intentional hazing was implemented in an effort to keep marbled
murrelets from diving or otherwise approaching ongoing construction activities that included
impact pile driving. This work was conducted in compliance with the terms and conditions of a
Biological Opinion addressing the construction activitiy and program of intentional hazing.
Entranco, Inc. and Hamer Environmental (2005) reported very little success at keeping marbled
murrelets (and other seabirds) away from the construction activity. Intentional hazing did not
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prevent the majority of birds from foraging, diving, and approaching the ongoing marine
construction. Appendix D includes excerpts from Entranco, Inc. and Hamer Environmental
2005); those excerpts are incorporated here by reference.
Other than this one example (Entranco, Inc. and Hamer Environmental 2005), the Service knows
of no other instances where marbled murrelets have been intentionally and systematically hazed
in the marine environment. However, the work reported by Speckman, Piatt, and Springer
2004) and Agness et al. (2008), which is discussed in the preceding sub-section (see Sound and
Visual Disturbance), does indicate that some breeding adults could incur added energetic costs
associated with avoidance diving and flights, or as a result of failed prey deliveries and bouts of
repeated foraging.
Unfortunately, the Service has little information to inform an assessment of potential exposures
and effects to marbled murrelets resulting from intentional hazing conducted on shellfish farms.
For example, there is no information to meaningfully describe where and how often murrelets
may be exposed to hazing practices, and what measurable outcomes may result for individuals.
Available information suggests that exposure of marbled murrelets to intentional hazing is likely
to occur very infrequently, if at all. We conclude that exposures are not discountable
extremely unlikely”). However, the Service is not able to demonstrate that potential exposures
to hazing are reasonably certain to result in a significant disruption of normal behaviors (i.e., the
ability to successfully feed, move, and/or shelter); measurable adverse effects to energetics,
growth, fitness, or long-term survival; or, direct injury or mortality.
Growers and farm operators who engage in intentional wildlife hazing should educate
themselves and understand their liabilities under the Migratory Bird Treaty Act, Bald and Golden
Eagle Protection Act, and ESA. Non-injurious and non-lethal methods must be implemented
and documented) before the issuance of a Depredation Permit is an option. Growers and farm
operators should consult with the Service and U.S. Department of Agriculture (Animal and Plant
Health Inspection Service, APHIS) before engaging in any practice that may represent an
enforceable violation under federal or State law.
Physical Entrapment and Stranding
The Corps has acknowledged the potential for physical entrapment or entanglement of fish and
wildlife in shellfish culturing equipment (Corps 2015, pp. 86, 110). The Corps and Services
developed conservation measures to address related, potential impacts, and the Corps has
included the conservation measures in their proposed action (Corps 2015, pp. 49-53).
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The Corps has stated (Corps 2015, p. 86):
Area nets used for clam and geoduck culture could potentially entrap fish, birds, or other
aquatic species if they become loose or dislodged … [However,] under the proposed
action … nets must be tightly secured to the substrate, maintained, and periodically
inspected in accordance with the Conservation Measures. This should minimize [the
Service would suggest “reduce”], but not necessarily eliminate, the number of loose or
dislodged nets.”
The Corps has included conservation measures addressing storage and security of culturing
equipment on the tidelands (conservation measure No.s 11, 18, and 19), and addressing patrols to
locate and remove debris (conservation measure No. 22)(Corps 2015, pp. 49-53). Farm plots are
patrolled by crews on a regular basis. Culturing equipment, not limited to nets, bags, racks,
stakes, longlines, tubes, anchors, screens, socks, ropes, and wires, are all routinely inspected to
ensure that they remain secure.
Although the Corps has included a number of conservation measures addressing the security of
culturing equipment (Corps 2015, pp. 49-53) and many growers and farm operators invest
significant time and resources to prevent the loss of equipment, the Service is aware of
information documenting instances where equipment such as nets and tubes have become
dislodged and moved from farmed areas by wind and waves. For example, as recently as
January 2015, the Corps and Service received information from a concerned member of the
public regarding a large quantity of discarded or dislodged and freely floating geoduck tubes on
Squamish Harbor, Hood Canal (P. Sanguinetti pers. comm. 2015)(Figure 38).
The Virginia Eastern Shorekeepers (Ayers 2006) looked at the distribution of lost, discarded, and
abandoned clam nets on the Atlantic barrier islands, and made observations regarding their
effects on substrates, vegetation, and nesting and migratory birds. They report (Ayers 2006, pp.
8, 9): “…there was a 41 percent reduction in the amount of clam net found on the barrier island
beaches … from spring 2004 to autumn 2006”; “there was no evidence of clam net disrupting or
disturbing any nesting birds … [and] no observed impacts on any mammals, reptiles, or
amphibians … there has been an anecdotal report of diamondback terrapins [Malaclemys
terrapin] trapped in net, but no evidence was produced to support this [claim].” Grower
education and public involvement have played a constructive role (Figure 39). Appendix D
includes excerpts from Ayers (2006); those excerpts are incorporated here by reference.
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Figure 38. Unsecured culturing equipment; Squamish Harbor, Hood Canal
P. Sanguinetti pers. comm. 2015)
Figure 39. Image of a “Clam Net Hotline” newspaper
advertisement
Ayers 2006, p. 14)
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The PCSGA and member growers/farm operators organize and conduct beach cleanups in the
south and north Puget Sound (PCSGA 2016). According to the PCSGA, “Twice a year, shellfish
farmers conduct beach cleanups near their farms, collecting tons of debris, the vast majority of
which is not related to shellfish farming … [A recent] effort recovered five dump truck loads of
debris – 85 percent of which had nothing to do with shellfish farming … Most of the debris
recovered by … fourteen shellfish companies was … ‘junk’ … [including] chunks of styrofoam
and] tires.” The PCSGA maintains and monitors a marine debris hotline (PCSGA 2016).
Historically, some oyster growers have used anchored vertical fencing or nets (drift fences or
oyster corrals) to stabilize and prevent oysters and oyster shell from being moved off the cultured
bed. Available information suggests this practice was never widely used in Washington State,
and the Corps’ programmatic consultation does not provide coverage for the practice or activity;
use of drift fences or oyster corrals is specifically excluded from coverage under the Corps
programmatic consultation (Corps 2015, p. 39).
The use of berms or dikes constructed on the upper intertidal bed is a practice of historical but
little apparent contemporary significance (Simenstad and Fresh 1995, pp. 46, 48). The Corps has
stated that their programmatic consultation will not provide coverage for the construction of new
berms or dikes, or “…the maintenance of current, authorized berms or dikes” (Corps 2015, p.
39). Despite the Service’s efforts to communicate concerns related to this practice (i.e., the risk
of fish stranding, entrapment, and mortality), the Corps has declined to provide any relevant
information to describe the ongoing use and prevalence of berms or dikes on the upper intertidal
bed.
The Corps has included a conservation measure which the Service hopes and expects will collect
and compile better, more comprehensive information to describe instances of fish and wildlife
entrapment, entanglement, and stranding. Conservation measure No. 23 requires the following
for all permitees seeking coverage under the programmatic Opinion (Corps 2015, p. 52):
When performing other activities on-site, the grower shall routinely inspect for and
document any fish or wildlife found entangled in nets or other shellfish equipment. In the
event that a fish, bird, or mammal is found entangled, the grower shall: 1) provide
immediate notice (within 24 hours) to WDFW (all species), the Services (ESA listed
species), or the Marine Mammal Stranding Network (marine mammals), 2) attempt to
release the individual(s) without harm, and 3) provide a written and photographic record
of the event, including dates, species identification, number of individuals, and final
disposition, to the Corps and Services. Contact the U.S. Fish and Wildlife Service Law
Enforcement Office at (425) 883-8122 with any questions about the preservation of
specimens.”
Anti-predator netting presents the most obvious potential for physical entrapment or
entanglement of fish and wildlife. Where clams and/or oysters are cultured directly on the
intertidal bed (bottom culture), anti-predator cover nets are frequently installed over a portion, or
all, of the planted area. These nets may be composed of either plastic or organic fibers, and are
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typically anchored at the periphery with embedded rebar or metal staking. Some growers bury
the net edges, or weigh-down the edges with a lead line. Once placed over a seeded clam bed,
anti-predator cover nets typically remain in place until harvest.
Geoduck culturing practices also use nets and tubes on the intertidal bed to prevent and minimize
losses of seed and immature clams. Many, perhaps most, geoduck growers and farm operators
install large, anti-predator, cover nets over the entire field of tubes. Cover nets minimize
predation losses, but also serve to prevent tubes from becoming dislodged.
Oysters and mussels are both grown in Washington State using methods that suspend nets,
screens, socks, ropes, wires, and/or longlines from floating rafts and buoys. Anti-predator
exclusion nets are typically hung around the perimeter of the rafts. Depending on the farm
location, these nets may only be necessary on a seasonal basis. Anti-predator, cover and
exclusion nets are available from a variety of commercial sources, in varying mesh size and
dimensions (Washington Sea Grant 2005, pp. 10, 17). Mesh size varies by application and/or
preference, typically ranging from ¼ x ¼ inch to ¾ x ¾ inch or larger.
The Service is aware of anecdotal information suggesting that fish (especially small schooling
fish) and wildlife do occasionally become entrapped or entangled in culturing equipment,
including anti-predator cover and exclusion nets. Unfortunately, it appears that most instances
have not been well-documented, and State and/or federal fish and wildlife authorities have rarely
been contacted in Washington State. In most cases it seems plausible, indeed highly likely, that
entrapped or entangled birds and marine fish quickly fall victim to predation, or are scavenged,
and little or no evidence of the event may persist after only a short time.
Concerned citizens have documented instances of entrapment involving larger vertebrates,
including birds. An instance of bald eagle (Haliaeetus leucocephalus) entrapment was reported
to the advocacy group ProtectOurShoreline.org (Protect Our Shoreline 2015). Photos and a
short narrative document the events (Figure 40), said to occur on July 23, 2006, wherein a
juvenile bald eagle was observed by citizens to be caught and entrapped by an anchored geoduck
net on the exposed intertidal bed off Harstene Island, Washington. The eagle is reported to have
been exhausted, but not injured. Incapable of flight for a period of time, it appears the eagle
became repeatedly entrapped or entangled as it attempted to walk across the geoduck net (Protect
Our Shoreline 2015).
Another, similar instance of bald eagle entrapment was reported recently, during October 2014
P. Sanguinetti pers. comm. 2014). A concerned citizen reported to the Corps that multiple eye
witnesses observed a bald eagle and scoter entangled by nets on the shores of Henderson Bay
near Burley Lagoon), upper Carr Inlet, Washington. It appears, in these cases, that eye
witnesses observed the animals struggling, but ultimately both succeeded in releasing themselves
and did not require rescue (P. Sanguinetti pers. comm. 2014). These examples present evidence,
albeit incomplete, that the risk of physical entrapment or entanglement is real and not
hypothetical.
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Figure 40. Juvenile bald eagle caught in anti-predator net on Harstene Island, Washington
Protect Our Shoreline 2015)
Bendell (2015) reviewed the efficacy and impacts of anti-predator netting used on intensively
farmed British Columbia tidelands, including Baynes Sound:
While there are studies which have addressed the effectiveness of [anti-predator netting]
APN) in the exclusion of crabs, there are few that have addressed the effectiveness of
APN in preventing clam predation by sea ducks and shore birds. In Puget Sound, Taylor
Shellfish report that significant losses would occur without the use of APN (Bill Dewey,
pers comm. April 2014). But, the lines of evidence for Baynes Sound, BC and clam
farming regions in Europe suggest differently” (p. 23).
Nets do not effectively exclude epibenthic predators such as crabs and fish. Indeed the
findings of Bendell (2014) indicate that seeding is acting as an attractant for bivalve
predators such as small fish and crabs … Poor husbandry of the nets results in gaps in the
APN allowing for predation. Nets are often in disarray and not firmly attached” (p. 24).
Nets … wash up on shore [and present] hazards to humans and wildlife alike … APN
entrains wildlife and poses a real threat to forage fish, such as [Pacific] herring, which
use the intertidal regions for spawning [Figure 41]” (Bendell 2015, pp. 25, 26).
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Figure 41. Marine forage fish entrapped in anti-predator netting
Bendell 2015, p. 26)
Related or Additional Considerations (Ingestion of Plastics and Microplastic Pollution)
Shellfish culturing activities commonly place a significant amount of plastic material onto the
tidelands (platic tubes, ties, nets, bags, etc.). These materials are subject to tidal, wind, and wave
action that may in some instances dislodge and remove them from farm locations. These
materials also breakdown in the marine environment and can become a source of microplastic
pollution.
According to Moore (2014, pp. 207, 208), “The equipment used for both aquaculture and capture
fishing up until the 1960s consisted of metal, wood, and natural fibers … The plastic age ushered
in materials so resistant to natural decay that lost plastic aquaculture gear can last for centuries
Plastic exposed to sunlight becomes embrittled, principally through photodegradation and the
leaching of monomeric conditioning agents into the surrounding water, and eventually breaks
into bite-sized bits that last far longer than natural materials.”
Moore (2014, pp. 208, 213, 214) claims that “…evidence from remote beaches and the high seas
implicates aquaculture as a significant contributor to the ocean’s plastic load,” and bottom trawl
survey estimates document tens of thousands of displaced geoduck tubes in the south Puget
Sound alone. “The enormous amount of uncovered expanded polystyrene docks and floats used
in aquaculture, and its tendency to readily fragment, means that untold trillions of particles the
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size of plankton and fish eggs are becoming a part of the marine food web” (Moore 2014, p.
215).
Davis and Murphy (2015) have summarized results of two independent studies evaluating the
abundance of anthropogenic debris on beaches bordering the Salish Sea in Washington State and
plastic debris in surface waters of the Salish Sea and the Inside Passage to Skagway, Alaska:
No previous studies have broadly documented plastic in enclosed waters of western
North America with substantial urbanization [such as the Salish Sea], or the
transboundary waters of the Inside Passage of Washington, British Columbia, and
Alaska” (p. 169).
Both studies concluded that foam, primarily expanded polystyrene was the dominant
pollutant … Plastic was found in surface waters the full length of the Inside Passage but
was concentrated near harbors” (p. 169).
Anthropogenic debris was found in 363 of 402 quadrats (90.3 percent) … Foam
comprised nearly 70 percent of the total count of anthropogenic debris … Plastic
fragments and glass followed with approximately 11 percent each … 77 percent of the
total count was microdebris … By weight plastic fragments and glass dominated with 37
percent and 32 percent of the total, respectively … Other components accounted for an
additional 17 percent and foam was just under 7 percent … While microdebris dominated
the count, it was only about 8 percent of the total weight” (p. 173).
Foam, virtually all of it expanded polystyrene, dominated the anthropogenic debris
found in samples of surface water collected in the Inside Passage … Microfoam
accounted for 94.7 percent of all anthropogenic debris collected, with another 1.4 percent
being macro foam … Expanded polystyrene foam was particularly common in the
vicinity of harbors/marinas the full length of the Inside Passage and low in remote areas”
p. 174).
Williams et al. (2011) assessed … [patterns] in coastal British Columbia … [and found]
the most abundant types of debris detected were Styrofoam (48.8 percent), plastic bottles
14.7 percent), plastic grocery bags (10.5 percent), and fishing gear (6.3 percent) … It is
interesting that, as in our studies, foam was by far the dominant pollutant” (Davis and
Murphy 2015, pp. 175, 176).
Cole et al. (2011) have reviewed available literature examining microplastics as contaminants in
the marine environment; they report the following:
Secondary microplastics describe tiny plastic fragments derived from the breakdown of
larger plastic debris, both at sea and on land (Ryan et al. 2009; Thompson et al. 2004) …
Over time a culmination of physical, biological, and chemical processes can reduce the
structural integrity of plastic debris, resulting in fragmentation (Browne et al. 2007)” (p.
2589).
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Owing to their small size, microplastics are considered bioavailable to organisms
throughout the food-web … Their composition and relatively large surface area make
them prone to adhering waterborne organic pollutants and to the leaching of plasticisers
that are considered toxic … Ingestion of microplastics may therefore be introducing
toxins to the base of the food chain, from where there is potential for bioaccumulation
Teuten et al. 2009)” (p. 2589).
Plastic debris on beaches … have high oxygen availability and direct exposure to
sunlight … will degrade rapidly, in time turning brittle, forming cracks and ‘‘yellowing’’
Andrady 2011; Barnes et al. 2009; Moore 2008) … With a loss of structural integrity,
these plastics are increasingly susceptible to fragmentation resulting from abrasion,
wave-action, and turbulence (Barnes et al. 2009; Browne et al. 2007) … This process is
ongoing, with fragments becoming smaller over time until they become microplastic in
size (Fendall and Sewell 2009; Rios et al. 2007; Ryan et al. 2009)” (p. 2590).
Plastics consist of many different polymers and, depending on their composition,
density and shape, can be buoyant, neutrally buoyant or sink … As such, microplastics
may be found throughout the water column” (p. 2592).
Incomplete polymerisation during the formation of plastics allows additives to migrate
away from the synthetic matrix of plastic … Commonly used additives, including
polybrominated diphenyl ethers, phthalates and the constituent monomer bisphenol A, are
renowned for being endocrine-disrupting chemicals as they can mimic, compete with or
disrupt the synthesis of endogenous hormones (Talsness et al. 2009)” (p. 2595).
A range of marine biota, including seabirds, crustaceans, and fish, can ingest
microplastics (Blight and Burger 1997; Tourinho et al. 2010) … In all these examples,
animals might have ingested microplastics voluntarily, which they confuse for their prey
Alternatively, microplastic ingestion may result from eating lower trophic organisms
that have themselves consumed microplastics (Browne et al. 2008; Fendall and Sewell
2009)” (Cole et al. 2011, p. 2594).
Lindborg et al. (2012) analyzed dietary habits and the presence of plastic in glaucous-winged
gulls (Larus glaucescens) from the Salish Sea; they report the following:
Glaucous-winged gulls are common seabirds in the Salish Sea (USA), Washington,
whose plastic ingestion has not been well documented … Glaucous-winged gulls are
omnivorous opportunists that feed on forage fish, invertebrates, and other birds (Trapp
1979; Schmutz and Hobson 1998)” (p. 2351).
Plastics comprise a notable but not dominant portion of gull bolus material, with 12.2
percent of collected boluses containing plastic … dominated by plastic film of the type
used in plastic bags and wrappers … Hard plastic fragments were found in 4.1 percent of
all boluses … [and] Filaments (such as fishing line), foam (such as polystyrene), and pre-
production pellets were found less frequently, in 1.4 percent, 1.4 percent and 0.5 percent
of all boluses, respectively” (p. 2353).
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The] Impact of ingestion of large quantities of plastic on gulls is at present unknown …
While gulls regurgitate indigestible materials, Procellariiformes [albatross and petrels] in
general do not” (Lindborg et al. 2012, p. 2355).
Avio et al. (2015) have examined microplastic pollutant bioavailability and toxicological risk for
marine mussels:
Ingestion of microplastics has been demonstrated in various marine organisms with
different feeding strategies; this phenomenon may negatively influence both the feeding
activity and nutritional value of a plankton-based diet, particularly in those species which
can not discriminate the food source (Moore et al. 2001; Browne et al. 2008)” (p. 211).
Recent evidences also suggest the potential role of microplastics as vectors of chemical
pollutants, either used as additives during the polymer synthesis, or adsorbed directly
from seawater (Rios et al. 2007; Teuten et al. 2009; Engler 2012)” (p. 211).
The results [here] … obtained with exposed mussels provide the first clear evidence that
pyrene adsorbed on contaminated microplastics was transferred to organisms and
concentrated in tissues … Significant immunological effects were observed … [and]
Exposure to microplastics also determined the onset of various forms of genotoxicity”
Avio et al. 2015, pp. 218, 220).
Cauwenberghe and Janssen (2014) have examined microplastics found in bivalves cultured for
human consumption:
Bivalves are of particular interest since their extensive filter-feeding activity exposes
them directly to microplastics present in the water column” (p. 66).
Our results show that microplastic particles are present in shellfish, more specifically
bivalves, cultured for human consumption” (p. 67).
Mathalon and Hill (2014) detected microfibres in wild and farmed mussels … Farmed
mussels had significantly higher concentrations of microplastics compared to wild
mussels: on average 178 microfibres per farmed mussel compared to an average of 126
microfibres per wild mussel in the most polluted site … These plastic body burdens are
500 times higher than the concentrations in mussels reported in [our] study” (p. 67).
This report is the first … on possible consequences of marine microplastics for humans
The presence of microplastics in seafood” (Cauwenberghe and Janssen 2014, p. 68).
The proposed action will introduce plastic debris that could exacerbate threats to marine life
through direct ingestion of plastics/debris, indirect ingestion via prey, or bioaccumulation of
toxic compounds in the food chain. These materials and debris may sink or float, but there is
limited information to discern quantities that would sink or float. While available information
clearly indicates significant amounts of plastic and microplastic pollution in the action area, it is
not clear that shellfish activities contribute significantly to this pollution. The Service does
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expect that some amount of plastic shellfish culturing material will persist in the marine
environment for long durations and will progressively break down into smaller and smaller
fragments.
Among seabirds the highest prevalence of ingested plastics has been documented in surface
feeders (Robards et al. 1997, p. 71). Blight and Burger (1997, p. 323) found plastics in the
stomachs of surface-feeding seabirds, but not in pursuit dive-feeding seabirds, including marbled
murrelets. Bond et al. (2013, p. 192) found that 7 percent of pursuit-dive feeding murres had
ingested plastic, and Provencher et al. (2010, p. 1406) found that 11 percent of murres had
plastic debris in their gastrointestinal tracts. Robards et al. (1997, p. 74) examined more than 80
marbled murrelets and found none that showed evidence of ingested plastic. Avery-Gomm et al.
2013, p. 1) have made a similar finding.
Bull trout and marbled murrelets prey on marine forage fish and may thereby indirectly ingest
plastics, chemical plastic additives, and adsorbed contamination. Persistent, bioaccumulative,
and toxic substances are found on recovered plastic debris (Hirai et al. 2011), bioaccumulate in
foodwebs (Teuten et al. 2009), and are linked with several adverse effects including endocrine
disruption (Guillette et al. 1994).
Plastic particles are reported in the gut content of several species of fish from pelagic habitats,
estuaries, and bays (Rochman et al. 2013, p. 2). They concluded that polyethylene ingestion is a
vector for the bioaccumulation of persistent, bioaccumulative, and toxic substances in fish, and
that toxicity resulting from plastic ingestion is a consequence (Rochman et al. 2013, p. 5).
Risk of Exposure to Physical Entrapment and Stranding (Bull Trout and Murrelet)
The Service has little information to inform an assessment of the risk of entrapment,
entanglement, or stranding for bull trout and marbled murrelets that forage in and around
shellfish farms. To our knowledge, there have been no reported instances of these species
becoming entrapped or entangled in shellfish culturing equipment. To our knowledge, there
have been no reported instances of bull trout, or larger salmonids, becoming stranded behind
berms or dikes, or within pools impounded by or around shellfish culturing equipment.
An earlier portion of the Opinion discussed derelict nets and fishing gear (see Current Condition
in the Action Area (Marbled Murrelet), Factors Responsible for the Condition of the Species).
Carter, McAllister, and Isleib (1995) documented accidental capture and mortality in commercial
gill nets as one of the major threats to marbled murrelet populations. Laist (1997) compiled a
comprehensive list of species with marine debris entanglement and ingestion records, described
factors influencing entanglement rates, and problems associated with collecting and analyzing
entanglement data. Good et al. (2010) reported on the progress made removing derelict gear in
Puget Sound and the Northwest Straits (i.e., Canadian waters of the Salish Sea), and the pattern
of remaining threats. Appendix D includes excerpts from Carter, McAllister, and Isleib (1995);
Laist (1997); and, Good et al. (2010); those excerpts are incorporated here by reference.
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Good et al. (2010) have reported the following:
Of the 902 derelict fishing nets recovered from Puget Sound and the Northwest Straits as of
June 2008, 876 were gillnets. The remaining nets were purse seines (n = 23), trawl nets (n =
2), and aquaculture nets (n = 1) … 25 percent were derelict for somewhere between 5 and 24
years”; most of the recovered and removed gillnets were located in the San Juan Island
archipelago and north Puget Sound (pp. 42, 43).
Nets] are especially lethal for marine fish, as [most of these] nets are designed specifically
for catching and killing them … [But nets] are also deadly for marine birds and mammals,
which must periodically surface to breathe air … Diving birds and marine mammals appear
to fall prey to nets while pursuing fish underwater … some of the forage fish and smaller fish
species aggregate in and under the relative safety of the netting” (Good et al. 2010, pp. 48,
49).
Unfortunately, the Service has little information to inform an assessment of potential exposures
and effects to marbled murrelets resulting from entrapment or entanglement in shellfish culturing
equipment and gear. There is no information to meaningfully describe where and how often
marbled murrelets may be exposed, and what measurable outcomes may result for individuals.
Available information suggests that exposure of marbled murrelets is likely to occur very
infrequently, if at all. We conclude that exposures are not discountable (“extremely unlikely”).
However, the Service is not able to demonstrate that potential exposures are reasonably certain to
result in a significant disruption of normal marbled murrelet behaviors (i.e., the ability to
successfully feed, move, and/or shelter) or instances of direct injury or mortality.
The Corps has stated the following (Corps 2015, p. 110):
Given the prevalence of nets, inconsistent husbandry practices, difficulty fully securing
nets in the aquatic environment, proximity to major spawning rivers, and the 20 year time
period of the [programmatic], some unknown amount of bull trout entanglement in nets is
likely to occur. Rack and/or bag culture may function in a similar manner resulting in the
entrapment and/or stranding as the tide retreats from these areas … These would be
considered adverse effects to this species.”
We agree with the Corps and believe that the best available scientific information supports this
conclusion. However, considering the size and mobility of subadult and adult anadromous bull
trout, the Service believes that the incidence rate of entanglement, entrapment, and/or stranding
must be very low across the whole of the industry. Despite the fact that shellfish farms occupy
tens of thousands of nearshore marine acres in Washington State, and overlap significantly with
habitats that are seasonally and regularly used by anadromous bull trout (e.g., approximately
12,000 acres of designated bull trout critical habitat), the Service expects that there will be very
few instances of individual bull trout injury or mortality over the 20-year term of the
programmatic (2016 to 2036).
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The Service concludes that instances of bull trout injury or mortality resulting from
entanglement, entrapment, and/or stranding are reasonably certain to occur over the 20-year term
of the programmatic. We expect that instances of bull trout injury or mortality will occur more
frequently in the north Puget Sound, where anadromous bull trout are relatively more abundant,
and will occur less frequently in the other four geographic sub-areas (Willapa Bay, Grays
Harbor, Hood Canal, and south Puget Sound). We expect that a maximum of six (6) subadult or
adult bull trout will be injured or killed in the north Puget Sound geographic sub-area over the
20-year term of the programmatic. We expect that a maximum of two (2) subadult or adult bull
trout will be injured or killed in each of the other four geographic sub-areas (Willapa Bay, Grays
Harbor, Hood Canal, and south Puget Sound) over the 20-year term of the programmatic (2016
to 2036).
The Service expects that plastic shellfish culturing materials will not float on the surface or in the
water column long enough to be a significant direct ingestion threat for bull trout or marbled
murrelets. While there may be a small risk that bull trout or marbled murrelets will accidentally
ingest debris, we expect that it is extremely unlikely to occur. Direct effects from exposure to
these materials are extremely unlikely, and therefore considered discountable.
Based on available information regarding degradation of plastics in the marine environment and
bioaccumulation of associated contaminants in the marine food web, we conclude that some
individual bull trout and marbled murrelets are likely to be exposed to microplastic pollution and
associated contaminants. These exposures may adversely affect some individuals. However, the
Service is not able to demonstrate that potential exposures are reasonably certain to result in a
significant disruption of normal behaviors (i.e., the ability to successfully feed, move, and/or
shelter), instances of direct injury or mortality, or fitness consequences.
Persistent Stressors, Long Duration or Long-Term Exposures, and Effects
Indirect effects are caused by or result from the proposed action, are later in time, and are
reasonably certain to occur. Indirect effects may occur outside of the area directly affected by
the action.
Shellfish activities result in measurable and potentially significant effects to water quality,
substrate condition, physical habitat structure and function, and benthic/epibenthic community
structure and composition. Earlier portions of the Opinion discussed temporary stressors
resulting from shellfish activities, and resulting short-term exposures and effects to the bull trout
and marbled murrelet.
Shellfish activities alter physical, chemical, and biological conditions on varying temporal scales.
Many of these effects to the physical, chemical, and biological environment (i.e., potential
stressors) correspond closely to cycles of production and harvest. However, some of these
effects also reflect variable patterns and rates of recovery from disturbance, and/or interactions
with unrelated activities in the same nearshore environments. While earlier portions of the
Opinion discussed temporary stressors resulting from shellfish activities, this portion addresses
persistent stressors of long duration (months, years), including potential indirect effects that may
result from altered patterns of prey availability and productivity (“prey-mediated effects”), and
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potential long-term effects to natural forms of nearshore marine habitat structure, function, and
complexity. This portion of the Opinion describes long-term, direct and indirect effects on large
spatial scales, corresponding to hundreds of farms and farm operations, and thousands of
affected nearshore marine acres.
When viewed from a landscape perspective, or even from the perspective of a single waterbody
e.g., Willapa Bay) or portion thereof (e.g., Totten Inlet, Samish Bay), shellfish activities are
variable in density and spatially discontinuous. At some locations, cultured tidelands extend
with only occasional interruption along extended lengths of the nearshore. At other locations,
cultured tidelands are interspersed along shorelines that support a range of other uses (residential,
recreational, etc.). Where cultured tidelands extend with only occasional interruption,
interspersed uncultured areas may experience direct or indirect effects, and are therefore
considered part of the action area. The discernable direct and indirect effects of shellfish
activities are generally superimposed on, and further influenced by, natural variability, patterns
of disturbance and recovery from natural events, and the confounding effects of concurrent,
unrelated activities occurring in the same nearshore environments and watersheds.
The Corps has stated the following (Corps 2015, p. 83):
The effects [of individual activities] may be relatively short-term or longer lasting … Of
equal or more relevance to ESA listed species are the effects of the collective activities,
their frequency, duration, timing, geographic location, and general scale across the
landscape.”
We agree with the Corps and believe that the best available scientific information supports this
conclusion. Our Opinion finds that the most significant and biologically relevant effects are
those that result in aggregate to nearshore marine habitat structure, function, and productivity,
ecological processes, and ecosystem services. The sub-sections that follow attempt, where
possible, to evaluate these effects to the physical, chemical, and biological environment on two
scales: 1) the scale of a single large farm or grouping of smaller farms (e.g., 50 to 500 acres);
and, 2) the scale of a large grouping of small and large farms, occupying a significant portion of
a single waterbody (e.g., Willapa Bay) or portion thereof (e.g., Totten Inlet, Samish Bay). For
wide-ranging species that depend on the action area’s variety of nearshore marine environments
and resources (e.g., anadromous bull trout, the marbled murrelet), it is ultimately at these larger
scales that we can best interpret the significance of potential stressors, exposures, and responses.
Effects to Ecosystem Services, including Water Quality
Ecosystem services are benefits that people and communities derive or obtain from natural and
managed ecosystems. They are commonly described as supporting, provisioning, regulating,
and cultural services (Millennium Ecosystem Assessment 2005 in Saurel et al. 2014, p. 267). A
number of authors have argued that bivalves and other filter-feeding shellfish, whether occurring
naturally or in farmed/cultured settings, provide measurable benefits in the form of ecosystem
services (Newell 2004; Coen et al. 2007; Forrest et al. 2009; Saurel et al. 2014; Banas and
Cheng 2015).
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Newell (2004) focused on bivalve feeding, “top-down” control of phytoplankton, “bottom-up”
control of nutrient processing and regeneration, and how these processes interact and can
contribute to improved marine and estuarine water quality. Coen et al. (2007) and Forrest et al.
2009) both emphasized filtration, benthic-pelagic coupling, interactions leading to the enhanced
heath or recovery of submerged aquatic vegetation, and the provision of refugia and habitat for
both sessile and mobile species. Saurel et al. (2014, p. 267) claim that cultured bivalves provide
all four forms of ecosystem services, supporting, provisioning, regulating, and cultural. Banas
and Cheng (2015 In Washington Sea Grant 2015) use an oceanographic circulation model
developed for the south Puget Sound to demonstrate how naturally occurring and
farmed/cultured bivalves could “…act as a brake on eutrophication” (p. 62).
Suspension-feeding bivalves serve to couple pelagic and benthic processes … [and] can be
extremely important in regulating water column processes … Verwey (1952) was the first to
identify the important ecological role of bivalves … as key agents in benthic-pelagic coupling …
Bivalves can exert ‘top-down’ grazer control on phytoplankton and in the process reduce
turbidity … [potentially] extending the depth to which ecologically important … plants …
seagrasses and benthic algae can grow” (Newell 2004, p. 51). “Bivalves can also exert ‘bottom-
up” nutrient control … by changing nutrient regeneration processes within the sediment … Large
amounts of undigested particulate organic nitrogen [N] and phosphorus [P] are transferred to the
sediment surface in feces and pseudofeces (biodeposits) …[where they] gradually become
incorporated” (Newell 2004, pp. 51, 52).
Newell (2004, pp. 55) claims that one aspect of this ‘bottom-up control’ is frequently
overlooked. “Burial of N and P, and removal of N from the ecosystem via denitrification, is
enhanced by bivalve biodeposition … Within the anaerobic sediments, denitrifying bacteria
reduce the … [N] to N2 gas … [which] passes to the atmosphere without stimulating further
primary production … [However, this requires] a close juxtaposition between oxygenated
conditions that support nitrifying bacteria and anaerobic conditions that support denitrifying
bacteria (Kaspar et al. 1985; Kristensen 1988).” Newell (2004, pp. 57) also claims that
extractive aquaculture’ can play a role in regulating or controlling nutrient levels and the
impacts resulting or associated with eutrophication; when bivalves are harvested, N and P are
permanently removed from the marine and estuarine ecosystems in the forms of tissue and shell.
Coen et al. (2007) and Forrest et al. (2009) both review published findings suggesting that
bivalves create and enhance habitats for submerged aquatic vegetation, marine invertebrates, and
finfish. Appendix D includes excerpts from Coen et al. (2007) and Forrest et al. (2009); those
excerpts are incorporated here by reference, and are also addressed by a sub-section that follows
see Effects to Nearshore Habitat Structure and Function).
Bivalve aquaculture may be seen as a green industry, providing ecosystem goods and services
Jackson et al. 2001; Smaal et al. 2001; Newell 2004; Coen et al. 2007, zu Ermgassen et al.
2013) that include: (1) reduction of turbidity and nutrient control through filtration of organic
matter (Forrest et al. 2009; Carlsson et al. 2012; Pollack et al. 2013); (2) water quality
improvement through reduction of primary eutrophication symptoms, thereby minimizing
secondary symptoms such as hypoxia (Bricker et al. 2003; Ferreira et al. 2007); (3) provision of
habitat for early stages of invertebrates, and food for local predators (Inglis and Gust 2003;
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Dealteris et al. 2004; Segvic-Bubic et al. 2011); and (4) potential improvement of shellfish
recruitment in adjacent areas, thereby helping restoration (Wilbur et al. 2005)” (Saurel et al.
2014, p. 256). Numerous authors have described how living bivalves, shells/shell fragments, and
their aggregations in reefs or banks create novel substrates and contribute to spatially
heterogenous habitats (Gutierrez et al. 2003; Sousa, Gutierrez, and Aldridge 2009; Gutierrez et
al. 2011). Appendix D includes excerpts from Gutierrez et al. (2003); Sousa, Gutierrez, and
Aldridge (2009); and, Gutierrez et al. (2011); those excerpts are incorporated here by reference,
and are also addressed by a sub-section that follows (see Effects to Nearshore Habitat Structure
and Function).
Banas and Cheng (2015 In Washington Sea Grant 2015) used an oceanographic circulation
model developed for the south Puget Sound to investigate the potential influences of shellfish
aquaculture on water quality and trophic status. “Results suggest a strong gradient in residence
time from the central, deep channels to the small, western inlets, creating a potential for localized
effects on water quality … Results suggest that Henderson Inlet, Eld Inlet, Totten Inlet,
Hammersley Inlet, Oakland Bay, and upper Case Inlet have combinations of long residence time
and high densities of aquacultured filter-feeders such that aquaculture operations there may
potentially control local phytoplankton concentrations … One might hypothesize that these inlets
are at noticeably lower risk of eutrophication than they would be in the absence of shellfish
aquaculture” (Banas and Cheng 2015 pp. 59, 66). Appendix D includes excerpts from Banas and
Cheng (2015); those excerpts are incorporated here by reference.
Bivalves and other filter-feeding shellfish, whether occurring naturally or in farmed/cultured
settings, provide important benefits in the form of ecosystem services. The Service expects that
shellfish activities will generally, and in the majority of cases, provide long-term benefits in the
form of improved water quality and sequestration of carbon and nutrients. These ecosystem
services may be important as a means to control and prevent the effects of excess nutrient
additions occurring elsewhere in the contributing watersheds and may lessen or counteract the
potential for climate-induced ocean acidification and hypoxia.
Carrying Capacity
Ecological carrying capacity is a useful concept for thinking about the possible erosion or loss of
ecosystem services, and resulting consequences, under a scenario of pervasive and extremely
high shellfish culturing densities. In its widest use, “carrying capacity” generally refers to the
maximum production of a population (or output) in relation to available, finite resources (or
inputs) that does not cause an unacceptable (or irreversible) change in the ecosystem. According
to the Pacific Shellfish Institute (2014), the concept is similar to, but broader than the principle of
maximum and optimum sustainable yield”.
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Newell (2004, pp. 54, 55) observed the following:
In waters with substantial rates of bivalve grazing … [this] may possibly adversely affect
food quality for other suspension-feeders … In systems that are either less productive, have
limited water circulation, or have very high levels of bivalve biomass … competition for
food may occur between natural and aquaculture stocks … There is likely to be an
exponential increase in interspecific competition for food as bivalve stocks increase in a
location from low to high.”
Newell (2004, pp. 56, 57) also observed the following, regarding biodeposition and sediment
overenrichment:
The ecosystem effects of an increase in bivalves on sediment nutrient regeneration … will
vary depending on bivalve population density and the rate of mixing of oxygenated water
down to the sediment surface … Excess biodeposition, especially in low flow environments
may cause] sediments to become anoxic … and sediment-bound P to be mobilized …
Local adverse effects can be ameliorated by moderate water currents or wave action that
allows biodeposits to be spread across a larger bottom area … The adverse effects of
sediment overenrichment … have been [most] often observed in sediments underlying …
suspended raft culture … Findings suggest that extremely dense bivalve communities can
adversely affect sediment microbial processes by shifting them from aerobic to anaerobic
metabolism.”
Similarly, Forrest et al. (2009, p. 3) reported the following:
Extreme enrichment effects as a result of oyster farming have been described historically
only for suspended culture systems in Japan, and been attributed to repeated culturing and
overstocking (Ito and Imai 1955; Kusuki 1981) … Hence, it is apparent that the magnitude of
benthic enrichment from elevated intertidal culture [of shellfish] is generally relatively minor
by comparison with suspended subtidal culture of fish (e.g. Brown et al. 1987; Karakassis et
al. 2000; Forrest et al. 2007a) … The magnitude of effects from enrichment will depend
primarily on stocking density and biomass in relation to the flushing characteristics of the
environment (Pearson and Black 2001) … Additionally, the level of biodeposition for a given
stocking density, and the assimilative capacity of the environment, may vary seasonally
Kusuki 1981; Souchu et al. 2001; Mitchell 2006) … The capacity of the environment to
assimilate and disperse farm wastes will mainly depend on water current velocity and wave
action (Souchu et al. 2001), as these factors control the size and concentration of the
depositional ‘footprint’ … Generally, well-flushed aquaculture sites can be expected to have
depositional footprints that are less intense but more widely dispersed than shallow or poorly
flushed sites (Pearson and Black 2001).”
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Forrest et al. (2009, p. 6) also directly addressed the science related to carrying capacity:
There has been considerable research into food depletion and modelling of carrying capacity
for oyster culture (e.g. Ball et al. 1997; Bacher et al. 1998; Ferreira et al. 1998) as well as for
other bivalves and polyculture systems (e.g. Carver and Mallet 1990; Prins et al. 1998; Smaal
et al. 1998; Gibbs et al. 2002; Nunes et al. 2003) … Typically, this work has focused on
phytoplankton depletion and maximum production capacity within growing regions … The
literature in this field primarily addresses the role of natural or cultivated bivalve populations,
whereas the filter-feeding activities of fouling organisms and other biota associated with
shellfish cultures can also be functionally important (e.g. Mazouni et al. 2001; Mazouni
2004; Decottignies et al. 2007).”
Influences from oyster aquaculture on estuarine carrying capacity are inextricably linked to
the issues of nutrient cycling, [solid particulate matter (SPM)] depletion, and coupling
between the seabed and water column … There is compelling evidence that bivalve
aquaculture can affect nutrient cycling and the quantity and quality of SPM across a range of
spatial scales (Prins et al. 1998; Cerco and Noel 2007; Coen et al. 2007; Lin et al. 2009) …
Empirically, phytoplankton depletion is certainly evident at local scales in the vicinity of
oyster cultures (Dumbauld et al. 2009) or intensive culture zones (Lin et al. 2009), and serial
depletion among multiple adjacent farms at larger spatial scales has been described for other
types of suspended bivalve culture (Gibbs 2007; Grant et al. 2007).”
The potential for wider effects on ecological carrying capacity as a result of SPM depletion
is invariably situation specific and scale-dependent … (Anderson et al., 2006) …
Carrying capacity is also … temporally variable, as the amount of phytoplankton and other
SPM in estuaries is likely to be influenced by factors operating from tidal time scales to
longer term climatic events … (Dame and Prins 1998; Prins et al. 1998; Zeldis et al. 2000)”
Forrest et al. 2009, p. 6).
High shellfish culture density may … impact the ecosystem through food competition with wild
filter-feeders (Dame and Prins 1997) and cause shifts in the phytoplankton community (Prins et
al. 1997) … In general, [however] sediment organic enrichment due to shellfish farming is
considered to be limited (Crawford et al. 2003; Forrest et al. 2009); farmers understand that
stocking densities leading to these effects do not benefit production, due to high mortality and
reduced growth rates” (Saurel et al. 2014, p. 256).
Meseck et al. (2012) investigated the influence of a commercial FLUPSY on water quality and
sediment chemistry in a small temperate embayment. They reported the following (Meseck et al.
2012, pp. 65, 70, 71, 75, 77):
The output from the FLUPSY was compared to estuarine transects in the bay to determine if
any outputs from the FLUPSY could be detected within the embayment … The FLUPSY
was a source of total ammonia … and nitrate+nitrite … throughout the season … [However,]
the output of total ammonia from the FLUPSY was within the concentration range observed
in the embayment … The FLUPSY was a very minor source of total ammonia when
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compared to the salt marsh and sediments … Our results clearly show that the net effects of
the FLUPSY … on the chemistry of the water column and the sediments were minimal
compared to the temporal variability of the system.”
Appendix D includes excerpts from Meseck et al. (2012); those excerpts are incorporated here
by reference.
Greene et al. (2012) published a report evaluating the status of the Puget Sound’s nearshore
pelagic foodweb, a multi-trophic level assessment in six oceanographic basins. Greene et al.
report (2012, pp. 4, 43):
Land use rarely explained more than 5 percent of the variation in observed data,
indicating a dominant marine influence and the potential for resilience of the Puget
Sound’s pelagic waters to anthropogenic influence … [but] the strong spatial structure
observed in our results [does] indicate that different pelagic food webs exist across the
system.”
Hood Canal and south [Puget] Sound were rated the lowest [or least ‘healthy’] in our
system … As has been summarized recently by EPA and the Department of Ecology,
Hood Canal is naturally challenged by its unique geography and oceanography, and a
recent report determined that it is premature to assign all these problems to anthropogenic
activities (Kope and Roberts 2012).”
The work and findings reported by Greene et al. (2012) provide a useful context in which to
consider available information regarding Puget Sound carrying capacity and the potential effects
of intensive shellfish aquaculture. However, despite the growing interest in this topic, to date
there has been little work performed that evaluates a scenario of pervasive and extremely high
shellfish culturing densities in Washington’s inland marine waters. Appendix D includes
excerpts from Greene et al. (2012); those excerpts are incorporated here by reference.
Ferriss et al. (2015, pp. 15-33 In Washington Sea Grant 2015) used a trophic model
incorporating mediation functions to examine potential food web implications associated with a
future growth in central Puget Sound geoduck production. Ferriss et al. report (2015, pp. 21,
22):
A 120 percent increase in cultured geoduck biomass had a limited impact on
phytoplankton biomass and measures of ecological resilience … The addition of cultured
geoducks into the central Puget Sound food web without any mediation functions had
very little impact on the simulated biomasses of other food web members.”
Habitat modification and facilitation are the predominant ecological effects of geoduck
aquaculture in a highly productive system such as central Puget Sound … The trophic
impacts of cultured geoducks as both grazers and prey were not influential at the system
level … Cultured geoducks did not substantially reduce the availability of phytoplankton
for other species.”
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The work and findings reported by Ferriss et al. (2015 In Washington Sea Grant 2015) suggest
that understanding the ecological effects of shellfish culturing will require going beyond the
modeling of direct trophic-level effects and must incorporate non-trophic information when
possible. Appendix D includes excerpts from Ferriss et al. (2015 In Washington Sea Grant
2015); those excerpts are incorporated here by reference.
According to the Pacific Shellfish Institute (2015), an expanded definition of carrying capacity
should include the physical, production, ecological, and social carrying capacity elements
including public perception and acceptance). Saurel et al. (2014, pp. 255, 256) observed the
following:
The aquaculture industry must comply with a broad range of natural and social
conditions (Jonell et al. 2013; Maltby 2013): (1) social acceptance; (2) comprehensive
governance with consistent environmental regulations and sustainable culture practices;
3) new culture technologies; (4) stakeholder collaboration and incentives; and (5)
compliance … with best management practices.”
Nevertheless, there is some controversy in Puget Sound concerning the use of intertidal
areas (beaches) for shellfish cultivation, and licensing of new farms.”
While we do not deny the role or significance of social carrying capacity and public acceptance,
those aspects are beyond the scope of the Service’s considerations, and therefore we limit here
our discussion of carrying capacity to the physical and ecological (habitat) elements.
Totten Inlet Primary Productivity and Consumption (A Case Study)
Totten Inlet currently supports some of the highest densities of shellfish culturing in Puget Sound
and a significant portion of the statewide subtidal wild geoduck resource (Corps 2015, pp. 40-49;
Figures 26-33, pp. 66-72). In addition, based on projected or estimated future growth of the
industry over the next 20 years (Corps 2015, pp. 40-43, 80), an increase of approximately 14
percent is expected in the south Puget Sound.
In support of their proposal to establish a new, large floating mussel raft facility (50 to 60
individual rafts) on north Totten Inlet, Taylor Resources, Inc. commissioned two studies and
reports (MEC-Weston Solutions, Inc. 2004; New Fields Northwest 2008) evaluating potential
direct and indirect effects to the “…physical, chemical, and biological characteristics of the
water column; specifically, currents, dissolved oxygen, nutrients, phytoplankton abundance,
biomass, primary productivity … [and] carbon-flow in the Totten Inlet food web” (New Fields
Northwest 2008, p. vi). The studies evaluated potential near-field, mid-field, and far-field
impacts, with the far-field area extending to all of Totten Inlet (MEC-Weston Solutions, Inc.
2004, pp. 1, 2).
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MEC-Weston Solutions, Inc. (2004) found:
Carbon removed [as] mussel tissue and associated fouling organisms is equivalent to
approximately 0.06 percent of the Totten Inlet water column carbon … production
annually … This does not address the additional transfer of approximately 0.11 percent
from the water column to the sediment, some of which would be regenerated … The
total loss of carbon … as a result of the proposed mussel rafts would range from 0.06 to
0.17 percent … [at the scale of] Totten Inlet” (p. 2).
Zooplankton standing stock was projected to decrease by 0.016 percent … Effects … to
forage fish and juvenile salmonids … are substantially less, primarily due to the dilution
effect with additional trophic transfer … Juvenile salmonids and forage fish are predicted
to have standing stock reductions of 0.0016 and 0.0021 percent, respectively” (p. 3).
Fish on the fourth trophic level [e.g., adult salmonids] would be relatively unaffected,
with 0.0006 to 0.0008 percent reductions in standing stock” (MEC-Weston Solutions,
Inc. 2004, p. 70).
New Fields Northwest (2008) found:
Primary production by phytoplankton in Totten Inlet was estimated to be 40,614,000 kg
C/year during the spring/summer period … Of this total production, [just] 7.4 percent is
consumed by primary consumers … The proposed mussel raft was predicted to consume
1 percent of the production during the spring/summer period” (pp. vii, viii).
Based on the mean and [upper confidence interval] consumption estimates, the proposed
mussel rafts [were] predicted to remove 0.1 to 0.4 percent of the primary production for
Totten Inlet during the spring/summer period” and “0.1 to 0.7 percent … in the
fall/winter period” (p. 79).
Relative to 10 percent of the area of Totten Inlet, the [proposed] rafts [are] predicted to
remove 1.1 to 7.3 percent of the seasonal [phytoplankton] production [Figure 42] …
These comparisons were made with the upper confidence interval values and can be
considered a conservative estimate” (New Fields Northwest 2008, pp. 83, 86).
Appendix D includes excerpts from New Fields Northwest (2008); those excerpts are
incorporated here by reference.
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Figure 42. Incremental increase in phytoplankton depletion predicted for the proposed north
Totten Inlet mussel rafts
New Fields Northwest 2008, p. 81)
Totten Inlet’s current natural/wild and cultured shellfish biomass is large, but available
information suggests a relatively muted or small influence on primary production and trophic
state. There is no indication that the Totten Inlet phytoplankton resource has been substantially
diminished over time as a result of shellfish activities, and it appears that primary production still
greatly exceeds the basin-scale demand of primary consumers. Even with the projected future
growth of the industry in south Puget Sound, available information suggests little or no
likelihood of approaching the ecological carrying capacity of this system.
While it would be premature to extend these tentative conclusions to the whole of Puget Sound
or to all of Washington’s marine waters), the Service does have confidence that Totten Inlet and
the south Puget Sound are an appropriately conservative geography and setting for considering
these potential effects. Totten Inlet, like several of the other “small” western inlets, exhibits the
conditions of extended (long) residence time and high densities of natural and cultured filter
feeders (Banas and Cheng 2015 pp. 59, 66). Available information leads us to conclude it is
unlikely that the projected 20-year future growth of the industry will approach or exceed
ecological carrying capacity within the action area.
Effects to Nearshore Habitat Structure, Function, and Productivity
Shellfish culturing and harvesting have direct and indirect effects to nearshore marine habitat
structure, function, and productivity. These effects may have significance for how well these
habitats support the essential behaviors and needs of listed species. The sub-sections that follow
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discuss long-term and persistent effects to substrates and sediment; eelgrass, kelp, and
submerged aquatic vegetation; benthic/epibenthic community structure and composition; and
predator-prey dynamics and productivity (“prey-mediated effects”).
Where possible, we evaluate these stressors and effects at two scales: 1) the scale of a single
large farm or grouping of smaller farms (e.g., 50 to 500 acres); and, 2) the scale of a large
grouping of small and large farms, occupying a significant portion of a single waterbody (e.g.,
Willapa Bay) or portion thereof (e.g., Totten Inlet, Samish Bay). For wide-ranging species that
depend on the action area’s variety of nearshore marine environments and resources (e.g.,
anadromous bull trout, the marbled murrelet), it is ultimately at these larger scales that we can
best interpret the significance of potential stressors, exposures, and responses. The most
significant and biologically relevant effects are likely to be those that result in aggregate to
nearshore marine habitat structure, function, and productivity.
The final sub-sections included here synthesize and evaluate the patterns of foreseeable spatial
and temporal effects to nearshore habitat structure, function, and productivity, and interpret their
significance for the bull trout and marbled murrelet. This is followed by a description of the
foreseeable direct and indirect effects to designated bull trout critical habitat, including natural
forms of nearshore marine habitat structure and complexity.
Effects to Substrates and Sediment
Here we evaluate long-term and persistent effects to substrates and sediment. We consider a
variety of shellfish activities and culturing techniques, including bed preparation; frosting and
graveling; placement of culturing equipment and materials on and over the bed; mechanical
leveling and harrowing; mechanical dredge harvesting; other mechanical harvesting techniques;
and, geoduck harvest.
Bed preparation: Intertidal beds are almost always prepared for ground-based culturing of
oysters, clams, or geoduck clams with some amount of raking and light grading, regardless of
whether the farm uses direct bottom culturing, bag, rack-and-bag, stake, or longline culturing
techniques. This is typically accomplished with the use of hand tools and may coincide with pre-
harvest (also, see mechanical leveling and harrowing). Bed preparation with hand tools
generally only disturbs the shallowest substrates. Available information suggests there are
unlikely to be any measurable effects that persist more than a few days, or a few high and low
tide cycles.
Frosting and graveling: Frosting and graveling are used to coarsen and firm substrates, either
to promote and encourage a natural set of seed, or to improve conditions for the maturing and
growth of planted clams or seeded cultch. Several thin layers of material are typically placed
over a period of days. Some growers/farm operators gravel or frost their beds on an annual
basis, while others do so less frequently.
The Corps and Services developed conservation measures under a SLOPES process, and the
Corps has included the conservation measures in their proposed action (Corps 2015, pp. 49-53).
The Corps has incorporated a conservation measure which limits the amount of material placed
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annually, and which should also prevent excessive mounding or piling of placed material (Corps
2015, p. 49). At the rates/amounts proposed we would not expect to see wholesale conversion of
the substrate type, and no significant effects to sediment chemistry or nutrient status.
Placement of culturing equipment and materials on and over the bed: Equipment and
materials placed on and over the bed directly influence hydrodynamics, including current
velocities and patterns of localized sediment deposition and scour. Equipment and materials
e.g., nets, bags, racks, stakes, longlines, tubes) interact with currents, wave action, and natural
patterns of sediment transport in ways that can be difficult to predict or generalize across
individual sites. However, there is information to suggest that these localized effects to
hydrodynamics, deposition, and scour can result in changes to grain size and other characteristics
of the substrate. Over the long-term (i.e., “grow-out” and cycles of production), substrate
characteristics are strongly influenced by the interactions between these physical characteristics,
the benthic community, and intensively cultured shellfish.
When defining disturbance resulting from intertidal aquaculture, Simenstad and Fresh (1995, p.
45) included the “…altering [of] sediment structure by mechanical modification … or addition of
different sediments … and altering [of] natural hydrologic and sedimentary regimes.” “In
addition to obvious shifts in substrate composition, other physicochemical characteristics and
processes may be altered that are important to intertidal biota … Thompson (1995) and Thom et
al. (1994) indicate that substrate modification … can significantly … increase benthic respiration
and… nutrient fluxes … The magnitude of these responses, however, tend to be very site-
specific” (Simenstad and Fresh 1995, p. 50).
Discussing the influence of nets placed on the intertidal bed, Simenstad and Fresh (1995, p. 54)
reported that “… grain size was consistently finer in netted plots than on the natural beach … the
increase in sediments <1-2 mm … implied that nets decreased near-bed resuspension and trapped
more material … thus promoting a comparatively … muddier substrate.” “Decreased current
velocities at high tide due to the presence of intertidal structure may … increase the deposition of
fine] organic particles” (Madsen et al. 2001 in Hosack et al. 2006, p. 1157).
Forrest et al. reported (2009, pp. 3-5):
Changes in seabed topography … have been described beneath oyster farms in several
studies (Ottmann and Sornin 1982; Everett et al. 1995; Forrest and Creese 2006) … Such
changes can result from the accumulation of shell and inorganic debris, and erosion or
accretion of sediment beneath and between farm structures (Forrest and Creese 2006) …
Sedimentation rates directly beneath cultures are generally elevated by comparison with non-
culture areas (Mariojouls and Sornin 1986; Sornin et al. 1987; Nugues et al. 1996), being as
much as three times greater directly beneath farm structures than at control sites (Forrest and
Creese 2006).”
Excessive sediment build-up within Pacific oyster leases can occur at sites where cultivation
structures are in high density or aligned perpendicular to tidal currents, resulting in the
entrapment of suspended sediments (Kirby 1994; Handley and Bergquist 1997).”
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Biodeposits are heavier than their constituent particles, and readily settle on the seabed
beneath culture areas (Haven and Morales-Alamo 1966; Kusuki 1981; Mitchell 2006) …
Since biodeposits are organic-rich and consist of a substantial proportion of fine particles (i.e.
silt and clay), seabed sediments beneath oyster cultures can become organically enriched and
fine-textured relative to surrounding areas … (Forrest and Creese 2006)” (Forrest et al. 2009,
pp. 3-5).
Appendix D includes fuller excerpts from Forrest et al. (2009); those excerpts are incorporated
here by reference.
When discussing the history of intertidal culturing of Pacific oysters in Willapa Bay, Simenstad
and Fresh (1995, p. 48) reported the following:
Once Pacific oysters became the focus of culturists, they were grown primarily on
littoral flats above MLLW … Presently, ground-cultured oysters are distributed over
broad intertidal flats in a relatively thin layer (at most one oyster thick) in order to
maximize growth … Consequently, oyster culture appears to have changed the nature of
oyster habitat from a thick reef-like structure to one that is analogous to fine sediments
with a thin layer of large substrates (i.e., oysters) over it.”
Mechanical leveling and harrowing; mechanical dredge harvesting: Mechanical leveling and
harrowing turn over the surficial substrates and shallow subsurface. This has measurable effects
on particle size, sediment chemistry, nutrient status, and aspects of benthic-water column
dynamics (Rhoads and Germano 1986, Newell 2004, Forchino 2010, Gutierrez et al. 2011).
Mechanical leveling and harrowing, and for that matter mechanical dredge harvesting, also
disturb, physically alter, and can damage or kill benthic infauna and microalgae, sessile
epibenthic invertebrates, and attached submerged aquatic vegetation. Some of these topics will
be discussed in greater detail by a following sub-section (see Effects to Eelgrass, Kelp, and
Submerged Aquatic Vegetation and Effects to Benthic/Epibenthic Community Structure and
Composition).
Species richness and functional group diversity are inherent to undisturbed benthic systems,
including within seemingly “plain” or “barren” sand and mud flats (Rhoads and Germano 1986,
pp. 293, 294; Forchino 2010, pp. 16, 17; Gutierrez et al. 2011, pp. 39-45). Benthic communities
are not static and the functional groups that dominate at points along the course of infaunal
succession (Figure 37, p. 105) influence important benthic ecosystem attributes, including
secondary production, nutrient cycling, and hypoxia (Rhoads and Germano 1986, pp. 291, 298-
301). “Infaunal ‘ecosystem engineers’ affect three-dimensional structure and thus the diversity
of microhabitats in marine soft sediments … When infaunal organisms recruit into soft sediment
habitats, they seek refuge by entering into the sediments and – in many cases – by producing
shells, tubes, or burrows (Marinelli and Woodin 2002) … All these structures generate a
remarkably more diverse environment within the sediment matrix relative to the originally
smooth soft sediment” (Gutierrez et al. 2011, pp. 44).
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Infaunal succession commonly requires years, and therefore benthic species assemblages and
their functional relationships can be disrupted by sources of disturbance. “[Disturbances that
cause] long-term degradation … frequently involve the loss of equilibrium species … high-order
seres are replaced by pioneering seres … [and] changes in organism-sediment relations and
population dynamics accompany this change” (Rhoads and Germano 1986, p. 295).
Appendix D includes excerpts from Rhoads and Germano (1986), Forchino (2010), and
Gutierrez et al. (2011); those fuller excerpts are incorporated here by reference.
There can be no question whether the acute physical disturbance caused by mechanical leveling,
harrowing, and dredge harvesting measurably and significantly changes substrate conditions and
the benthic community. These shellfish activities act as intense pulse disturbances, and clearly
they will in many cases either interfere with or reset normal patterns of infaunal succession and
development. [Geoduck harvesting may also act as an intense pulse disturbance, though
generally it occurs at a much reduced frequency (e.g., once every 7 to 9 years).] The
implications for sediment chemistry, nutrient status, benthic-water column dynamics, and
benthic community richness and evenness are very difficult to predict or generalize across
individual sites. However, when we consider that many sites and farms are harrowed and
dredged repeatedly over the course of a single or successive cycles of shellfish culturing, it
becomes obvious that many of these sites and farms are managed in a more or less permanently
or chronically) “disturbed” state.
Complex physicochemical and ecological linkages among estuarine organisms and
communities can be altered over the long-term by persistent disturbances that exceed natural
regimes … Large-scale disturbances, such as those associated with some intensive oyster
practices, may induce chronic shifts in the benthic community by removing or reducing the
influence of community dominants such as eelgrass or … [by] altering the apparent …
relationship between them” (Simenstad and Fresh 1995, pp. 65, 66). The sub-sections that
follow will discuss these topics in greater detail (see Effects to Eelgrass, Kelp, and Submerged
Aquatic Vegetation and Effects to Benthic/Epibenthic Community Structure and Composition).
Other mechanical harvesting techniques: Bottom cultured clams are sometimes harvested
mechanically, most notably in Samish Bay. Mechanical clam harvesters are driven or pulled
across the exposed bed at low tide, and the clams are “swept” onto a conveyor belt. Another
type of mechanical harvesting equipment, the hydraulic escalator, has been mostly or completely
phased out and is excluded from coverage under the Corps programmatic consultation (Corps
2015, p. 26).
The mechanical clam harvesters used in Samish Bay, and perhaps at a growing but uncertain
number of additional locations, are repurposed and re-configured tulip harvesters (Saurel et al.
2014, p. 263). While only a few studies considering the use of this equipment are either
completed or underway, available information suggests that the practice is relatively benign and
no significant impacts to substrates or sediment have been observed (Saurel et al. 2014, p. 263).
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Geoduck harvest: Geoduck are harvested from intertidal beds at low tide (“beach harvest”), or
by divers at middle or high tides (“dive harvest”). In either case, geoduck clams are typically
harvested using hand-operated water jet probes. Seawater pumped at a pressure of
approximately 40 pounds per square inch, and 20 gallons per minute, is injected at the vicinity of
each harvestable geoduck, liquefying the substrate and allowing extraction of the clam by hand.
Geoduck… [harvest] may alter abiotic conditions in the sediment (e.g., grain size, oxygen
and] nutrient levels)” (Straus et al. 2013, p. 20). Willner (2006) considered the effects of
geoduck dive harvest and observed the following:
This method of harvesting is considered to be the most environmentally benign method
available (Palazzi et al. 2001)” (p. 11).
However,] The physical disturbance associated with … geoduck harvest has the potential
to alter] the availability and distribution of physical microhabitat and biogenic structures”
p. 2).
Disturbances, such as geoduck harvesting, homogenize the area by breaking up structures
and disturbing materials … reducing the structural complexity of the area (Hewitt et al.
2005) … As the water jet overturns sediments, organic material and organisms in and
adjacent to the harvesting hole are resuspended and/or buried” (p. 31).
With larger particles settling quickly and finer materials being carried away, the result is a
larger sediment grain composition with a lower concentration of nutrients” (pp. 31, 32).
Artificially resuspended sediments have important implications for nutrient cycling
Pilskaln et al. 1998) … Resuspension can result in higher nutrient concentrations in the
water column … [and] increase[d] oxygen consumption … (Tengberg et al. 2003)” (Willner
2006, pp. 45, 46).
Appendix D includes excerpts from Willner (2006); those fuller excerpts are incorporated here
by reference.
All of the shellfish activities and culturing techniques that have been described here result in
measurable effects to substrates and sediment. Some of these shellfish activities and culturing
techniques are more likely than others to result in measurable long-term and persistent effects.
Based on the available information, we conclude that the placement of culturing equipment and
materials on and over the bed, mechanical leveling and harrowing, and mechanical dredge
harvesting, are most likely to result in measurable long-term and persistent effects to substrates
and sediment.
Mechanical leveling, harrowing, and dredge harvesting act as intense pulse disturbances, and
clearly they will in many cases either interfere with or reset normal patterns of infaunal
succession and development. When we consider that many sites and farms are harrowed and
dredged repeatedly over the course of a single or successive cycles of shellfish culturing, it
becomes obvious that many of these sites and farms are managed in a more or less permanently
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or chronically) “disturbed” state. The sub-sections that follow will discuss these topics in
greater detail (see Effects to Eelgrass, Kelp, and Submerged Aquatic Vegetation and Effects to
Benthic/Epibenthic Community Structure and Composition).
Effects to Eelgrass, Kelp, and Submerged Aquatic Vegetation
Here we evaluate long-term and persistent effects to eelgrass, kelp, and submerged aquatic
vegetation. We consider a variety of shellfish activities and culturing techniques, including bed
preparation; frosting and graveling; placement of culturing equipment and materials on and over
the bed; mechanical leveling and harrowing; mechanical dredge harvesting; other mechanical
harvesting techniques; and, geoduck harvest.
The local ecology and function of eelgrass and kelp: Phillips (1984) described the Ecology of
Eelgrass Meadows in the Pacific Northwest. Mumford (2007) described the ecology of Kelp and
Eelgrass in Puget Sound. These excellent reports discuss in detail how submerged aquatic
vegetation contributes to and influences natural marine and estuarine functions (biotic and
abiotic). Appendix D includes excerpts from Phillips (1984) and Mumford (2007); those
excerpts are incorporated here by reference.
Interactions between submerged aquatic vegetation and shellfish activities: Interactions
between submerged aquatic vegetation (native eelgrass, rooted kelp) and shellfish activities are
complex and not easily characterized with simple generalizations. These interactions include
competition for space, competition for light (or shading), and physical damage that results from
some activities, practices, and techniques. However, not all of these interactions are detrimental
to the health of native eelgrass and rooted kelp. For instance, shellfish culturing provides a
source of nutrient enhancement, which supports plant growth and vigor, and frequently improves
water quality. Furthermore, when evaluating potential interactions and outcomes, we must also
consider that the current conditions for submerged aquatic vegetation in the action area represent
at many locations a dynamic equilibrium influenced by shellfish and other activities conducted
over years and decades. Despite the intensive shellfish culturing that has characterized the recent
history at the scale of whole sub-basins (Samish Bay) and whole waterbodies (Willapa Bay),
submerged aquatic vegetation continues to show good or consistent health in some of these same
geographies (Gaeckle et al. 2011, 2015)(see Environmental Baseline, Puget Sound and Hood
Canal, Existing Conditions for Native Eelgrass).
Competition for space: While studies considering the potential role of shading and competition
for light have produced inconclusive or equivocal findings, they demonstrate more consistently
that cultured shellfish compete directly with eelgrass for space. “Oysters use space in direct
competition with eelgrass … Eelgrass shoots cannot grow in areas occupied by shell, so direct …
competition [should] lower eelgrass density” (Tallis et al. 2009, p. 256).
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Wagner et al. (2012) looked specifically at density-dependent effects of oyster cultivation on
native eelgrass:
A key consideration for the coexistence of bivalves and eelgrass involves the functional
shape of potential tradeoffs (Koch et al. 2009) … specifically, thresholds beyond which
eelgrass responds more strongly than expected from the effects of displacement and space
competition with bivalves alone” (p. 150).
Steep declines [in eelgrass shoot density and size,] indicating density-dependent space
competition, occurred at different thresholds after 1 (1.3 percent oyster cover), 2 (12.4
percent), and 3 years (21.9 percent) … Eelgrass responded to the presence of oysters
both live adults and empty shells) by reducing shoot density and size” (pp. 149, 157).
The superior fit … models relating eelgrass density to oyster cover … [show]
exponential declines in eelgrass shoot density when oyster cover exceeded 10 to 20
percent” (p. 158).
Our results indicate that low densities of oysters can be compatible with eelgrass … but
that tradeoffs reliably occur both after initial establishment and above 20 percent oyster
cover … Ecological consequences … are likely to be location-specific and density
dependent … [but] our results indicated disproportionately large tradeoffs between space
occupants at high oyster density” (Wagner et al. 2012, p. 158).
Appendix D includes excerpts from Wagner et al. (2012); those fuller excerpts are incorporated
here by reference.
Distribution of eelgrass reflects a balance of space competition, pulse disturbance, and
recovery, and is therefore at dynamic equilibrium on aquaculture beds” (Dumbauld, Ruesink,
and Rumrill 2009, p. 196). “If eelgrass impact reduction, rather than avoidance, is identified as
the management goal, the degree of tradeoff between eelgrass habitat and oyster production can
be minimized by managing aquaculture methods or oyster planting densities, depending on the
eelgrass measure of interest” (Tallis et al. 2009, p. 251). “Similar to Tallis et al. (2009), we
noted a negative relationship between eelgrass above-ground biomass and culture density”
Skinner, Courtenay, and McKindsey 2013, p. 115).
Life history characteristics and growth forms would suggest that competition for space is a
significant interaction for kelp species too: “The habitat requirements for kelp include not only
those conditions needed for the large kelp plant, but also for the tiny and cryptic gametophytes,
for induction of reproduction, and for fertilization (Foster and Schiel 1985; Dayton 1985; Druehl
and Wheeler 1986)” (Mumford 2007, p. 4). “Competitors of kelp … include any shallow …
space-occupying organism … The tiny gametophytes and small sporophytes can be out-
competed for space or light by a variety of algae and sessile invertebrates … Once grown out of
these small stages, however, kelps can outcompete most other seaweeds and sessile invertebrates
because of their rapid elongation (10 cm per day in Nereocystis) and large adult size … Even the
smaller, non-floating kelps can overtop and shade other algae” (Mumford 2007, p. 12).
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Physical damage: “Eelgrass rhizomes are buried … up to 20 cm (8.0 inches) deep in sediment,
depending on the sediment consistency … In firmer substrates, rhizomes may be only half as
deep as in soft muddy substrates” (Phillips 1984, p. 9). “Significant injury to roots, rhizomes,
and meristems is lethal to seagrass shoots” (Neckles et al. 2005, p. 58). “Eelgrass may … be
impacted by dredging, harrowing, and leveling, all of which extensively disrupt surface
sediments … destroy aboveground eelgrass shoots and leaves, and perhaps belowground roots
and rhizomes as well” (Simenstad and Fresh 1995, p. 54). “Direct stressors to eelgrass include
harrowing or roto-tilling for on-ground oyster culture and damage from propellers … Similarly,
for] kelp, if … [cut] below the meristem, or growing region, [this] will result in the death of the
entire plant” (Mumford 2007, p. 14).
The extent to which a particular disturbance alters structure or function and thereby affects
recovery time depends on the frequency and/or duration of the disturbance (den Hartog 1971),
the physiological condition of the plants, and the characteristics of the particular seagrass species
involved (McRoy and Lloyd 1981; Zieman and Zieman 1989; Williams 1990; Alberte et al.
1994) … Additionally, recovery from disturbance can vary depending on the level of damage
sustained” (Short and Wyllie-Echeverria 1996, p. 18). “The effect of physical disturbance on
plant communities depends on the size, frequency, and intensity of disruption, and on ecological,
physiological, and life history characteristics affecting ecosystem recovery (Pickett and White
1985)” (Neckles et al. 2005, p. 58).
Fishing gear has been shown repeatedly to reduce the structural complexity of benthic habitats
by smoothing sedimentary bedforms and physically removing biota that produce habitat structure
Auster and Langton 1999, National Research Council 2002) … Mobile gear has been found to
affect seagrass beds similarly through removal of the vegetation (Fonseca et al. 1984, Peterson et
al. 1987, Orth et al. 2002; but see Meyer et al. 1999) … Mussel dragging … had a comparably
severe impact on localized habitat structure by eliminating large amounts of vegetation … Our
model of within-bed eelgrass recovery emphasized the importance of initial dragging intensity”
Neckles et al. 2005, pp. 67-69).
Previous work has shown that recovery periods for eelgrass following oyster harvest vary
depending on a combination of factors, including the type of oyster culture, duration of culture,
spatial configuration of culture operations and nearby meadows, and the frequency of oyster
harvest events (Waddell 1964; Orth et al. 2002) … Our data have important management
implications … but we know little about how these results vary among sites (either within or
among estuaries) … Tidelands used for aquaculture in Willapa Bay comprise a mosaic of
disturbance … some beds may have little to no eelgrass cover due to frequent harvest and
management activities, while other beds are left unmanipulated for long periods, enabling dense
stands of eelgrass to form and persist” (Wisehart et al. 2007, pp. 78, 79).
Studies of onground culture systems have … demonstrated physical effects during intermittent
shellfish harvesting, and the recovery of soft-sediment communities in a matter of weeks to
months in unvegetated habitats (McKindsey et al. 2006 and references therein) … By contrast,
recovery from physical disturbance by eelgrass … may take several years (McKindsey et al.
2006; Dumbauld et al. 2009 and references therein)” (Forrest et al. 2009, p. 4). “Published
recovery rates of eelgrass are almost all slower than reported for other soft-sediment organisms
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exposed to intertidal shellfish harvest; they appear more similar to [the approximate] 2-year
recovery rates of biogenic habitats (corals and sponges) after subtidal trawling or dredging
Kaiser et al. 2006)” (Ruesink and Rowell 2012, p. 718).
Individual activities act as pulse disturbances and the recovery of eelgrass … to pre-disturbance
levels is variable [2 to 5 years] … The extent of disturbance depends on the aquaculture practice
and the distribution of eelgrass reflects a balance of space competition, pulse disturbance, and
recovery, and is therefore at dynamic equilibrium on aquaculture beds” (Dumbauld, Ruesink,
and Rumrill 2009, p. 196). “The negative and positive effects of aquaculture on eelgrass are
likely caused by the direct disturbance of aquaculture and the indirect response of plants to that
disturbance … Although eelgrass does grow back in the beds over time (both via rhizomes and
seeds; Wisehart et al. 2007), densities may not reach those of uncultivated beds within the
typical harvest cycle (approximately 3 years)” (Tallis et al. 2009, p. 256). Damage to eelgrass
may be lessened if activities are conducted during winter months, when aboveground shoot
densities are lowest (Wisehart et al. 2007, p. 72).
Recovery from physical damage: Eelgrass recovery from physical damage is influenced by a
number of factors, including capacity for seed production, germination, and seedling survival;
capacity for vegetative patch expansion; the persistence of remnant, undisturbed or lightly
disturbed patches of eelgrass; intraspecific competition; and a host of other variable (and
sometimes site-specific) environmental and culturing conditions and factors. Neckles et al.
2005), Wisehart et al. (2007), and Tallis et al. (2009) have each reported relevant findings.
Neckles et al. (2005) reported:
Dramatic differences in the habitat characteristics of disturbed and reference sites were
seen in the areas of the most recent [mussel] dragging activity” (p. 63).
The broadly overlapping zones of statistical similarity in measured plant characteristics
suggest considerable variability in the actual length of time that would be required for
newly vegetated substrate to achieve reference conditions” (p. 66).
The measured effect of disturbance … depended on the scale of observation and the
apparent intensity of [mussel] dragging effort … Presumably, the number, sizes, and
distribution of remnant patches of eelgrass following dragging are a function of the
dragging intensity, with patches occurring on substrate that was missed by the dredge …
This difference in dragging intensity most likely reflects the pattern of mussel distribution
rather than any difference in gear efficiency” (Neckles et al. 2005, p. 68).
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Wisehart et al. (2007) reported:
Oyster growers have reported that eelgrass rapidly reappears in areas planted with
oysters … There are two potential mechanisms to explain high recruitment: (1) oysters
influence eelgrass seed production, seed germination, and/or seedling survival by altering
the nutrient or light environment … or by trapping/protecting seeds, and (2) aquaculture
disturbance affects eelgrass seed production, seed germination, and/or seedling survival
by removing neighboring adult eelgrass plants” (p. 72).
More seeds were produced in the dredged beds than in the reference beds” (p. 74).
We found higher seedling densities in dredged beds … compared to reference areas
where adult density was significantly greater … When neighbors were removed,
seedlings survived better … and were significantly larger … Dredge harvest of oysters,
which results in decreased eelgrass density due to the removal of above ground plant
structures, may facilitate seed germination and/or seedling growth and survival, by
reducing competition for light or other resources” (Wisehart et al. 2007, p. 77).
Tallis et al. (2009) reported:
Surprisingly, eelgrass relative growth rates were faster in dredged and hand picked beds
than in uncultivated areas … [However,] In contrast, all aquaculture areas had smaller
plants (above-ground biomass) and lower production than uncultivated areas” (p. 254).
Higher growth rates of eelgrass in oyster beds are likely related to lower eelgrass density
rather than the direct effect of oysters per se … Eelgrass growth is generally light limited
in this region (Thom and Albright 1990, Wisehart et al. 2007), so lower eelgrass densities
in dredged and hand picked beds … may release individual plants from intraspecific
competition, increasing light levels, and leading to higher relative growth rates” (p. 256).
When the cumulative effects of oyster aquaculture (oysters and practices) are
considered, higher growth rates in dredged, and perhaps hand picked beds are cancelled
out by lower plant densities and size in these areas … As a result, all current aquaculture
methods have … relatively large impacts on plant size and eelgrass production” (Tallis et
al. 2009, p. 257).
Appendix D includes excerpts from Neckles et al. (2005), Wisehart et al. (2007), and Tallis et al.
2009); those fuller excerpts are incorporated here by reference.
The Corps has stated “… for recovery times on the order of years, such as [recovery from]
disturbance to eelgrass, an annual or every few year repeat disturbance may never allow a full
recovery” (Corps 2015, p. 92). We agree with the Corps and believe that the best available
scientific information supports this conclusion. However, the number and variety of factors
influencing eelgrass recovery suggest the potential for significant site-by-site and temporal
variability. It is therefore difficult (or impossible) to state with certainty the likely pattern or rate
of recovery, at either a fine or coarse scale. Furthermore, there appear to be few general rules
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that accurately characterize this complex set of interactions. Nevertheless, the weight of
available evidence does lead the Service to conclude that in most cases and settings where
shellfish activities result in physical damage to eelgrass beds, and/or displace eelgrass beds or
other submerged aquatic vegetation, they will result in at least temporal loss of production and
associated ecosystem services, including habitat functions (Figure 43).
Figure 43. Diagrammatic representation of the interim or temporal loss of ecosystem services
Fonseca et al. 1998, p. 68)
Longline culturing: A number of studies have looked specifically at longline culturing
techniques, damage to eelgrass, and recovery, including those reported by Wisehart et al. (2007),
Tallis et al. (2009), and Rumrill and Poulton (2004). Where intertidal longline culturing is
practiced, oysters are grown in clusters, attached to rope lines suspended above the bed between
upright stakes. Stakes and longlines prevent oysters from sinking and smothering, and also serve
to control and minimize exposure to predators inhabiting the intertidal bed.
Wisehart et al. (2007) reported the following:
Significantly fewer seedlings were observed in the longline beds compared to [both] the
dredged and reference beds, which did not significantly differ” (p. 74).
More seeds were produced in the dredged beds than in the reference beds, and lowest
seed production occurred in the longline beds” (p. 74).
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We observed very few naturally recruiting seedlings in longline areas, and survivorship
of seedlings in longline seed addition plots was zero … Our data suggest that seed
production and seed bank densities are high in dredged areas compared to longline areas
Longlines may also act as ‘clotheslines,’ causing plants to become entwined in the
ropes at high tide resulting in severe desiccation at low tide, thus reducing the density of
both vegetative and flowering shoots (Pregnall 1993, Everett et al. 1995)” (p. 78).
Seed dispersal and deposition in longline beds may be limited due to altered water flow
the reduction in flow causes longline areas to accrete sediment at much greater rates
than would naturally occur (Everett et al. 1995) and could lead to burial of seeds and
young seedlings” (Wisehart et al. 2007, p. 78).
Tallis et al. (2009) reported the following:
Both on-bottom aquaculture methods (hand picked and dredge) had lower eelgrass
densities than uncultivated areas … [but] results were less clear for long line beds … We
found that long lines and hand-picking tend to have smaller effects on eelgrass density
than dredging … There was no clear link between oysters, aquaculture structures, and
eelgrass density in long line areas” (p. 254).
We show that tradeoffs exist between oyster aquaculture and native eelgrass populations
None of the existing aquaculture methods in this region can be conducted whereas
avoiding all impacts on eelgrass … Oysters can be cultivated using long lines with the
least impact on eelgrass density, but eelgrass biomass (shoot size) and production will
decline (as will eelgrass seed recruitment, Wisehart et al. 2007)” (Tallis et al. 2009, p.
260).
Rumrill and Poulton (2004) reported the following:
It is clear … that intensive commercial cultivation of oysters typically results in chronic
and variable levels of disturbance to eelgrass beds and their associated communities
Simenstad and Fresh 1995; Griffin 1997; Dumbauld 1997) … [However,] empirical
studies are needed to investigate the ecological impacts of oyster cultivation on long-lines
suspended between stakes” (p. 3).
Twelve study sites were established … with variable spacings of 1.5 [ft], 2.5, 5, and 10
ft] between the suspended lines … We conducted additional field sampling … to
compare eelgrass presence, size, and biomass in the experimental plots … [and]
commercial long-line plots” (p. 6).
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We observed a strong trend toward decreased spatial cover and density … with
decreased distance between suspended oyster long-lines … Low eelgrass metrics were
consistently observed within the narrow line spacing / high-density oyster plots [1.5 and
2.5 ft], where eelgrass cover was generally less than 15 percent … [However,] eelgrass
beds in the ‘wide’ oyster long-line spacing plots [5 ft] were intermediate (35-45 percent
cover) … and high spatial cover (55-65 percent cover) and density values … were
observed in the ‘very wide’ oyster longline plot [10 ft spacing]” (p. 11).
Results suggest that the shading effect of oyster long-lines … is probably negligible …
and] factors other than light availability are probably responsible for the reduced
abundance of eelgrass in closely-spaced off-bottom oyster culture sites … Changes in
sediment deposition and erosion were clearly evident in the plots with high densities of
oyster lines [1.5, 2.5, and 5 ft spacing] … The seasonal build-up of sediments was
particularly evident … around the PVC stakes that support the oyster lines … Substantial
and rapid sediment deposition was observed … [but] these soft and flocculent sediments
were … [also] eroded away … Sediments were deposited more slowly over time within
the 10 ft spacing] oyster long-line plot” (Rumrill and Poulton 2004, pp. 15, 16).
Geoduck cultivation and harvest: Studies conducted in the Pacific Northwest demonstrate that
geoduck cultivation also results in measurable impacts to eelgrass. A 2-year experiment
investigating seasonal effects of geoduck production at a site in the south Puget Sound found that
the largest impacts (70 percent shoot loss) occurred during harvest (Ruesink and Rowell 2012, p.
718).
Horwith (2013) investigated changes in eelgrass over a 5-year crop cycle in Samish Bay, located
in the north Puget Sound:
Immediately following harvest … eelgrass remained patchily distributed within the farm
being present in 64 percent of quadrats), but where it was present, Z. marina was now 78
percent more dense in the unfarmed area ... Eelgrass was no longer present on the farm 1
year after harvest … following a period of heavy [algae] biofouling on the blanket nets”
p. 111).
However] … the first signs of recovery for eelgrass began 1 year after the removal of
tubes and nets, and continued evidence for recovery appeared in the following year …
Geoduck aquaculture practices do not appear to have made this site unsuitable for later
recolonization by eelgrass” (Horwith 2013, p. 112).
Saurel et al. (2014, pp. 261, 264) considered the effects of fouling (algal growth) on geoduck
cover nets:
A macroalgal individual growth model was implemented to simulate fouling of predator
nets by seaweeds … [The] model simulates sweeping at regular intervals, and the
subsequent new growth of macroalgae on the nets … Increased fouling in farm sections
with larger clams (higher year classes) is … [evident] and reflects a greater emission of
ammonia [nutrient] from … larger animals.”
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Summary: Interactions between submerged aquatic vegetation (eelgrass, kelp) and shellfish
activities are complex. The number and variety of factors influencing recovery from disturbance
or damage suggest the potential for significant temporal and site-by-site variability. However, in
most cases and settings where shellfish activities result in physical damage to submerged aquatic
vegetation, they will result in at least temporal loss of production and associated ecosystem
services, including habitat functions (Figure 43, p. 151).
Not all of the potential interactions with shellfish activities are detrimental to the health of native
eelgrass and rooted kelp. For instance, shellfish culturing provides a source of nutrient
enhancement, which supports plant growth and vigor, and frequently improves water quality.
Therefore, when evaluating potential interactions and outcomes, we must also consider that the
current conditions for submerged aquatic vegetation in the action area represent at many
locations a dynamic equilibrium influenced by shellfish and other activities conducted over years
and decades. Despite the intensive shellfish culturing that has characterized the recent history at
the scale of whole sub-basins (Samish Bay) and whole waterbodies (Willapa Bay), submerged
aquatic vegetation continues to show good or consistent health in some of these same
geographies (Gaeckle et al. 2011, 2015)(see Environmental Baseline, Puget Sound and Hood
Canal, Existing Conditions for Native Eelgrass).
Landscape scale interactions and dynamics: Whereas there have been many studies
evaluating interactions and outcomes at the scale of a single bed or a single farm, there have been
relatively few that describe interactions between submerged aquatic vegetation and shellfish
activities on a landscape scale in the Pacific Northwest.
Dumbauld and McCoy (2015) evaluated the effect of oyster aquaculture on eelgrass at the
estuarine landscape scale in Willapa Bay:
We … use [several] factors to predict Z. marina distribution for each aquaculture bed,
and compare the model-predicted, interpolated, and actual quantities … [We] determine
whether any impacts of oyster aquaculture … were chronic or transitory by analyzing
data from 3 separate years” (p. 31).
We predicted that mechanically harvested beds would either exhibit chronically low
proportions of Z. marina, if the effects of dredging are long-lived, or high variability, due
to a rapid removal (mechanical harvest) and recovery (regrowth), relative to more stable
hand-picked beds” (p. 34).
The total area of Z. marina estimated to be missing using a model prediction in 2005
and 2006 was only 22 and 8 ha, respectively … In 2009, there were 0.4 ha, more Z.
marina present than predicted by the model … The total area … estimated to be missing
using the interpolation prediction was higher for all years, at 80, 84, and 60 ha,
respectively … Although large in aggregate, even the highest estimate is <1.5 percent of
the total amount of Z. marina cover found in Willapa Bay in these 3 years” (p. 35).
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The majority of beds exhibited expected levels of Z. marina with low variation across
years … [However,] All of the beds with <65 percent of the mean expected amount of …
cover (n = 24) were mechanically harvested beds and demonstrated a chronically low
level of Z. marina cover … across years” (p. 36).
While the total area of Z. marina declined slightly over time in our study, <1.5 percent
of either the total predicted or interpolated amount … was missing (maximum of 80 ha)
and could thus potentially be attributed to aquaculture in any single year … This lack of
substantial overall impact is similar to the few studies conducted at the estuarine
landscape scale elsewhere” (p. 38).
Our results suggest that the majority of oyster aquaculture impacts are not persistent at
the landscape scale … Our results suggest that current oyster aquaculture practices do not
substantially reduce and may even enhance the presence of Z. marina at the estuarine
landscape scale” (Dumbauld and McCoy 2015, p. 41).
Appendix D includes excerpts from Dumbauld and McCoy (2015); those fuller excerpts are
incorporated here by reference.
These findings direct appropriate attention to the scale of observation, but do not wholly
undermine or refute the position voiced previously by some of these same authors: “Bivalve
culture clearly modifies estuarine habitat at local community and at landscape scales … Effects
are most often evaluated against existing structured habitat in the form of submerged aquatic
vegetation” (Dumbauld, Ruesink, and Rumrill 2009, p. 196).
Impacts to submerged aquatic vegetation resulting from programmatic shellfish activities:
The BA submitted by the Corps in support of programmatic consultation provides an excellent
summary of available data, and the limitations of available data, to describe eelgrass distribution
in the action area, and its co-location with continuing shellfish activities (Corps 2015, pp. 90, 94,
95; Appendix D). The Service regards these data, and the Corps’ analyses, as the best available
information to describe the likely physical extent of potential impacts to submerged aquatic
vegetation resulting from programmatic shellfish activities in Washington’s marine waters. The
Service does acknowledge that there is no current, comprehensive mapping of eelgrass and kelp
in Puget Sound, Hood Canal, or the coastal embayments of Willapa Bay and Grays Harbor.
The Corps has stated the following regarding potential impacts to native eelgrass (Corps 2015,
pp. 94, 95):
The continuing active and fallow [shellfish] acres could potentially occur in areas with
eelgrass … A geographic analysis was conducted to estimate the acreage potentially co-
located with eelgrass … There is substantial overlap between eelgrass and much of the
continuing active and fallow [shellfish] acreage … This pattern occurs in all the
geographic regions … An estimated 11,227 acres … [continuing fallow] would be co-
located with eelgrass.”
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Activities (active and fallow) are more often than not co-located with eelgrass in
Willapa Bay, Grays Harbor, and the north Puget Sound region … In the Hood Canal
region, acreage is equally split between areas with and without eelgrass … The south
Puget Sound region appears to be the notable exception where a minority of the acreage
is collocated with eelgrass … Continuing activities would occur in 49 percent of the total
mapped eelgrass acreage in Willapa Bay, and 21 percent of the [total mapped eelgrass
acreage] in Hood Canal … Percentages are less in the other [geographic] regions.”
Table 8 presents the Service’s best approximation of the likely physical extent of potential
impacts to submerged aquatic vegetation resulting from programmatic shellfish activities in
Washington’s marine waters. Across the geographies and acreages summarized here, the Service
expects there will be measurable losses of production and associated ecosystem services,
including habitat functions.
Table 8. Likely physical extent of potential impacts to submerged aquatic vegetation
GEOGRAPHY
Affected
Nearshore Acres
Action Area)
Continuing
Shellfish Activities (Acres)
Affected
Submerged
Aquatic
Vegetation
Acres)2TotalCo-Located
with Eelgrass
Willapa Bay 30,000 25,840 19,618 Approx. 19,620
Grays Harbor1 4,000 2,965 1,918 Approx. 1,920
Hood Canal1 3,000 1,356 685 Approx. 790
North Puget Sound1 5,000 3,687 3,370 Approx. 3,370
South Puget Sound 5,000 3,133 275 Approx. 320
Total 45,000 to 50,000 ~37,000 ~25,900 Approx. 26,000
1 These geographies include designated bull trout critical habitat (see Table 4, p. 77).
2 All estimates reflect a degree of uncertainty and imprecision. In Hood Canal and south Puget Sound, our
estimates include an additional 15 percent to account for potential co-location with rooted kelp.
However, the Service also expects that many of these impacts and measurable losses will be
temporary. In most cases, and in most settings where continuing shellfish activities result in
physical damage to submerged aquatic vegetation, we expect that much of the lost production
and function will be recovered over time. Furthermore, we expect that the conservation
measures included by the Corps as elements of their proposed action (see Project Description,
Conservation Measures) will largely avoid and effectively reduce impacts to submerged aquatic
vegetation that might otherwise result from proposed, new shellfish activities and farms.
Native eelgrass, rooted kelp, and other submerged aquatic vegetation experience loss and
recovery on continuing farms. Native eelgrass and other submerged aquatic vegetation will also
experience loss and recovery when fallow farms or farm footprints are re-cultivated and put into
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production. The Service acknowledges that chronic suppression of eelgrass growth and
production may be a reality on some farms. We also acknowledge that fallow farm footprints are
extensively co-located with submerged aquatic vegetation; most extensively and importantly for
bull trout, in the north Puget Sound (approximately 2,239 acres) (Corps 2015, p. 95).
The weight of available evidence suggests and leads the Service to conclude that permanent
losses of submerged aquatic vegetation (native eelgrass and rooted kelp), production, and
function will not be typical of most outcomes. While it is likely there will be instances where
limited, permanent losses (or chronic suppression) are attributable to shellfish activities, the
Service expects that permanent losses will me small (e.g., a fraction of the submerged aquatic
vegetation resource) at the scale of the five geographic sub-areas (Willapa Bay, Grays Harbor,
Hood Canal, south and north Puget Sound), at the scale of any whole waterbody (e.g., Willapa
Bay), or sub-basin (e.g., Totten Inlet, Samish Bay).
Effects to Benthic/Epibenthic Community Structure and Composition
Here we evaluate long-term and persistent effects to benthic/epibenthic community structure and
composition. We consider a variety of shellfish activities and culturing techniques, including
pre-harvest; bed preparation; frosting and graveling; placement of culturing equipment and
materials on and over the bed; mechanical leveling and harrowing; mechanical dredge
harvesting; other mechanical harvesting techniques; and geoduck harvest.
Pre-harvest: Pre-harvest removes marketable product and removes, or more commonly
relocates, undesirable species. Native shellfish predators, which are sometimes actively removed
from farm plots, include moon snails, sea stars, and sand dollars, including the eccentric sand
dollar or sea-cake. The non-native eastern oyster drill and Japanese oyster drill are commonly
removed from oyster beds. For a period following pre-harvest, and until the cultured species and
colonizing species become re-established, most cultured farm plots exhibit a benthic community
that is reduced in abundance, biomass, and diversity (Corps 2015, p. 85; Straus et al. 2013, p. 20;
Vanblaricom et al. 2015, pp. 171, 178, 180).
Simenstad and Fresh (1995) reviewed the scale and intensity of disturbance, and the response of
intertidal communities to aquaculture activities in Pacific Northwest estuaries. The authors state,
On a community scale, responses to chronic, low intensity or infrequent, intermediate intensity
disturbances tend to be within the scope of behavioral or ecological adaptability of the flora and
fauna … Dispersal of most epibenthic populations is often continuous and dynamic as a function
of tidal advection and resuspension … [and] meiofaunal animals tend to have high … turnover
rates that facilitate rapid recolonization” (Simenstad and Fresh 1995, p. 62).
Bed preparation: Intertidal beds are almost always prepared for ground-based culturing of
oysters, clams, or geoduck clams with some amount of raking and light grading, regardless of
whether the farm uses direct bottom culturing, bag, rack-and-bag, stake, or longline culturing
techniques. This is typically accomplished with the use of hand tools and may coincide with
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pre-harvest (also, see mechanical leveling and harrowing). Bed preparation with hand tools
generally only disturbs the shallowest substrates. Available information suggests there are
unlikely to be measurable effects that persist more than a few days, or a few high and low tide
cycles.
Frosting and graveling: Frosting and graveling are used to coarsen and firm substrates, either
to promote and encourage a natural set of seed, or to improve conditions for the maturing and
growth of planted clams or seeded cultch. Several thin layers of material are typically placed
over a period of days. Some growers/farm operators gravel or frost their beds on an annual
basis, while others do so less frequently.
The Corps and Services developed conservation measures under a SLOPES process, and the
Corps has included the conservation measures in their proposed action (Corps 2015, pp. 49-53).
The Corps has incorporated a conservation measure which limits the amount of material placed
annually, and which should also prevent excessive mounding or piling of placed material (Corps
2015, p. 49). At the rates/amounts proposed we would not expect to see wholesale conversion of
the substrate type.
Simenstad et al. (1991 In Simenstad and Fresh 1995, p. 52) found that these practices can alter
the benthic infaunal community, especially the dominant or co-dominant taxa, but unless there is
total replacement of the natural substrate, effects to the epibenthic community (crustaceans and
decapod crustaceans, mobile and sessile echinoderms, mobile and sessile gastropods, etc.) are
less pronounced and often site-specific. The authors do acknowledge that (Simenstad and Fresh
1995, p. 50), “the Washington Department of Fisheries has investigated differences in benthic
infauna composition and densities at sites that have been graveled to enhance clam production …
and] their results (Washington Department of Fisheries 1988; Thompson and Cooke 1991;
Thompson, 1995; Washington Department of Fisheries and Fisheries Research Institute,
University of Washington unpublished data) indicate a shift away from communities numerically
dominated by glycerid, sabellid, and nereid polychaetes [bloodworms, feather duster tube
worms, and rag or clam worms] to ones dominated by bivalve molluscs and nemerteans
ribbonworms].”
Placement of culturing equipment and materials on and over the bed: The benthic
community interacts with, and is influenced by, equipment and materials placed on and over the
bed (e.g., nets, bags, racks, stakes, longlines, tubes), currents, wave action, patterns of sediment
transport, and the intensively cultured shellfish. Over the long-term (i.e., “grow-out” and cycles
of production), benthic community structure and composition may be strongly influenced by
these interactions.
Straus et al. (2013), when discussing the effects of geoduck cultivation, have emphasized the
following:
The effects of shellfish aquaculture on benthic faunal communities are strongly debated,
as many contrasting effects have been reported” (p. 18).
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In general, effects on benthic infauna are most pronounced in soft sediment habitats
directly below, or immediately adjacent to, shellfish aquaculture operations as a function
of organic enrichment via biodeposits (Dumbauld et al. 2009) … Crawford et al. (2003)
found that benthic community structure was not significantly different between farm
and reference sites … Greater differences in benthic infauna were found among farms
than between farm and reference sites, suggesting that local conditions may dictate how
the benthic environment is affected by shellfish aquaculture” (pp. 18, 19).
Grant et al. (1995) found relatively minor changes … Reference sites showed higher
abundance of benthic macrofauna but lower biomass, and species diversity was higher at
the farm sites … Conversely, the benthic community under a … longline mussel farm
experienced dramatic declines in species diversity, from a healthy and diverse complex
to a community consisting entirely of infaunal polychaetes (Kaspar et al. 1985)” (p.
19).
In studies comparing benthic habitats in Willapa Bay… abundance was higher in on-
bottom oyster aquaculture and eelgrass beds than in unstructured mudflat (Hosack et al.
2006), and diversity was similar (Ferraro and Cole 2007)” (p. 19).
Hard structures placed on or above low-relief mud or sand habitats represent a novel
substrate in the form of solid surfaces fixed in space (e.g., Wolfson et al. 1979) …
Mobile consumers such as fish and macroinvertebrates are often drawn to structures on
low-relief soft-sediment habitats (e.g., Davis et al. 1982) … Moreover, these structures
may serve as refugia that reduce predation risk (e.g., Dealteris et al. 2004), especially for
juvenile life-history stages (e.g., Powers et al. 2007)” (Straus et al. 2013, p. 19).
Numerous authors have described how living bivalves, shells/shell fragments, and their
aggregations in reefs or banks create novel substrates and contribute to spatially heterogenous
habitats (Gutierrez et al. 2003; Sousa, Gutierrez, and Aldridge 2009; Gutierrez et al. 2011).
Coen et al. (2007) and Forrest et al. (2009) both review published findings suggesting that
bivalves create and enhance habitats for submerged aquatic vegetation, marine invertebrates, and
finfish. Appendix D includes excerpts from Gutierrez et al. (2003); Coen et al. (2007); Forrest et
al. (2009); Sousa, Gutierrez, and Aldridge (2009); and, Gutierrez et al. (2011); those excerpts are
incorporated here by reference.
Dealteris et al. (2004) assessed the structural habitat complexity inherent to submerged aquatic
vegetation, shallow nonvegetated seabeds, and shellfish aquaculture gear, and the abundance,
composition, and diversity of associated benthic communities. Appendix D includes excerpts
from Dealteris et al. (2004); those excerpts are incorporated here by reference.
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Dealteris et al. (2004, pp. 867, 873) concluded that, “Shellfish aquaculture gear … has habitat
value at least equal to and possibly superior to submerged aquatic vegetation.” However, we do
not reach the same conclusion, and for reasons made evident by this same study. Dealteris et al.
2004) reported:
The [shellfish aquaculture gear] habitat showed consistently lower Smith and Wilson
species evenness values than either the [submerged aquatic vegetation] or [shallow
nonvegetated seabeds] because a few species tended to dominate this habitat … The
shellfish aquaculture gear] habitat was significantly lower in species evenness than
either the [submerged aquatic vegetation] or [shallow nonvegetated seabed] habitats” (p.
870).
The [shellfish aquaculture gear] habitat had consistently lower evenness than the other
ecotypes because of the hyperdominance of several species within the aquaculture gear
In contrast, the [submerged aquatic vegetation] habitat was rarely dominated by a few
species, but rather supported a more equal distribution of organisms” (p. 873).
The species evenness data clearly show that whereas the abundances may be greater in
the [shellfish aquaculture gear] habitat, the [shellfish aquaculture gear] habitat is
dominated by a few species” (Dealteris et al. 2004, p. 873).
Thrush et al. (2001) and Gutierrez et al. (2011) have both emphasized the often-ignored
structural and biological diversity of soft-sediment habitats. “We found local variation in
surficial sediment characteristics and the presence of other immobile features, many of which are
biogenic, to be strongly related to diversity” (Thrush et al. 2001, p. 262). “The overall abiotic
impact of an engineered structure will also depend on the baseline abiotic state … While mussels
have little influence on the availability of hard substrates on rocky shores, they have a very large
effect in soft-sediment systems (Gutierrez et al. 2003) … Initial establishment of mussels in
areas dominated by soft-substrates increases the availability of hard substrate (i.e., abiotic
change) with a positive feedback effect on subsequent mussel recruitment (Bayne 1964)”
Gutierrez et al. 2011pp. 10-12). Appendix D includes excerpts from Thrush et al. (2001) and
Gutierrez et al. (2011); those excerpts are incorporated here by reference.
Ferraro and Cole (2012) investigated recurring empirical relationships between operationally-
defined biotic communities and habitat types in Willapa Bay, Grays Harbor, and Tillamook Bay,
Oregon. They observed the following:
Bathymetry, sediment type, and the presence of ecosystem engineering (Jones et al.
1994) or niche constructing (Boogert et al. 2006) species are habitat characters that
operationally define estuarine habitats with different benthic macrofaunal communities in
the U.S. Pacific Northwest (Posey 1986; Ferraro and Cole 2004, 2007, 2011;
Berkenbusch and Rowden 2007)” (p. 2).
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There were a total of 107 benthic macrofauna taxa … Twenty-three … species were
collected in one and only one habitat type … [but] unique species accounted for <1
percent of the benthic macrofaunal abundance in the habitat in which they were found …
Even though many of the more common benthic macrofaunal taxa occurred in multiple
habitats … and few benthic macrofaunal species were unique to a single habitat …
benthic macrofaunal Bray-Curtis similarity was significantly different among the
habitats” (pp. 5, 6).
The benthic macrofaunal habitat usage patterns … surpass in detail common
generalizations, such as that benthic macrofaunal species richness, abundance, and
diversity are typically greater in more structurally complex habitats (Hemminga and
Duarte, 2000)” (Ferraro and Cole 2012, p. 10).
Appendix D includes excerpts from Ferraro and Cole (2012); those fuller excerpts are
incorporated here by reference.
Hosack et al. (2006) compared the fish and invertebrate communities occupying intertidal
mudflat, eelgrass, and oyster habitats in Willapa Bay. They observed the following:
The introduction of estuarine organisms, such as oysters or other forms of aquaculture,
that compete with existing forms of habitat structure, such as seagrass, may affect the
availability of important habitat refugia and foraging resources for mobile estuarine fish
and decapods” (p. 1150).
Habitat types were distinct … between-habitat dissimilarities ranged 82–88 percent, but
within-habitat dissimilarities ranged 31–63 percent” (pp. 1153).
Densities of epibenthic invertebrates, harpacticoid copepods, and benthic invertebrates
varied significantly among habitat types and were generally higher in structured eelgrass
and oyster habitats … The assemblage composition … differed between adjacent patches
of low intertidal eelgrass, oyster, and unvegetated mudflat” (p. 1156).
Results for mobile fish and decapods were somewhat different than the generally
accepted view of greater diversity and abundance in vegetated versus unvegetated
habitats (Heck et al. 1989; Connolly 1994; Edgar and Shaw 1995) … While the
composition of fish and decapods varied strongly across both time and space, habitat type
explained little of the variation in composition, richness, or size of this component” (p.
1156).
Species richness of fish and decapods was not related to habitat [type] … and abundance
was [also] unrelated to habitat type” (p. 1155).
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Benthic invertebrate densities were significantly higher in eelgrass … The rhizome
structure of eelgrass beds may support high densities of benthic invertebrates … [But,]
Reduced diversity and density of benthic infauna on open mudflats, particularly those
adjacent to structured habitat, could be due to increased predation (Orth et al. 1984;
Summerson and Peterson 1984)” (p. 1157).
The fish and decapod assemblage as a whole, which is highly mobile relative to
epifauna and infauna, showed little habitat association in Willapa Bay, despite the
habitat-specific associations of the invertebrate organisms that would be expected to
serve as important prey resources … Fish and decapods frequently exhibit diel cycles in
habitat use … Fish [and decapods] caught in this study were sufficiently mobile to forage
over much larger spatial scales than the patches of habitat we selected for sampling”
Hosack et al. 2006, p. 1158).
Appendix D includes excerpts from Hosack et al. (2006); those fuller excerpts are incorporated
here by reference.
These studies and findings indicate to us that culturing equipment and materials placed on and
over the bed (including nets, bags, racks, stakes, longlines, and tubes), and the intensively
cultured shellfish (many of which are non-native species), modify habitat and may create new
habitat types (or habitat variants). Culturing equipment/materials and intensively cultured
shellfish do clearly influence benthic community structure and composition. However, the
weight of available evidence leads the Service to conclude that the direction of these influences
are variable (e.g., toward greater abundance and biomass, but reduced species evenness), and the
nature of some relationships remains poorly understood. Issues of scale and spatial resolution
are evident, exemplified by a general lack of appreciation for the structural and biological
diversity inherent to seemingly “barren” or “plain” soft-sediment habitats. The significant roles
played by ecosystem engineering or niche constructing species (e.g., eelgrass, oysters, other),
and biogenic structures (e.g., kelp forest, oyster reef, other), are also evident.
Mechanical leveling and harrowing: Mechanical leveling and harrowing turn over the surficial
substrates and shallow subsurface. This has measurable effects on the benthic community,
particle size, sediment chemistry, and nutrient status. Mechanical leveling and harrowing, and
for that matter mechanical dredge harvesting, also disturb, physically alter, and can damage or
kill benthic infauna and microalgae, sessile epibenthic invertebrates, and attached submerged
aquatic vegetation.
Mechanical dredge harvesting: Mechanical dredge harvesting is among the most physically-
intrusive and disruptive of all the shellfish activities discussed in this Opinion. Dredge
harvesting directly impacts substrate conditions, submerged aquatic vegetation (including its
many important physical, chemical, biological, and habitat functions), and the benthic
community.
Disturbances that cause] long-term degradation … frequently involve the loss of equilibrium
species … These high-order seres are replaced by pioneering seres … Changes in organism-
sediment relations and population dynamics accompany this change … High-order seres … are
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deeply burrowing errant or tube-dwelling infauna … for example, maldanid, pectinid, and
orbinid polychaetes, caudate holothurians, protobranch bivalves, infaunal ophiuroids, and
irregular urchins … [while] early or low-order successional stages … [include] tubiculous
polychaetes or oligochaetes … [which] feed at, or near, the sediment surface … A transitional
stage [and sere] … [may include] a diverse assemblage of tubiculous amphipods, molluscs, and
polychaetes” (Rhoads and Germano 1986, p. 295).
Simenstad and Fresh (1995, p. 65, 66) state: “Complex physicochemical and ecological linkages
among estuarine organisms and communities can be altered over the long-term by persistent
disturbances that exceed natural regimes … Large-scale disturbances, such as those associated
with some intensive oyster practices, may induce chronic shifts in the benthic community by
removing or reducing the influence of community dominants … or [by] altering the apparent …
relationship between them.”
Collie et al. (2000) published a meta-analysis looking at the effects of towed bottom-fishing gear
on benthic communities. They observed the following:
Fishing gears used to catch demersal fish and shellfish often disturb both the seabed and
the organisms living within or on it … The potential impact of this disturbance has
become a subject of heated debate (Malakoff 1998) … The results of any single study are
highly specific with respect to fishing gear, disturbance regime, habitat, and environment
Viewing each study in isolation makes it difficult to draw general conclusions” (p.
785).
We found 57 different manipulations or observations of the effects of fishing
disturbance on benthic fauna and communities, extracted from 39 separate publications
they examine] … gear type … regime [or] number of discrete periods of disturbance
and] habitat” (p. 786).
Most (89 percent) of the studies were undertaken at depths less than 60 m; of these 13
23 percent) were intertidal … All the intertidal studies were conducted at small spatial
scales (<50 m) … The largest scale studies were those that compared commercially-
fished grounds with closed areas or areas of different fishing intensity … We used the
regime’ variable to distinguish experimental studies (acute disturbance) from the 12
studies comparing fished and unfished areas (chronic disturbance)” (p. 789).
Dredging had a more negative impact than trawling, which is not surprising as dredges
tend to penetrate deeper into the sediments than trawls … The mean response for number
of species was … a 27 percent reduction … Larger impacts were observed in mud and
gravel habitats than in sand … Intertidal dredging had the most negative impact on
species richness” (p. 790).
Gear type was highly significant, with intertidal dredging having the most negative
impact, followed by scallop dredging, and inter-tidal raking” (pp. 790).
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The variable ‘Class’ also had a significant effect on the response to disturbance …The
largest negative impacts were observed for Anthoza and Malacostraca … Polychaetes
were more negatively affected than oligochaetes, which appeared to be the least sensitive
class … None of the predicted means were positive … Taxa differed in their response to
disturbance, but on average, none increased in abundance” (p. 791).
The genera least impacted by disturbance were bivalves … Many of these bivalves are
small in size or have particularly well armoured shells that protect them from physical
damage” (p. 792).
Patterns of recovery … Depth and scale were either insignificant or had inconsistent
effects among models … With respect to gear type, the plots suggest that the source of
the statistically significant interaction term is the greater initial impact for intertidal
dredging … Intertidal dredging gives the greatest initial responses because it is the most
efficient gear … [often] completely removing the … fauna” (pp. 792, 793).
It is clear that intensively fished areas are likely to be maintained in a permanently
altered state, inhabited by fauna adapted to frequent physical disturbance” (Collie et al.
2000, p. 795).
Appendix D includes excerpts from Collie et al. (2000); those fuller excerpts are incorporated
here by reference.
There can be no question whether the acute physical disturbance caused by mechanical leveling,
harrowing, and dredge harvesting measurably and significantly changes substrate conditions and
the benthic community. These shellfish activities act as intense pulse disturbances, and clearly
they will in many cases either interfere with or reset normal patterns of infaunal succession and
development. The implications for sediment chemistry, nutrient status, and benthic community
richness and evenness are very difficult to predict or generalize across individual sites.
However, when we consider that many sites and farms are harrowed and dredged repeatedly over
the course of a single or successive cycles of shellfish culturing, it becomes obvious that many of
these sites and farms are managed in a more or less permanently (or chronically) “disturbed”
state. We can expect that initial effects or impacts to ecological and habitat functions will persist
for durations extending months or years. If, however, on some sites and farms the disturbance
regimes routinely and repetitively exceed natural patterns of frequency and intensity, those sites
may never recover, or may only recover after long periods in a fallowed state.
Other mechanical harvesting techniques: As stated earlier, bottom cultured clams are
sometimes harvested mechanically, most notably in Samish Bay. Mechanical clam harvesters
are driven or pulled across the exposed bed at low tide, and the clams are “swept” onto a
conveyor belt. Another type of mechanical harvesting equipment, the hydraulic escalator, has
been mostly or completely phased out and is excluded from coverage under the Corps
programmatic consultation (Corps 2015, p. 26).
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The mechanical clam harvesters used in Samish Bay are repurposed and re-configured tulip
harvesters (Saurel et al. 2014, p. 263). The practice is relatively benign; no significant impacts
to benthos have been observed (Saurel et al. 2014, p. 263).
Geoduck cultivation and harvest: For a full description of the species life history,
reproduction, distribution, and habitat, and for a review of relevant research findings regarding
the ecological effects of geoduck cultivation (including effects to benthic community dynamics
and predator-prey relationships), the reader is referred to the Washington Sea Grant publication
Effects of Geoduck Aquaculture on the Environment: A Synthesis of Current Knowledge (Straus
et al. 2013, pp. 1- 22).
Environ International Corporation (2011) has cited several studies that suggest geoduck culturing
and harvest have only a modest impact on benthic invertebrates:
Ecological theory suggests that many species typical of wave-exposed sandy
environments … exhibit behaviors that enable them to survive daily tidal scouring events
Gorselany and Nelson 1987 as cited in Dernie et al. 2003) … It is generally assumed
that benthos found in more dynamic sandy habitats will recover more quickly following
physical disturbance than those found in less energetic muddy habitats, based on the
adaptive strategies of the respective assemblages found in these environments (Kaiser et
al. 1998, Ferns et al. 2000) … Microcosm studies appear to support this hypothesis
Dernie et al. 2003)” (p. 50).
Pearce et al. (2007, unpublished) … observed that recovery rates of benthic
invertebrates varied in response to timing (season), magnitude, and location of the
disturbance in relation to the species involved and level of mobility of those organisms …
Kaiser et al. (2006) commented that recovery may take longer in cases where
recolonization through larval recruitment is the dominant mechanism” (p. 51).
Spencer et al. (1997 as cited in Straus et al. 2008) found that the netting used to reduce
Manila clam predation led to an increase in surface deposit-feeding worms compared to a
community dominated by subsurface deposit-feeding worms in non-netted plots” (p. 51).
Fleece et al. (2004, unpublished) completed a dive study at three locations in Case Inlet
that compared epibenthic fauna between geoduck beds with individually netted tubes,
adjacent eelgrass beds, and control sites … The authors observed a higher density of
epibenthic fauna in geoduck beds in relation to control sites, and similar densities in
relation to adjacent eelgrass beds … The structure created by tubes most likely provides
additional habitat structure for many epibenthic invertebrate species” (Environ
International Corporation 2011, p. 53).
Appendix D includes excerpts from Environ International Corporation (2011); those fuller
excerpts are incorporated here by reference.
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Brown and Thuesen (2011) assessed the biodiversity of mobile benthic fauna in cultured south
Puget Sound geoduck beds. They observed the following:
Both sites were commercial-scale geoduck farming operations and were representative
of typical geoduck farms in Puget Sound” (p. 772).
Using Coleman rarefaction analysis, species richness was significantly higher (P < 0.05)
in the structured geoduck site … compared with its control site … However, there was no
significant difference observed between the [un-structured] geoduck grow-out site …
and] its control” (p. 773).
At the structured Eld Inlet site] low species evenness was observed … [At the un-
structured Nisqually Reach site] there was greater species evenness … [Graceful crab] C.
gracilis was [still] the most abundant species, comprising 35.0 percent of the individuals
but] staghorn sculpin, Leptocottus armatus, and red rock crab, Cancer productus,
each made up 26.5 percent of the individuals” (p. 773).
In southern Puget Sound, even small differences in habitats can demonstrate broad
variability in community member assemblages, as evidenced by the differences between
the study sites in Eld Inlet and Nisqually Reach” (Brown and Thuesen 2011, p. 774).
Appendix D includes excerpts from Brown and Thuesen (2011); those fuller excerpts are
incorporated here by reference.
McDonald et al. (2013) looked at the effects of geoduck aquaculture gear on resident and
transient macrofaunal communities. They report the following:
The Shannon index was utilized to compare differences in diversity between plots …
This measure is commonly used in ecological studies and combines aspects of species
richness and relative abundance … (Shannon 1948, Shannon and Weaver 1949) … A
higher index value indicates higher diversity” (p. 54).
All sites were characterized by substantial seasonal variation … We collected and
identified 68 taxa … [Our] analyses illustrate differences in community structure across
months …, plot types, and phases at each site … Within each site … community data
from the pre-gear phase were similar at culture and reference plots … Similarly, there
were no significant differences … for culture and reference plots at any site when
aquaculture structures were in place (gear-present)” (p. 54).
Taxa showed no consistent response to geoduck aquaculture … Only two taxa
experienced persistent negative effects: the polychaete Families Spionidae … and
Orbiniidae” (p. 55).
Of the significant functional groups, true crab and other nearshore fish show[ed]
strongest associations with culture plots during the gear-present phase, when PVC tubes
and nets were in place” (p. 55).
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Resident invertebrate communities were characterized by strong seasonal patterns of
abundance and site-specific differences in composition … Effects on resident … infauna
and epifauna may be site-specific … Elucidating potential mechanisms responsible for
differences in the response of infauna will require additional study” (p. 56).
Unlike resident macrofauna, the transient fish and macroinvertebrate community was
clearly affected by aquaculture activities … Presence of PVC tubes and nets significantly
altered abundance and composition, but not diversity, of transient macrofauna … Over
two times more organisms were observed during surveys at the culture plots than at
reference areas during the structured phase of geoduck aquaculture, indicating that
geoduck aquaculture gear created favorable habitat for some types of Puget Sound
macrofauna” (McDonald et al. 2013, p. 56).
Appendix D includes excerpts from McDonald et al. (2013); those fuller excerpts are
incorporated here by reference.
Geoduck clams are typically harvested using hand-operated water jet probes. Seawater is
pumped under pressure into the substrate, liquefying the substrate and allowing extraction of the
clam by hand. Willner (2006) considered the effects of geoduck dive harvest. Appendix D
includes excerpts from Willner (2006); those excerpts are incorporated here by reference.
Vanblaricom et al. (2015) recently reported the findings of a multi-site study evaluating the
effects of geoduck harvest on benthic infaunal communities in the south Puget Sound. The
authors use a treatment and control experimental design to describe spatial and temporal (i.e.,
seasonal) patterns of abundance and diversity, and to evaluate the effects of harvest both on and
adjacent to cultured farm plots. “There was scant evidence of effects on the community structure
and] no indications of significant ‘spillover’ effects of harvest on uncultured habitat adjacent
to cultured plots” (p. 171). The authors suggest: “…a principal reason for the apparent
insensitivity of resident infauna … is accommodation of the infaunal assemblage to a significant
natural disturbance regime ... natural disturbances typical of the area provide a rate of physical
intervention … substantially greater than rates of significant disturbance caused by geoduck
aquaculture operations in a given plot” (p. 183). The authors go on to say, “…the prevailing
natural disturbance climate in the region has effectively selected the infaunal assemblage toward
tolerance of and resilience to the types of disturbances associated with geoduck aquaculture
operations”, but also warn that “…the data may not provide a sufficient basis for unequivocal
extrapolation to cases when a given plot is exposed to a long series of successive geoduck
aquaculture cycles” (Vanblaricom et al. 2015, pp. 183, 184).
Summary: Interactions between benthic/epibenthic communities and shellfish activities are
complex. Culturing equipment and materials placed on and over the bed, and the intensively
cultured shellfish that they promote (many of which are non-native species), modify habitat,
and/or create new habitat types (or habitat variants). Shellfish activities do clearly influence
benthic community structure and composition. However, studies consistently indicate significant
seasonal and site-by-site variability, issues of scale and spatial resolution are evident, and the
nature of some relationships remains poorly understood. Some interactions with shellfish
activities do appear to benefit and favor specific benthic/epibenthic taxa and functional groups.
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Mechanical leveling, harrowing, and dredge harvesting act as intense pulse disturbances.
Geoduck harvesting may also act as an intense pulse disturbance, though generally it occurs at a
much reduced frequency (e.g., once every 7 to 9 years). These activities have implications for
substrate conditions, sediment chemistry, nutrient status, and benthic community richness and
evenness. While clearly they will in many cases either interfere with or reset normal patterns of
infaunal succession and development, and many sites and farms are therefore managed in a
chronically disturbed state, the long-term implications for benthic/epibenthic community health
are difficult to predict or generalize across individual sites. When evaluating potential
interactions and outcomes, we must consider that the current conditions in the action area
represent at many locations a dynamic equilibrium influenced by shellfish and other activities
conducted over years and decades. The significant roles played by ecosystem engineering or
niche constructing species (e.g., eelgrass, oysters, other), and biogenic structures (e.g., kelp
forest, oyster reef, other), are evident.
Effects to Predator-Prey Dynamics and Productivity (Prey-Mediated Effects)
Here we evaluate potential effects to predator-prey relationships and dynamics, and prey
productivity and availability. Shellfish activities have measurable, persistent or long-term effects
to substrates, submerged aquatic vegetation, and benthic/epibenthic community structure and
composition. These, in turn, may influence habitat function and productivity for a variety of
prey resources that are important to listed species.
Unfortunately, there are relatively few studies that provide relevant and specific information to
describe interactions between shellfish activities and the prey resources that are considered most
important to bull trout and marbled murrelets foraging in the marine environment (e.g., marine
forage fish, juvenile salmonids). Further complicating matters, conditions resulting from
shellfish activities reflect variable patterns and rates of recovery from disturbance, and the
discernable direct and indirect effects of shellfish activities are generally also superimposed on,
and further influenced by, natural variability, patterns of disturbance and recovery from natural
events, and the confounding effects of concurrent, unrelated activities occurring in the same
nearshore environments and watersheds.
Simenstad and Fresh (1995, pp. 44, 63) offered useful examples to help explain potential
interactions, and also warned of potential cascading trophic affects:
In [the] Pacific Northwest … a number of economically-important fishes feed
preferentially on specific taxa of intertidal soft-bottom meiofauna and small macrofauna
Of prime interest are juvenile chum, Chinook, and coho salmon that exhibit a high
fidelity for shallow estuarine habitats … These fish feed on a restricted suite of
epibenthic harpacticoid copepods, gammarid amphipods, [and] cumaceans … When
feeding in estuarine habitats, particularly in eelgrass meadows and mud flats, juvenile
chum salmon prey extensively on only a few taxa of harpacticoid copepods such as
Harpacticus uniremis, Tisbe spp., and Zaus sp. (Healey 1979; Simenstad et al. 1982,
1988; D’Amours 1987, 1988) … A number of other species, including smelts ([Family]
Osmeridae), sand lances ([Family] Ammodytidae), and sticklebacks ([Family]
Gasterosteidae) also prey heavily on these same prey taxa … early in their life histories
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Simenstad et al. 1988) … Similarly, amphipods such as Corophium salmonis and C.
spinicorne and cumaceans are preyed upon extensively by juvenile Chinook salmon
Dunford 1975; Northcote et al. 1979; Levy and Northcote 1982; Simenstad et al. 1982)
and by migratory waterfowl and shorebirds such as sandpipers [Family Scolopacidae]
and dunlin (Caladris alpina) … (Albright and Armstrong 1982; Baldwin and Lovvorn
1994).”
Aquaculture … may disturb benthic-epibenthic habitats beyond natural intensities or
frequencies, perhaps for years or decades … When scales of human disturbance exceed
that of natural regimes … effects can potentially cascade … to affect production of other
estuarine, marine, and anadromous populations” (Simenstad and Fresh 1995, pp. 44, 63).
Doney et al. (2012) also emphasize the significance of altered species interactions and trophic
pathways: “Shifts in the size structure, spatial range, and seasonal abundance of populations …
in turn, lead to altered species interactions and trophic pathways as change cascades from
primary producers to upper-trophic-level fish, seabirds, and marine mammals … in both bottom-
up and top-down directions … Investigating the responses of individual species to single forcing
factors, although essential, provides an incomplete story and highlights the need for more
comprehensive, multispecies- to ecosystem-level analyses” (Doney et al. 2012, p. 12).
The nusery-role concept: There is wide acknowledgement that eelgrass meadows, kelp forests,
and other structured habitats of the estuarine environment (e.g., oyster reefs, estuarine wetlands,
mangroves) provide a diversity of microhabitats (Figure 44), and may also confer significant
benefits in the forms of enhanced growth, survival, and recruitment for a huge variety of
organisms. These structured habitats are therefore frequently described as “nurseries”. A
number of authors have examined and critiqued the nusery-role concept as it relates to the
function and value of structured estuarine habitats, including eelgrass meadows.
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Figure 44. The eelgrass meadow; a world of microhabitats
Mumford 2007, p. 3)
Beck et al. (2001) have argued that “…a better understanding of the habitats that serve as
nurseries for marine species, and the factors that create site-specific variability in nursery quality,
will improve conservation and management.” They observed the following:
Comparisons are often limited to vegetated versus unvegetated habitats (Edgar and
Shaw 1995, Gray et al. 1996) … Generally, an area has been called a nursery if a juvenile
fish or invertebrate species occurs at higher densities, avoids predation more successfully,
or grows faster there than in a different habitat” (p. 634).
The few studies that have focused on differences in juvenile survival … indicate that
survival of a species is generally greater in vegetated than in unvegetated habitats (Orth et
al. 1984, Heck and Crowder 1991, Able 1999) … [But] Even fewer studies have focused
on the effects … [to] growth of fish and invertebrates (Heck et al. 1997, Phelan et al.
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2000) … In seagrass meadows, evidence regarding growth is, surprisingly, equivocal …
Only about half of the studies report that the growth rate of individuals is higher in
seagrass habitats than in adjacent habitats (Heck et al. 1997)” (p. 634).
There is growing recognition that there are exceptions to the nursery-role concept …
few] species of fish and invertebrates appear to rely exclusively on seagrass meadows …
Heck et al. 1995) … (Able and Fahay 1998) … Instead, most of these species use
seagrass meadows opportunistically but can survive well in unvegetated areas” (p. 635).
The ecological processes operating in nursery habitats, as compared with other habitats,
must support greater contributions to adult recruitment from any combination of four
factors: (1) density, (2) growth, (3) survival of juveniles, and (4) movement to adult
habitats” (p. 635).
The nursery value of seagrass meadows … may vary geographically … Many biotic and
abiotic factors can influence the nursery value of habitats for a species [including
predation, competition, food availability, water depth, location, tidal regime, disturbance
regime, fragmentation, and connectivity] … For example, Heck and Crowder (1991)
found that predation on target species in seagrass beds was lower in more structurally
complex beds, which suggests that more complex beds may serve as better nurseries for
many species because they increase survivorship” (Beck et al. 2001, p. 638).
Heck, Hays, and Orth (2003) used meta-analytic techniques to examine whether seagrass
meadows function as effective nursey grounds. They observed the following:
Surprisingly, few significant differences existed in abundance, growth, or survival when
seagrass meadows were compared to other structured habitats, such as oyster or cobble
reefs, or macroalgal beds … Nor were there decreases in harvests of commercially
important species that could be clearly attributed to significant seagrass declines in 3 well
studied areas … One important implication of these results is that structure per se, rather
than the type of structure, appears to be an important determinant of nursery value” (p.
123).
Of the total 193 comparisons, 89 (46 percent) showed greater abundance in seagrass, 50
26 percent) showed greater abundance in other habitats, and 54 (28 percent) showed no
difference between seagrass and other habitats … Thus, for slightly more than half of the
species studied, seagrass meadows did not support abundances that were significantly
greater than those in surrounding habitats … [However,] There is stronger evidence of
the importance of seagrass meadows in the northern hemisphere, where 58 of 77
comparisons (75 percent) showed significantly greater abundances in seagrass” (pp. 126,
127).
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When all studies were considered together in the unlumped data set, seagrasses had a
significantly positive effect on juvenile survival when compared to other habitats …
But] The effect of seagrass meadows on juvenile survival clearly varied across species
with no discernible patterns by taxonomy (fish vs decapod crustaceans) or geography
tropical vs temperate)” (pp. 127, 129).
The enhanced survival of organisms in seagrass compared to that observed on
unvegetated substrates seems to be due primarily to the simple effect of structure and not
some intrinsic property of the seagrasses themselves … [Still] Over a period of more than
20 years, virtually all studies have found significantly greater survival in the presence
than in the absence of seagrasses, whether in the laboratory (Nelson 1979, Coen et al.
1981, Main 1987, Mattila 1995) or in the field (Leber 1985, Heck and Wilson 1987, Heck
and Valentine 1995)” (p. 131).
Growth was also significantly greater in seagrass than on unvegetated substrates,
although there was little difference between growth in seagrass and other structured
habitats … It may well be that greater growth in structured habitats occurs because
structure provides more protection from predators and thereby allows more time for
feeding, and thus significantly greater growth rates, than is possible in unstructured
habitats … It is also true that structure provides more substrate for food resource to grow
upon, which can be an important factor influencing growth rates” (Heck, Hays, and Orth
2003, p. 132).
Appendix D includes excerpts from Beck et al. (2001) and Heck, Hays, and Orth (2003); those
fuller excerpts are incorporated here by reference.
Sheaves, Baker, and Johnston (2006) have argued that tests of the nursery-role hypothesis are
often overly simplistic, and therefore likely to misunderstand and/or misrepresent important
relationships:
While some species use particular habitats within an area as ‘nurseries’, for others
nursery ground value is derived from the whole area (Aiken et al. 2002) … In essence,
nursery ground provision needs to be considered at different scales for different species”
p. 304).
In many cases, the situation is complex, with many habitat types or habitat areas
contributing to support juvenile nutrition and provide refuge from predation (Dorenbosch
et al. 2004a, Niklitschek and Secor 2005, Sheaves 2005) … Where this occurs,
untangling the contribution of the various constituents of the mosaic could prove very
difficult … The effectiveness of habitats may be additive, with many different habitats
utilised over time and space (Hernandez et al. 2001, Pederson and Peterson 2002,
Niklitschek and Secor 2005), making identification of the exact contribution of each, and
unambiguously quantifying the importance of a particular habitat, fraught with
difficulties” (p. 304).
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Breaking complex systems into simpler units can provide insights, but it is dangerous to
apply such piece-by-piece understanding in isolation from the complexity … The
approach of applying a rigid and overly simplistic ‘recipe book’ classification of complex
and dynamic systems may lead to a failure to adequately recognise and understand
critical links and processes which support marine nurseries” (Sheaves, Baker, and
Johnston 2006, pp. 304, 305).
Landscape scale interactions and dynamics: Bostrom, Jackson, and Simenstad (2006)
reviewed and synthesized a large body of literature describing the landscape ecology of
seagrasses and their effects on associated fauna; they observed the following:
Patterns (e.g., abundance, diversity, biomass) and processes (e.g., recruitment,
predation, flows and productivity) at a specific site can only be fully understood by
including broad-scale … variables and landscape attributes … We review landscape
patterns and [the] processes that cause them, and then present models for faunal
distribution” (pp. 383, 384).
The landscape mosaic model … [takes] into account that organisms rarely show a
preference for a specific structured habitat, i.e. seagrass, oyster reefs, macroalgae, and
mangrove … An alternative view is to see the species/process/question-specific
landscape as a mosaic of different habitats (McGarigal and Cushman, 2002) … [The
model] proposes that optimal foraging, movement, and fitness strategies vary for
different animals within a mosaic” (p. 386).
A total of 33 papers published between 1994 and 2004 met our search criteria …
skewed towards the temperate northern latitudes … Zostera spp. … [were among] the
most studied landscape-forming genera/species … 50 percent of the papers examined the
role of patch size and 43 percent examined edge effects, i.e., possible differences in
response variables between the seagrass boundary and the interior parts of a patch or
meadow” (pp. 391, 392).
About 50 percent of all studies focused on some aspect of seagrass ecosystem
configuration based on a variety of partly correlating metrics, including fragmentation,
proximity, connectivity, isolation, fractal dimension, total linear edge, number of patches,
edge contrast, and patch orientation … At its simplest, fragmentation is usually observed
as a reduction in seagrass cover and a decrease in patch size over time, causing an
increase in the proportion of habitat edge and distance between patches, i.e. decreased
connectivity and increased amount of unvegetated corridors” (p. 393).
In two thirds of the studies examined, seagrass patch size was a significant predictor of
faunal] density (n = 7), growth (n = 5), and mortality (n = 4), respectively … However,
half of the studies examined showed non-significant results for the same response
variables, mainly due to confounding effects of sites, seasons, and target taxa … This
exemplifies the difficulty in linking effects of seagrass landscape pattern to faunal
structure” (p. 393).
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We found mixed effects of fragmentation in seagrass landscapes, with about equal
proportions of significant … and non-significant effects … suggesting that seagrass
fragmentation is not necessarily detrimental for associated animals” (p. 396).
Studies in terrestrial landscapes have demonstrated critical thresholds in fragmentation,
where mobility and diversity patterns change dramatically and nonlinearly (Gardner and
Milne, 1987; Rosen, 1989) … Demonstration of such threshold responses … [in seagrass
landscapes] warrants further investigation” (p. 396).
In accordance with Turner et al. (2001), it might be summarized that effects of spatial
patterns/fragmentation on organisms are not likely to be important if habitat patches are
abundant … and well connected, edge effects are not central to the process/species under
study, and movement between suitable habitats is relatively unlimited” (p. 397).
The importance of unvegetated strips as corridors for large mobile predators (e.g.,
Irlandi et al., 1995) is likely to vary depending on target species and water depth … In
very shallow seagrass landscapes, where the leaf canopy reaches the water surface,
unvegetated corridors may provide the only avenue for movement/foraging in an
unstructured environment, while in deeper seagrass landscapes the space above the leaf
canopy can also be utilized by mobile fauna” (p. 398).
Nonlinear relationships between ensemble faunal variables and landscape metrics were
identified by a number of studies, and are to be expected when assessing species with
different perception of the seagrass landscape … This may also account for the lack of
relationships in some studies and the opposing results of comparable studies … In order
to contrast patterns across regions and to allow the synergistic development of our
knowledge in this field, we need to standardise our use of landscape metric and terms in
relation to seagrass landscapes … Perhaps the more daunting need is a much better
understanding of the various processes operating at various scales and possible cascading
effects across scales that influence fauna-environment relationships in seagrass
landscapes … It is obvious from this literature that they are complex, difficult to predict,
and still relatively under-studied” (Bostrom, Jackson, and Simenstad 2006, p. 399).
Appendix D includes excerpts from Bostrom, Jackson, and Simenstad (2006); those fuller
excerpts are incorporated here by reference.
Summary: There are relatively few studies that provide relevant and specific information to
describe interactions between shellfish activities and the prey resources that are considered most
important to bull trout and marbled murrelets foraging in the marine environment (e.g., marine
forage fish, juvenile salmonids). Lacking information from these types of studies, we have
instead considered available information describing the nursery function of structured estuarine
habitats, including eelgrass meadows, and available information regarding the altered species
assemblages, and altered species and trophic interactions, that are likely to result from loss or
fragmentation of structured estuarine habitat.
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Whereas, we have already concluded that (1) shellfish activities resulting in physical damage to
submerged aquatic vegetation will result in losses of production and associated ecosystem
services (including habitat functions), and (2) some activities (e.g., mechanical leveling,
harrowing, and dredge harvesting) will in many cases either interfere with or reset normal
patterns of infaunal succession and development, available information regarding predator-prey
relationships, and prey productivity and availability, is more ambiguous and therefore also less
compelling. Further complicating matters, conditions resulting from shellfish activities are
generally superimposed on, and further influenced by, natural variability, patterns of disturbance
and recovery from natural events, and the confounding effects of concurrent, unrelated activities
occurring in the same nearshore environments and watersheds. While there is some information
to indicate a decline in the health of marine forage fish resources in the action area (see
Environmental Baseline, Willapa Bay, Grays Harbor, Puget Sound and Hood Canal), and the
decline of many salmonid populations is both obvious and widespread, there is little or no
information attributing those conditions to shellfish activities specifically.
Furthermore, not all of the potential shellfish interactions are detrimental to the health of native
eelgrass and rooted kelp, or nearsore habitat complexity, function, and productivity. Bivalves
and other filter-feeding shellfish, whether occurring naturally or in farmed/cultured settings, do
provide important benefits in the form of ecosystem services (e.g., improved water quality;
sequestration of carbon and nutrients). Culturing equipment and materials, and the intensively
cultured shellfish that they promote, create new habitat types (or habitat variants).
Biodeposition, as a source of nutrient enhancement supporting plant growth and vigor, and
improved water quality may well act to enhance eelgrass and kelp health in some settings. And,
importantly, cultured shellfish are themselves ecosystem engineering or niche constructing
species, and the habitat value of the biogenic structures they create is evident.
Impacts to marine forage fish spawning habitat resulting from programmatic shellfish
activities: The BA submitted by the Corps in support of programmatic consultation provides a
summary of available data, and the limitations of available data, to describe the distribution of
marine forage fish spawning habitat in the action area, and its co-location with continuing
shellfish activities (Corps 2015, pp. 90, 95-97; Appendix D). The Service regards these data, and
the Corps’ analyses, as the best available information to describe the likely physical extent of
potential impacts to marine forage fish spawning habitat resulting from programmatic shellfish
activities in Washington’s marine waters. The Service does acknowledge that there is no current,
comprehensive mapping of marine forage fish spawning habitat in Puget Sound, Hood Canal, or
the coastal embayments of Willapa Bay and Grays Harbor.
The Corps has stated the following regarding potential impacts to marine forage fish spawning
habitats located on fallowed farm footprints (Corps 2015, pp. 95-97):
There is substantial overlap between forage fish spawning locations and [shellfish]
activities … There are an estimated total of 3,297 fallow acres across all [geographic]
regions co-located with forage fish spawning areas … The analysis suggests that Willapa
Bay and north Puget Sound are the [geographic] regions where the most overlap may
occur on an acreage basis … Relative to the total mapped herring spawning area in each
region, activities in Willapa Bay tend to occur in well over half of the mapped spawning
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area, by far the largest proportion of any of the [geographic] regions … The north Puget
Sound region contains the most fallow acres (2,241 acres) potentially co-located with
forage fish spawning areas … Much of this is overlap with the herring spawning area in
Samish Bay.”
Table 9, below, presents the Service’s best approximation of the likely physical extent of
potential impacts to marine forage fish spawning habitat resulting from programmatic shellfish
activities in Washington’s marine waters. Across the geographies and acreages summarized
here, the Service expects there will be measurable, temporal losses of marine forage fish
spawning habitat and production. However, the Service also expects that most of these impacts
and measurable losses will be temporary. In most cases, and in most settings where continuing
shellfish activities result in temporal losses of marine forage fish production, we expect that
much of the lost function and production will be recovered over time. Furthermore, we expect
that the conservation measures included by the Corps as elements of their proposed action (see
Project Description, Conservation Measures) will largely avoid and effectively reduce impacts
to marine forage fish spawning habitat that might otherwise result from proposed, new shellfish
activities and farms.
Marine forage fish spawning habitat experiences loss and recovery on continuing farms. Marine
forage fish spawning habitat will also experience loss and recovery when fallow farms or farm
footprints are re-cultivated and put into production. The Service acknowledges that fallow farm
footprints are extensively co-located with marine forage fish habitat; most extensively and
importantly for bull trout, in the north Puget Sound (approximately 2,239 acres)(Corps 2015, p.
95).
The weight of available evidence suggests and leads the Service to conclude that permanent
losses of marine forage fish spawning habitat and production will be uncommon, and not typical
of most outcomes. The Service does not expect that permanent losses attributable to shellfish
activities will be measurable at the scale of the five geographic sub-areas (Willapa Bay, Grays
Harbor, Hood Canal, south and north Puget Sound), at the scale of any whole waterbody (e.g.,
Willapa Bay), or sub-basin (e.g., Totten Inlet, Samish Bay). We expect that these temporal
losses will rarely, if ever, occur at a scale, or with a duration or severity, sufficient to measurably
reduce the quality or availability of bull trout prey resources in any portion of the action area.
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Table 9. Likely physical extent of potential impacts to marine forage fish spawning areas.
GEOGRAPHY
Affected
Nearshore Acres
Action Area)
Continuing
Shellfish Activities (Acres)
Total Co-Located
with Mapped
Herring
Co-Located
with Mapped
Other2
Willapa Bay 30,000 25,840 2,710 ---
Grays Harbor1 4,000 2,965 73 ---
Hood Canal1 3,000 1,356 269 394
North Puget Sound1 5,000 3,687 2,670 195
South Puget Sound 5,000 3,133 93 989
Total 45,000 to 50,000 ~37,000 Approx. 5,815 Approx. 1,578
1 These geographies include designated bull trout critical habitat (see Table 4, p. 77).
2 Mapped “Other” combines mapped Pacific sand lance and mapped surf smelt spawning habitat.
Related or additional considerations for marine birds and shorebirds: Straus et al. (2013, p.
20) discuss briefly the variety of potential interactions with marine birds (waterfowl) and
shorebirds. Some of these interactions and effects are likely to be beneficial (e.g., increased
concentration of cultured bivalve prey, provision of perching and roosting structures), while
others are clearly not (e.g., disturbance, displacement, risk of entanglement). “Responses depend
largely on species-specific food and habitat requirements … waders (e.g., plovers and
oystercatchers) and divers (e.g., scaup and scoters) may benefit from an increased concentration
of … prey” (Straus et al. 2013, p. 20).
However, there are disturbing lines of evidence to suggest the severity of potential long-term
shellfish interactions and outcomes for marine birds (waterfowl), shorebirds, and raptors.
Studies conducted in Europe, Canada, and the United States have contributed a large body of
literature and findings addressing prey depletion and conversion or displacement from preferred,
highly productive foraging areas.
Coastal aquaculture and fisheries are expanding industries, and their further development is
accepted by society … With increasing industrialization of the landscape, it has also become
important to protect ecologically important habitats from further human impact” (Hilgerloh and
Young 2006, p. 535). “Coastal sites and habitats where birds are especially vulnerable have to
be identified, with modeling to predict the impacts of three particular effects: (1) habitat loss,
including bird exclosures, (2) competition for food between humans and birds, and (3)
disturbance … Behavior-based models employing optimal decision rules are needed to make
predictions on the fitness of birds, quantified in terms of survival rate and body condition”
Hilgerloh and Young 2006, p. 535).
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Norris, Bannister, and Walker (1998) reported evidence of prey depletion, its relationship to
fishery exploitation, and the numbers of oystercatchers remaining on overwintering grounds
during the spring:
The abundance of oystercatchers during spring (measured as total bird-days during
March and April) was positively correlated with the biomass of cockles at the start of the
winter, and negatively correlated with the biomass landed by the fishery over the winter
The most likely explanation for this is that birds disperse from the Burry Inlet earlier
in spring when the biomass of cockles at the start of the winter is small and/or the
biomass landed by the fishery is large” (p. 75).
The Burry Inlet cockle fishery is a low intensity fishery, removing < 25 percent of the
available stock, and using traditional fishing methods such as hand gathering … Even at
these low levels of fishing effort oystercatcher abundance was reduced during spring …
The introduction of more efficient modern fishing methods, such as tractor or suction
dredging, could therefore cause a decline in the abundance of oystercatchers within the
estuary, if the level of exploitation increased as a result” (p. 75).
Both autumn cockle biomass and winter cockle landings do seem to affect the number of
birds left in March and April at the end of the winter … Results suggest that the declining
trend in spring oystercatcher abundance has resulted from a decline in the biomass of
cockles and an increase in the biomass landed by the fishery during the winter” (Norris,
Bannister, and Walker 1998, p. 82).
Stillman et al. (2001) used a behaviour-based model to evaluate the impacts of current and
alternative shellfishery regimes on oystercatcher health, mortality, and population size:
This study explored the impacts of the present-day management regime of the mussel
fishery on the Exe estuary, south-west England … and of the cockle fishery on the Burry
inlet, south Wales … on the survival and numbers of overwintering oystercatchers … It
also explored the effect on birds of some possible alternative ways of managing these
shellfisheries” (p. 858).
Present-day methods and fishing effort did not affect the body condition of model
oystercatchers on either the Exe or Burry … But with increased shellfishing, and the use
of dredging, a point came when many oystercatchers could not compensate by feeding for
longer or eating more smaller prey … Unsuccessful birds then drew on their energy
reserves and so lost mass … The model predicted that increasing fishing effort
substantially above current levels would reduce the average mass of surviving birds for
all methods, except hand-raking cockles” (pp. 862, 863).
Mussel-fishing techniques that reduced bed area (hand-raking and dredging) both
reduced the food available and forced birds to feed at higher densities, thus increasing
both exploitation and interference competition” (p. 865).
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The simulations … showed that relatively small increases in mortality due to intensive
shellfishing could indeed greatly reduce population size … Small increases in mortality
caused by fishing should not be assumed to be of little importance” (p. 864).
Small changes in oystercatcher mortality caused larger changes in the long-term
population size because the oystercatcher population did not recover from the effects of
shellfishing between winters … The model predicted that the impact of shellfishing on
oystercatchers depends not only on fishing effort but also on environmental factors such
as the weather and overall food abundance” (Stillman et al. 2001, p. 866).
Godet et al. (2009) considered the effects of intensive clam cultivation on Lanice conchilega
sand mason worm] beds and found that beds were both degraded and less attractive to foraging
oystercatchers; they observed the following:
In 2005, we studied the impacts of Manila clam cultivation on the Chausey’s L.
conchilega beds focusing on the macrobenthic compartment (Toupoint et al., 2008) …
This study mainly revealed that clam cultivation induced a decrease of both the L.
conchilega densities and of the abundance and the diversity of the associated macrofauna
In this paper, we aimed at assessing the impacts of the degradation of Chausey’s L.
conchilega beds by this activity on the spatial distribution of a secondary consumer: the
Eurasian Oystercatcher Haematopus ostralegus” (p. 590).
Before the creation of the new clam concessions, L. conchilega beds were significantly
selected by Oystercatchers as a major feeding ground … We highlighted (Godet et al.,
2008) the important abundances of large bivalves especially the Cockle (Cerastoderma
edule) … known to be an important prey for the Oystercatcher (Cramp and Simmons,
1983)” (pp. 591, 593).
The present study revealed that the positive effects of the L. conchilega beds for birds
are ephemeral … The regression or the disappearance of L. conchilega beds involved
directly a loss of attractiveness for the feeding Oystercatchers” (p. 593).
During the first year of the production cycle, clam concessions are not attractive for
Oystercatchers because: (1) during six months nets prevent any predation, (2) during the
following months, clam are hardly large enough to be profitable for the birds, and (3) the
associated benthic macrofauna is less abundant in one-year concessions … Clam
concessions are potentially the most attractive during the second year of the production
cycle until the beginning of the third year, before harvesting … Nevertheless, we did not
find any differences between the different concessions of one, two, or three years for the
attractiveness of the birds” (p. 593).
The rapid … [growth] of shellfish farming activities along the world’s coasts may have
irreversible and increasing negative impacts on secondary consumers which have only
just begun to be explored by the scientific community” (Godet et al. 2009, p. 594).
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Kraan et al. (2009) provide evidence that intensive, landscape-scale shellfish activities have
caused or contributed to prey depletion, reductions in available foraging habitat, reduced
survival, and reduced numbers of red knots (Calidris canutus islandica):
Whether intertidal areas are used to capacity by shorebirds can best be answered by
large-scale manipulation of foraging areas … The recent overexploitation of benthic
resources in the western Dutch Wadden Sea offers such an ‘experimental’ setting … We
review the effects of declining food abundances on red knot [Calidris canutus islandica]
numbers, based on a yearly large-scale benthic mapping effort, long-term colour-ringing,
and regular bird-counts from 1996 to 2005 … We focus on the three-way relationships
between suitable foraging area, the spatial predictability of food, and red knot survival …
Over the 10 years, when accounting for a threshold value to meet energetic demands, red
knots lost 55 percent of their suitable foraging area … This ran parallel to a decrease in
red knot numbers by 42 percent … Densities of red knots per unit suitable foraging area
remained constant at 10 knots [per] ha between 1996 and 2005, which suggests that red
knots have been using the Dutch Wadden Sea to full capacity” (p. 1259).
The mechanical harvesting of cockles Cerastoderma edule, allowed in three-quarters of
the intertidal flats, has decreased both the quality (flesh-to-shell ratio) and the abundance
of available cockles for red knots Calidris canutus (Van Gils et al. 2006a)” (p. 1260).
Knots, visiting the area in winter … [over] the period 1996-2005 … were faced with a
decline in the extent of suitable foraging area, especially from 2002 onwards … For a
benthivorous predator, which also has to deal with tidal cycles (Van Gils et al. 2005b,
2006b, 2007), interference competition (Van Gils and Piersma 2004; Vahl et al. 2005),
and predation by raptors (Piersma et al. 1993; Van den Hout, Spaans and Piersma 2008),
these landscape-scale changes have population-level impacts” (p. 1265).
Following the … decline of suitable foraging area … survival of islandica knots
decreased from 89 percent to 82 percent … Reduced survival (with constant recruitment)
only explained … 42 percent of the loss in numbers: more red knots ‘disappeared’ from
the Dutch Wadden Sea than could be explained by the increased mortality (e.g. Van Gils
et al. 2006a) … Apparently, many surviving red knots emigrated permanently out of this
marine protected area … and reduced food abundance may have indirectly lead to
reduced breeding success (Ebbinge and Spaans 1995; Baker et al. 2004; Morrison,
Davidson and Wilson 2007) … In any case, the reduced annual survival clearly supports
the suggestion that the Wadden Sea was filled to capacity in the decade during which this
study took place (Goss-Custard 1985; Goss-Custard et al. 2002)” (Kraan et al. 2009, p.
1266).
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Bendell and Wan (2011) used high resolution aerial photography and Geographic Information
Systems to evaluate the effect of intensive, landscape-scale shellfish activities on patterns of
avian habitat utilization; they reported the following:
The case study presented here is unique in that the region under study is an Important
Bird Area … of global significance (Booth 2001) … The Baynes Sound region supports
globally important populations of the Western Grebe (Aechmophorus occidentalis), the
White-winged (Melanitta fusca) and Surf Scoter (Melanitta perspicillata), and the Pacific
Loon (Gavia pacifica) (Booth 2001) … It also serves as a major centre for the BC
shellfish aquaculture industry with half of the industries economies being generated from
this region (British Columbia Ministry of Sustainable Resource Management
BCMSRM) 2002)).”
On the west coast of BC … there has been [an] attempt by industry and the federal and
provincial governments to aggressively expand shellfish aquaculture, with the Manila
clam (Venerupis philippinarum), and Pacific oyster (Crassostrea gigas), the main product
farmed … Baynes Sound has a long history of shellfish aquaculture dating back to the
1900’s (BCMSRM 2002) … [But] The number of leases and the numbers of approved
species for farming on the individual leases has greatly increased since 1984 … In
addition to shellfish aquaculture, increasing urban development also results in habitat loss
within this region” (pp. 418, 419).
After the maximum and relevant intertidal [habitats] were digitized, regions of the
intertidal covered by anti-predator netting were determined … A multi-step analysis by
GIS modelling was applied to the four layers (maximum intertidal, viable intertidal,
antipredator netting, and oyster grow-out beds) to determine that region of the foreshore
not compromised by shellfish farming activities … We use the information obtained by
spatially characterizing the anthropogenic footprint to assess its role in influencing the
distribution of shore and water birds such as the dunlin, grebe, and scoter” (pp. 422, 423).
In Baynes Sound, netted areas … [and] oyster grow-out beds occupy 27 percent and 34
percent of the intertidal area respectively … The amount of foreshore habitat in Baynes
Sound used for shellfish farming is … 56 percent of the viable intertidal” (p. 424).
There were distinct differences in the locations of high bird use in 1980 as compared to
2003-2005 … In 2003-2005 birds were located all along the coastline, with no one
particular region of high use” (p. 425).
Within Baynes Sound, the primary change in intertidal use during this 30 year period
has been the development of the foreshore within polygons 33–46 for aquaculture, with
the true extent of its footprint determined by high resolution aerial photography coupled
with GIS … As the majority of overwintering birds are now found within the Courtenay
River Estuary (Comox Harbour) or are distributed along the coastline with no one
significant region of high bird use, it would appear that key habitat historically used by
these species is no longer available” (Bendell and Wan 2011, p. 429).
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Ferriss et al. (2015, pp. 15-33) used a trophic model incorporating mediation functions to
examine potential food web implications associated with a future growth in central Puget Sound
geoduck production; they reported the following:
The nontrophic effects of increased geoduck aquaculture, related to the influence of
anti-predator structure, had a stronger influence on the food web than the trophic role of
cultured geoducks as filter feeders and prey to other species … Increased geoduck culture
caused substantial increases in biomass densities of surf perches, nearshore demersal
fishes, and small crabs, and decreases in seabirds, flatfishes, and certain invertebrates
e.g., predatory gastropods and small crustaceans)” (p. 15).
The addition of cultured geoduck mediation functions had a notable impact on the food
web [Figure 45] … The biomass of food web members that were linked to geoduck
culture through mediation functions changed considerably, with the biomass densities of
some members increasing and decreasing by more than 20 percent (e.g., surf perches,
small crabs, predatory gastropods, and small mouth flatfishes) … In addition, changes in
the biomass of food web members directly linked to geoduck culture propagated through
the food web, contributing to additional changes in other members’ biomass … In total,
the biomasses of 9 of the 10 functional groups with cultured geoduck mediation functions
changed substantially” (pp. 21, 22).
Geoduck mediation functions linked to demersal fishes and small crustaceans had
substantial effects on the food web … For example, the cultured geoduck-demersal fish
mediation function resulted in decreases in herons (-23 percent) and resident birds (-17
percent), and increases in Pacific cod (+7 percent) and harbor seals (+7 percent) ... The
cultured geoduck–small crustacean mediation functions resulted in reductions in the
biomasses of juvenile wild salmon (-7 percent) and juvenile hatchery salmon (-4
percent)” (p. 22).
Geoduck predators (moon snails, starfish, flatfishes, red rock crab, and sea birds) are all
generalists to varying degrees and showed limited change in biomass in response to
increased geoduck aquaculture … However, the impact of antipredator structure (tubes
and nets) placed on geoduck plots had a larger influence on the surrounding food web by
providing predation refuge or by changing foraging opportunities … In turn, these effects
propagated throughout the food web” (p. 22).
The substantial decrease of most bird groups in the model is important to note, as these
are important ecologically, culturally, and socio-economically … [There was a] decrease
in eagle populations … [and] the biomass of other bird groups decrease[d], implying
bottom-up control … reduced access to key prey (e.g., demersal fishes and small
crustaceans) because of the predator refuge provided by anti-predator nets on geoduck
farms … Migratory shore birds (biomass increase) do not primarily prey upon demersal
fishes and small crustaceans, and are likely benefiting from a release of eagle predation
while not suffering prey depletion … Further empirical study is required to understand
the relationship between shellfish aquaculture and birds” (Ferriss et al. 2015, p. 24).
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Figure 45. Functional groups with the greatest change in relative biomass
Ferriss et al. 2015, p. 22)
Appendix D includes excerpts from Norris, Bannister, and Walker (1998); Stillman et al. (2001);
Godet et al. (2009); Kraan et al. (2009); Bendell and Wan (2011); and, Ferriss et al. (2015, pp.
15-33 In Washington Sea Grant 2015); those fuller excerpts are incorporated here by reference.
Exposures and Responses to Persistent Stressors (Bull Trout and Murrelet)
Shellfish activities alter physical, chemical, and biological conditions on varying temporal scales.
Many of these effects to the physical, chemical, and biological environment (i.e., potential
stressors) correspond closely to cycles of production and harvest. However, some of these
effects are more persistent, and also reflect variable patterns and rates of recovery from
disturbance, and/or interactions with unrelated activities in the same nearshore environments.
This portion of the Opinion has addressed persistent stressors of long duration (months, years),
including potential indirect effects that may result from altered patterns of prey availability and
productivity (“prey-mediated effects”), and potential long-term effects to natural forms of
nearshore marine habitat structure, function, and complexity. These portions of the Opinion
have described long-term, direct and indirect effects on large spatial scales, corresponding to
hundreds of farms and farm operations, and thousands of affected nearshore marine acres.
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Our Opinion finds that the most significant and biologically relevant effects are those that result
in aggregate to nearshore marine habitat structure, function, and productivity, ecological
processes, and ecosystem services. For wide-ranging species that depend on the action area’s
variety of nearshore marine environments and resources (e.g., anadromous bull trout), it is
ultimately at these larger scales that we can best interpret the significance of potential stressors,
exposures, and responses.
Bivalves and other filter-feeding shellfish, whether occurring naturally or in farmed/cultured
settings, do provide important benefits in the form of ecosystem services. The Service expects
that shellfish activities will generally, and in the majority of cases, provide long-term benefits in
the form of improved water quality and sequestration of carbon and nutrients. These ecosystem
services may be important as a means to control and prevent the effects of excess nutrient
additions occurring elsewhere in the contributing watersheds and may lessen or counteract the
potential for climate-induced ocean acidification and hypoxia.
Ecological carrying capacity is a useful concept for thinking about the possible erosion or loss of
ecosystem services, and resulting consequences, under a scenario of pervasive and extremely
high shellfish culturing densities. While we do not deny the role or significance of social
carrying capacity and public acceptance, those aspects are beyond the scope of the Service’s
considerations, and therefore we limit our consideration of carrying capacity to the physical and
ecological elements.
Our Opinion includes a case study of Totten Inlet primary productivity and consumption (MEC-
Weston Solutions, Inc. 2004; New Fields Northwest 2008). Totten Inlet’s current natural/wild
and cultured shellfish biomass is large, but available information suggests a relatively muted or
small influence on primary production and trophic state. There is no indication that the Totten
Inlet phytoplankton resource has been substantially diminished as a result of shellfish activities,
and it appears that primary production still greatly exceeds the basin-scale demand of primary
consumers. Even with the projected future growth of the industry in south Puget Sound,
available information suggests little or no likelihood of approaching the ecological carrying
capacity of this system. While it would be premature to extend these tentative conclusions to the
whole of Puget Sound (or to all of Washington’s marine waters), the Service does have
confidence that Totten Inlet and the south Puget Sound are an appropriately conservative
geography and setting for considering these potential effects. Available information leads us to
conclude it is unlikely that the projected 20-year future growth of the industry will approach or
exceed ecological carrying capacity within the action area.
Shellfish activities have direct and indirect effects to nearshore marine habitat structure, function,
and productivity. These effects may have significance for how well these habitats support the
essential behaviors and needs of listed species, including bull trout and marbled murrelets that
forage in the marine environment. This portion of the Opinion has discussed long-term and
persistent effects to substrates and sediment; eelgrass, kelp, and submerged aquatic vegetation;
benthic/epibenthic community structure and composition; and predator-prey dynamics and
productivity (“prey-mediated effects”).
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All of the shellfish culturing and harvesting practices that have been described here result in
measurable effects to substrates and sediment. Some of these shellfish activities and practices
are more likely than others to result in measurable long-term and persistent effects. Based on the
available information, we conclude that the placement of culturing equipment and materials on
and over the bed, mechanical leveling and harrowing, and mechanical dredge harvesting, are
most likely to result in measurable long-term and persistent effects to substrates and sediment.
Sites and farms that are harrowed and dredged repeatedly are managed in a chronically
disturbed” state.
Interactions between submerged aquatic vegetation (native eelgrass, rooted kelp) and shellfish
activities are complex and not easily characterized with simple generalizations. These
interactions include competition for space, competition for light (or shading), and physical
damage that results from some activities, practices, and techniques. However, not all of these
interactions are detrimental to the health of native eelgrass and rooted kelp. For instance,
shellfish culturing provides a source of nutrient enhancement, which supports plant growth and
vigor, and frequently improves water quality. Furthermore, when evaluating potential
interactions and outcomes, we must also consider that the current conditions for submerged
aquatic vegetation in the action area represent at many locations a dynamic equilibrium
influenced by shellfish and other activities conducted over years and decades. Despite the
intensive shellfish culturing that has characterized the recent history at the scale of whole sub-
basins and whole waterbodies, submerged aquatic vegetation continues to show good or
consistent health in some of these same geographies (Gaeckle et al. 2011, 2015)(see
Environmental Baseline, Puget Sound and Hood Canal, Existing Conditions for Native
Eelgrass).
The variety of factors influencing eelgrass recovery suggests the potential for significant site-by-
site and temporal variability. It is therefore difficult (or impossible) to state with certainty the
likely pattern or rate of recovery, at either a fine or coarse scale. Furthermore, there appear to be
few general rules that accurately characterize this complex set of interactions. Nevertheless, the
weight of available evidence does lead the Service to conclude that in most cases and settings
where shellfish activities result in physical damage to eelgrass beds, and/or displace eelgrass
beds or other submerged aquatic vegetation, they will result in at least temporal loss of
production and associated ecosystem services, including habitat functions and prey production
that are important to bull trout and marbled murrelets that forage in the marine environment.
Whereas there have been many studies evaluating interactions and outcomes at the scale of a
single bed or a single farm, there have been relatively few that describe interactions between
submerged aquatic vegetation and shellfish activities on a landscape scale in the Pacific
Northwest. However, Dumbauld and McCoy (2015) did recently complete a multi-year study
evaluating the effects of oyster aquaculture on eelgrass at the estuarine landscape scale in
Willapa Bay. Their findings suggest to us that culturing methods and techniques do have
variable effects to patterns of eelgrass disturbance, recovery, and persistence, but the majority of
these temporal impacts are not likely to be persistent at the estuarine landscape scale (Dumbauld
and McCoy 2015, pp. 38, 41).
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The Corps has provided an excellent summary of the available data, and the limitations of these
data, to describe eelgrass distribution in the action area, and its co-location with continuing
shellfish activities (Corps 2015, pp. 90, 94, 95; Appendix D). The Service used this information
to inform our best, conservative approximation of the likely physical extent of potential impacts
to submerged aquatic vegetation resulting from programmatic shellfish activities in
Washington’s marine waters (Table 8, p. 156). We conclude that regulated shellfish activities in
Washington State, specifically those for which this Opinion provides programmatic coverage,
are likely to directly or indirectly affect more than 26,000 acres of submerged aquatic vegetation,
including more than 6,000 acres located within or near designated bull trout critical habitat
Table 8, p. 156).
The Service expects that shellfish activities will result in measurable losses of eelgrass and kelp
production, and associated habitat functions and prey productivity that are important to
anadromous bull trout and marbled murrelets. However, the Service also expects that most of
these impacts and measurable losses will be temporary. In most cases and settings where
continuing shellfish activities result in physical damage to submerged aquatic vegetation, we
expect that much of the lost production and function will be recovered over time. And, we
expect that the conservation measures included by the Corps as elements of their proposed action
see Project Description, Conservation Measures) will largely avoid and effectively reduce
impacts to submerged aquatic vegetation that might otherwise result from proposed, new
shellfish activities and farms.
Native eelgrass, rooted kelp, and other submerged aquatic vegetation experience loss and
recovery on continuing farms. Native eelgrass and other submerged aquatic vegetation will also
experience loss and recovery when fallow farms or farm footprints are re-cultivated and put into
production. The Service acknowledges that chronic suppression of eelgrass growth and
production may be a reality on some farms. We also acknowledge that fallow farm footprints are
extensively co-located with submerged aquatic vegetation; most extensively and importantly for
bull trout, in the north Puget Sound (approximately 2,239 acres) (Corps 2015, p. 95).
The weight of available evidence suggests and leads the Service to conclude that permanent
losses of submerged aquatic vegetation (native eelgrass and rooted kelp), production, and
function will not be typical of most outcomes. While it is likely there will be instances where
limited, permanent losses (or chronic suppression) are attributable to shellfish activities, the
Service expects that permanent losses will me small (e.g., a fraction of the submerged aquatic
vegetation resource) at the scale of the five geographic sub-areas (Willapa Bay, Grays Harbor,
Hood Canal, south and north Puget Sound), at the scale of any whole waterbody (e.g., Willapa
Bay), or sub-basin (e.g., Totten Inlet, Samish Bay).
Interactions between benthic/epibenthic communities and shellfish activities are complex and not
easily characterized with simple generalizations. Shellfish activities clearly influence benthic
community structure and composition. However, studies consistently indicate significant
seasonal and site-by-site variability, and the nature of some relationships remains poorly
understood.
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Shellfish activities have measurable, persistent or long-term effects to substrates, submerged
aquatic vegetation, and benthic/epibenthic community structure and composition. These, in turn,
may influence habitat function and productivity for a variety of prey resources that are important
to listed species. Unfortunately, there are relatively few studies that provide relevant and
specific information to describe interactions between shellfish culturing and harvesting activities
and the prey resources that are considered most important to anadromous bull trout and marbled
murrelets. Lacking information from these types of studies, we instead considered available
information describing the nursery function of structured estuarine habitats, including eelgrass
meadows, and available information regarding the altered species assemblages, and altered
species and trophic interactions, that are likely to result from loss or fragmentation of structured
estuarine habitat.
Whereas, we have already concluded that (1) shellfish activities resulting in physical damage to
submerged aquatic vegetation will result in losses of production and associated ecosystem
services (including habitat functions), and (2) some activities (e.g., mechanical leveling,
harrowing, and dredge harvesting) will in many cases either interfere with or reset normal
patterns of infaunal succession and development, available information regarding predator-prey
relationships, and prey productivity and availability, is more ambiguous and therefore also less
compelling. Further complicating matters, conditions resulting from shellfish activities are
generally superimposed on, and further influenced by, natural variability, patterns of disturbance
and recovery from natural events, and the confounding effects of concurrent, unrelated activities
occurring in the same nearshore environments and watersheds. While there is some information
to indicate a decline in the health of marine forage fish resources in the action area (see
Environmental Baseline, Willapa Bay, Grays Harbor, Puget Sound and Hood Canal), and the
decline of many salmonid populations is both obvious and widespread, there is little or no
information attributing those conditions to shellfish activities specifically.
During 2008, the Service and NMFS approved a low-effect HCP developed in coordination with
the DNR for their commercial geoduck fishery. That record of HCP approval indicates minor
and small-scale effects resulting from elevated turbidity and sedimentation during harvest
activities (Service Ref. No. PRT-TE187810-0). The Service stated:
Pacific herring are the [marine forage fish ] species most likely to spawn on or near
commercial geoduck tracts … Injury and or mortality to juvenile and adult forage fish
from sediment are not anticipated … Temporary displacement of forage fish from
sediment plumes may occur during harvest activities … [but] will have little effect on
forage fish’s ability to feed … A small amount of Pacific herring egg mortality and the
temporary displacement of adult forage fish during geoducks harvest activities [are]
anticipated, but adverse effects to forage fish populations at the tract level or within the
action area are not anticipated” (USFWS 2009b, pp. 128-130).
The Corps has provided a summary of available data, and the limitations of available data, to
describe the distribution of marine forage fish spawning habitat in the action area, and its co-
location with continuing shellfish activities (Corps 2015, pp. 90, 95-97; Appendix D). The
Service used this information to inform our best, conservative approximation of the likely
physical extent of potential impacts to marine forage fish spawning habitat resulting from
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programmatic shellfish activities in Washington’s marine waters (Table 9, p. 177). We conclude
that regulated shellfish activities in Washington State, specifically those for which this Opinion
provides programmatic coverage, are likely to directly or indirectly affect more than 5,500 acres
of mapped Pacific herring spawning habitat, and more than 1,500 acres of mapped Pacific sand
lance and surf smelt spawning habitat, including more than 3,600 acres located within or near
designated bull trout critical habitat (Table 9, p. 177).
The Service expects there will be measurable, temporal losses of marine forage fish spawning
habitat and production. However, the Service also expects that most of these impacts and
measurable losses will be temporary. In most cases, and in most settings where continuing
shellfish activities result in temporal losses of marine forage fish production, we expect that
much of the lost function and production will be recovered over time. And, we expect that the
conservation measures included by the Corps as elements of their proposed action (see Project
Description, Conservation Measures) will largely avoid and effectively reduce impacts to marine
forage fish spawning habitat that might otherwise result from proposed, new shellfish activities
and farms. The weight of available evidence suggests and leads the Service to conclude that
permanent losses of marine forage fish spawning habitat and production will be uncommon, and
not typical of most outcomes.
Regulated shellfish activities occur on large spatial scales in Washington State (approximately
38,716 acres; Corps 2015, pp. 40-49, 77-82). The larger action area, where measurable direct
and indirect effects are likely to occur, is expansive (i.e., more than 45,000 acres of nearshore
marine habitat). There is also substantial overlap with designated bull trout critical habitat (i.e.,
approximately 12,000 acres in Grays Harbor, the north Puget Sound, and Hood Canal) which is
used seasonally by anadromous bull trout when foraging and migrating.
Nevertheless, given the above-described variable effects of regulated shellfish activities on
nearshore marine habitat structure, function, and productivity, ecological processes, and
ecosystem services (i.e., including those that are neutral or beneficial, some that are adverse, but
few that are measurable, persistent, and adverse), it is difficult to identify specific practices,
instances, or scenarios which will have measurable adverse effects to individual bull trout.
Available information suggests to us that mechanical leveling, harrowing, and dredge harvesting
are the most physically-intrusive and disruptive of all the shellfish activities discussed in this
Opinion. These practices are focused most intensively in Washington’s coastal embayments,
especially Willapa Bay. Bull trout have been documented in Willapa Bay and its tributaries,
though infrequently and in low numbers, and no portion of Willapa Bay has been designated as
bull trout critical habitat. Willapa Bay is one of the few geographies in Washington State where
landscape scale impacts have been evaluated (Dumbauld and McCoy 2015), and it appears that
temporal impacts to eelgrass meadows, a viable general habitat surrogate for natural nearshore
habitat complexity, are not likely to be persistent at the estuarine landscape scale.
The weight of available evidence suggests and leads the Service to conclude that permanent
losses of marine forage fish spawning habitat and production will be uncommon, and not typical
of most outcomes. The Service does not expect that permanent losses attributable to shellfish
activities will be measurable at the scale of the five geographic sub-areas (Willapa Bay, Grays
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Harbor, Hood Canal, south and north Puget Sound), at the scale of any whole waterbody (e.g.,
Willapa Bay), or sub-basin (e.g., Totten Inlet, Samish Bay). We expect that these temporal
losses will rarely, if ever, occur at a scale, or with a duration or severity, sufficient to measurably
reduce the quality or availability of bull trout prey resources in any portion of the action area.
Bull trout will be exposed to the measurable, persistent and long-term effects of regulated
shellfish activities. The Service expects that persistent and long-term stressors and exposures
resulting directly and indirectly from continuing and proposed, new shellfish activities and farms
will in some instances have adverse effects to bull trout. However, we are not able to
demonstrate that exposures are reasonably certain to result in a significant disruption of normal
bull trout behaviors (i.e., the ability to successfully feed, move, and/or shelter). The best
available information is currently insuffcient to demonstrate that persistent and long-term
stressors and exposures are reasonably certain to result in measurable adverse effects to
energetics, growth, fitness, or long-term survival (injury or mortality).
Marbled murrelets will be exposed to the measurable, persistent and long-term effects of
regulated shellfish activities. The Service expects that persistent and long-term stressors and
exposures resulting directly and indirectly from continuing and proposed, new shellfish activities
and farms will in some instances have adverse effects to marbled murrelets. However, we are
not able to demonstrate that exposures are reasonably certain to result in a significant disruption
of normal marbled murrelet behaviors (i.e., the ability to successfully feed, move, and/or shelter).
The best available information is currently insufficient to demonstrate that persistent and long-
term stressors and exposures are reasonably certain to result in measurable adverse effects to
energetics, growth, fitness, or long-term survival (injury or mortality).
Effects of Interrelated and Interdependent Actions
Interrelated actions are defined as actions “that are part of a larger action and depend on the
larger action for their justification”; interdependent actions are defined as actions “that have no
independent utility apart from the action under consideration” (50 CFR section 402.02).
No measurable effects to bull trout individuals, their prey base, or habitat are expected to result
from interrelated or interdependent actions. No measurable effects to marbled murrelet
individuals, their prey base, or habitat are expected to result from interrelated or interdependent
actions.
Effects to the PCEs of Designated Bull Trout Critical Habitat
In nearshore marine areas, the inshore extent of critical habitat is the MHHW line, including the
uppermost reach of the saltwater wedge within tidally influenced, freshwater heads of estuaries.
Critical habitat extends offshore to a depth of 10 meters (33 ft) relative to the MLLW line (75 FR
63935; October 18, 2010).
When viewed from a landscape perspective, or even from the perspective of a single waterbody
e.g., Willapa Bay) or portion thereof (e.g., Totten Inlet, Samish Bay), shellfish activities are
variable in density and spatially discontinuous. At some locations, cultured tidelands extend
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with only occasional interruption along extended lengths of the nearshore. At other locations,
cultured tidelands are interspersed along shorelines that support a range of other uses (residential,
recreational, etc.). Where cultured tidelands extend with only occasional interruption,
interspersed uncultured areas may experience direct or indirect effects, and are therefore
considered part of the action area.
The action area includes approximately 12,000 acres of designated bull trout critical habitat,
mostly located in Grays Harbor (approximately 4,000 acres), the north Puget Sound
approximately 5,000 acres), and Hood Canal (approximately 3,000 acres) (Corps 2015
Appendix H, Figures H-1 through H-8) (Table 4, p. 77). South of Tacoma, designated bull trout
critical habitat only extends as far as the Nisqually River delta. No portion of Willapa Bay has
been designated as critical habitat for the bull trout.
Within the action area, the current condition of designated bull trout critical habitat varies
considerably. Current conditions reflect natural variability, patterns of disturbance and recovery
from both natural and man-made events, and the effects of earlier and concurrent, unrelated
activities occurring in the same nearshore environments and watersheds.
Where shellfish activities have been conducted for many years and will continue to impact
habitat conditions, most of the action area cannot be regarded as pristine in its current state.
Also, at many locations this habitat exhibits the pervasive effects of shoreline development and
alteration. Armored and hardened shorelines, diking and filling of marine and estuarine areas,
and overwater structures are all characteristic of the action area. At many locations these
features impair important natural processes that create and maintain functional nearshore marine
habitat for bull trout and marine forage fish. Natural nearshore habitat complexity is either
mildly or moderately impaired throughout much of the action area. The same can be said for the
condition of bull trout prey resources. At some locations either or both of these functions may be
severely impaired.
An earlier portion of this Opinion identified the PCEs of designated bull trout critical habitat and
described their baseline condition in the action area (see Environmental Baseline, Current
Condition in the Action Area, Bull Trout Critical Habitat). This portion of the Opinion discusses
the foreseeable direct and indirect effects of the action, with reference to the specific PCEs which
are present and may be affected.
Note: New critical habitat regulations (81 FR 7214; February 11, 2016) use PBFs rather than
PCEs. The shift in terminology does not change the approach used in conducting a “destruction
or adverse modification” analysis, which is the same regardless of whether the original
designation identified PCEs, PBFs, or essential features. References here to PCEs should be
viewed as synonymous with PBFs.]
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The action area includes nearshore marine environments providing five of the nine PCEs of
designated bull trout critical habitat (50 FR 63898; October 18, 2010):
2) Migration habitats with minimal physical, biological, or water quality impediments between
spawning, rearing, overwintering, and freshwater and marine foraging habitats, including but
not limited to permanent, partial, intermittent, or seasonal barriers.
Within the action area this PCE is generally only mildly impaired and still functions well.
However, in locations where armored and hardened shorelines, marine and estuarine fill, and
overwater structures are more pervasive, this PCE is moderately or severely impaired.
Shellfish activities result in measurable, temporary impacts to water quality. Where these
temporary impacts to water quality are concerned, our primary focus is on four biologically and
behaviorally relevant water quality parameters: turbidity, DO, BOD, and nutrients (e.g., nitrogen
and ammonium). ENVIRON International Corp. (2011, p. 41) has observed that water quality
conditions typically reflect the pervasive influence of oceanic conditions, residence time, and
other human activities in these same nearshore environments and watersheds. Forrest et al.
2009, p. 5) have observed, “…the potential for adverse water quality-related effects … is low,
which is perhaps not surprising considering that intertidal farm sites are substantially or
completely flushed on every tidal cycle.” Shellfish activities result in temporary effects to water
quality that are localized, limited in physical extent, and low intensity.
During 2008, the Service evaluated the effects of commercial geoduck harvest. That review
indicated minor and small-scale effects resulting from elevated turbidity and sedimentation
during harvest activities. The described impacts to designated bull trout critical habitat included
temporary elevation of sediment levels, and temporary disruption of migratory corridors from
diver and vessel activities (USFWS 2009b, p. 134).
Shellfish culturing and harvest activities result in temporary impacts to the sound and visual
environment. Most activities associated with ground-based culturing are conducted as bouts of
intermittent activity, with each bout lasting a few hours. While some activities may be relieved
or partially relieved of strict timing constraints, many still target specific tidal elevations and
therefore proceed as bouts of intermittent activity. Effects to the sound and visual environment
are temporal and limited in physical extent, intensity, and duration.
Placement of culturing equipment and materials on and over the bed is the most obvious,
persistent or long-term effect to nearshore migratory habitat. These materials take a variety of
forms, including nets, bags, racks, stakes, longlines, and tubes. Culturing equipment and
materials placed on and over the bed, and the intensively cultured shellfish that they promote
many of which are non-native species), do modify habitat, and/or create new habitat types (or
habitat variants). The Service has concluded that regulated shellfish activities in Washington
State are likely to directly or indirectly affect more than 6,000 acres of submerged aquatic
vegetation (native eelgrass and rooted kelp) located within or near designated bull trout critical
habitat, mostly in Grays Harbor and the north Puget Sound (Table 4, p. 77; Table 8, p. 156).
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Although the Corps has included a number of conservation measures addressing the security of
culturing equipment (Corps 2015, pp. 49-53) and many growers and farm operators invest
significant time and resources to prevent the loss of equipment, the Service is aware of
information documenting instances where equipment has become dislodged and moved from
farmed areas by wind and waves (see Temporary Stressors, Resulting Exposures, and Effects;
Physical Entrapment and Stranding). However, to our knowledge, there have been no reported
instances of bull trout becoming entrapped or entangled in shellfish culturing equipment, and no
reported instances of bull trout becoming stranded within pools impounded by or around
shellfish culturing equipment.
Considering the size and mobility of subadult and adult anadromous bull trout, the Service
believes that the incidence rate of bull trout entanglement, entrapment, and/or stranding must be
very low across the whole of the industry. Aside from the rare instances where individual bull
trout become entangled, entrapped, or stranded, the Service expects that these structures and
materials do not generally pose a barrier to migration, or hinder or prevent bull trout movement
and migration though nearshore marine habitats.
The Service concludes that the proposed action, consisting of the issuance of Corps permits and
permit verifications for continuing and proposed, new shellfish activities and farms, will not
permanently degrade PCE #2 or prevent nearshore migratory corridors from functioning as
intended. The proposed action will result in temporary impacts to water quality and the sound
and visual environment, but these effects will be limited in physical extent, intensity, and
duration, and are not likely to measurably impair the current function of nearshore migratory
corridors. The proposed action will cause or contribute to losses of submerged aquatic
vegetation. However, we conclude that permanent losses of submerged aquatic vegetation,
production, and function will not be typical of most outcomes. The Service expects no
measurable adverse effects to PCE #2.
3) An abundant food base, including terrestrial organisms of riparian origin, aquatic
macroinvertebrates, and forage fish.
Within the action area this PCE is either mildly or moderately impaired. Across most portions of
the action area, it would appear that both salmonid and marine forage fish prey resources are
well below historic, long-term peaks of production. However, year-to-year and geographic
variability is significant and not easy to generalize with recognizable trends.
Shellfish culturing and harvesting have direct and indirect effects to nearshore marine habitat
structure, function, and productivity. These effects may have significance for how well these
habitats support the essential behaviors and needs of listed species, including bull trout that
forage in the marine environment.
The Service has concluded that regulated shellfish activities in Washington State are likely to
directly or indirectly affect more than 6,000 acres of submerged aquatic vegetation (native
eelgrass and rooted kelp) located within or near designated bull trout critical habitat, mostly in
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Grays Harbor and the north Puget Sound (Table 4, p. 77; Table 8, p. 156). The Service expects
that there will be measurable losses of native eelgrass, rooted kelp, and associated ecosystem
services, including habitat functions and prey productivity.
Interactions between benthic/epibenthic communities and shellfish activities are complex and not
easily characterized with simple generalizations. Culturing equipment and materials, and the
intensively cultured shellfish that they promote, create new habitat types. Cultured shellfish are
themselves ecosystem engineering or niche constructing species, and the habitat value of the
biogenic structures they create is evident.
Some shellfish culturing and harvesting activities have measurable, persistent or long-term
effects to substrates, submerged aquatic vegetation, and benthic/epibenthic community structure
and composition. Unfortunately, there are relatively few studies that provide relevant and
specific information to describe interactions between shellfish activities and the prey resources
that are considered most important to marine foraging bull trout (e.g., marine forage fish,
juvenile salmonids).
Whereas, we have already concluded that (1) shellfish activities resulting in physical damage to
submerged aquatic vegetation will result in losses of production and associated ecosystem
services (including habitat functions), and (2) some activities (e.g., mechanical leveling,
harrowing, and dredge harvesting) will in many cases either interfere with or reset normal
patterns of infaunal succession and development, available information regarding predator-prey
relationships, and prey productivity and availability, is more ambiguous and therefore also less
compelling. While there is some information to indicate a decline in the health of marine forage
fish resources in the action area (see Environmental Baseline, Willapa Bay, Grays Harbor, Puget
Sound and Hood Canal), and the decline of many salmonid populations is both obvious and
widespread, there is little or no information attributing those conditions to shellfish activities
specifically.
We conclude that regulated shellfish activities in Washington State, specifically those for which
this Opinion provides programmatic coverage, are likely to directly or indirectly affect more than
5,500 acres of mapped Pacific herring spawning habitat, and more than 1,500 acres of mapped
Pacific sand lance and surf smelt spawning habitat (Table 9, p. 177). This includes more than
3,600 acres located within or near designated bull trout critical habitat, mostly in the north Puget
Sound and Hood Canal (Table 4, p. 77; Table 9, p. 177).
Marine forage fish spawning habitat experiences loss and recovery on continuing farms. Marine
forage fish spawning habitat will also experience loss and recovery when fallow farms or farm
footprints are re-cultivated and put into production. The Service acknowledges that fallow farm
footprints are extensively co-located with marine forage fish habitat; most extensively and
importantly for bull trout, in the north Puget Sound (approximately 2,239 acres) (Corps 2015, p.
95).
The Service expects there will be measurable, adverse effects to PCE #3 associated with losses
of marine forage fish spawning habitat and production. However, the Service also expects that
most of these impacts and measurable losses will be temporary. In most cases, and in most
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settings where shellfish culturing and harvesting activities result in temporal losses of marine
forage fish production, we expect that much of the lost function and production will be recovered
over time.
The weight of available evidence suggests and leads the Service to conclude that permanent
losses of marine forage fish spawning habitat and production will be uncommon, and not typical
of most outcomes. The Service does not expect that permanent losses attributable to shellfish
activities will be measurable at the scale of the five geographic sub-areas (Willapa Bay, Grays
Harbor, Hood Canal, south and north Puget Sound), at the scale of any whole waterbody (e.g.,
Willapa Bay), or sub-basin (e.g., Totten Inlet, Samish Bay).
The Service concludes that the proposed action, consisting of the issuance of Corps permits and
permit verifications for continuing and proposed, new shellfish activities and farms, will not
permanently degrade PCE #3 or prevent nearshore marine critical habitat from functioning as
intended. The proposed action will result in instances of significant temporal loss of marine
forage fish spawning habitat and production (temporary adverse effects to PCE #3). We expect
that these temporal losses will rarely, if ever, occur at a scale, or with a duration or severity,
sufficient to measurably reduce the quality or availability of bull trout prey resources in any
portion of the action area.
4) Complex river, stream, lake, reservoir, and marine shoreline aquatic environments, and
processes that establish and maintain these aquatic environments, with features such as large
wood, side channels, pools, undercut banks and unembedded substrates, to provide a variety of
depths, gradients, velocities, and structure.
Within the action area this PCE is moderately impaired, but still functions. At some locations,
where armored and hardened shorelines, marine and estuarine fill, and overwater structures are
more pervasive, and where important natural processes that create and maintain functional
nearshore marine habitat are impeded, this PCE is severely impaired.
Shellfish culturing and harvesting have direct and indirect effects to nearshore marine habitat
structure, function, and productivity. These effects may have significance for how well these
habitats support the essential behaviors and needs of listed species, including bull trout that
forage in the marine environment.
Placement of culturing equipment and materials on and over the bed is an obvious, persistent or
long-term effect to nearshore habitat structure and complexity. These materials take a variety of
forms, including nets, bags, racks, stakes, longlines, and tubes. Culturing equipment and
materials placed on and over the bed, and the intensively cultured shellfish that they promote
many of which are non-native species), do modify habitat, and/or create new habitat types (or
habitat variants). Cultured shellfish are themselves ecosystem engineering or niche constructing
species, and the habitat value of the biogenic structures they create is evident.
Interactions between submerged aquatic vegetation (native eelgrass, rooted kelp) and shellfish
activities are complex and not easily characterized with simple generalizations. These
interactions include competition for space, competition for light (or shading), and physical
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damage that results from some activities, practices, and techniques. However, not all of these
interactions are detrimental to the health of native eelgrass and rooted kelp. For instance,
shellfish culturing provides a source of nutrient enhancement, which supports plant growth and
vigor, and frequently improves water quality. The variety of factors influencing eelgrass
recovery suggests the potential for significant site-by-site and temporal variability. Culturing
methods and techniques have variable effects to patterns of eelgrass disturbance, recovery, and
persistence, but the majority of these temporal impacts are not likely to be persistent at the
estuarine landscape scale.
The Service has concluded that regulated shellfish activities in Washington State are likely to
directly or indirectly affect more than 6,000 acres of submerged aquatic vegetation (native
eelgrass and rooted kelp) located within or near designated bull trout critical habitat, mostly in
Grays Harbor and the north Puget Sound (Table 4, p. 77; Table 8, p. 156). The Service expects
that there will be measurable losses of native eelgrass, rooted kelp, and associated ecosystem
services, including habitat functions.
Native eelgrass, rooted kelp, and other submerged aquatic vegetation experience loss and
recovery on continuing farms. Native eelgrass and other submerged aquatic vegetation will also
experience loss and recovery when fallow farms or farm footprints are re-cultivated and put into
production. The Service acknowledges that chronic suppression of eelgrass growth and
production may be a reality on some farms. We also acknowledge that fallow farm footprints are
extensively co-located with submerged aquatic vegetation; most extensively and importantly for
bull trout, in the north Puget Sound (approximately 2,239 acres) (Corps 2015, p. 95).
The Service concludes that the proposed action, consisting of the issuance of Corps permits and
permit verifications for continuing and proposed, new shellfish activities and farms, will not
permanently degrade PCE #4 or prevent nearshore marine critical habitat from functioning as
intended. The weight of available evidence suggests and leads the Service to conclude that
permanent losses of submerged aquatic vegetation (native eelgrass and rooted kelp), production,
and function will not be typical of most outcomes. While it is likely there will be instances
where limited, permanent losses (or chronic suppression) are attributable to shellfish activities,
the Service expects that permanent losses will be relatively small (e.g., a fraction of the
submerged aquatic vegetation resource) at the scale of the five geographic sub-areas (Willapa
Bay, Grays Harbor, Hood Canal, south and north Puget Sound), at the scale of any whole
waterbody (e.g., Willapa Bay), or the sub-basin (e.g., Totten Inlet, Samish Bay).
The proposed action will have spatially and temporally adverse effects to PCE #4. The action
will result in instances of significant loss of submerged aquatic vegetation and associated habitat
function. The action will reduce natural forms of nearshore marine habitat structure and
complexity at some locations.
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5) Water temperatures ranging from 2 to 15 °C (36 to 59 °F), with adequate thermal refugia
available for temperatures that exceed the upper end of this range. Specific temperatures within
this range will depend on bull trout life-history stage and form; geography; elevation; diurnal
and seasonal variation; shading, such as that provided by riparian habitat; stream flow; and
local groundwater influence.
Conditions are not degraded. Within the action area this PCE is fully functioning, with little or
no significant impairment.
The proposed action will not cause or contribute to measurable increases in surface water
temperature, or degrade thermal refugia within the action area. We conclude that foreseeable
effects to PCE #5 will not be measurable, and are therefore considered insignificant. Within the
action area this PCE will retain its current level of function (fully functioning).
8) Sufficient water quality and quantity such that normal reproduction, growth, and survival are
not inhibited.
Water and sediment quality conditions are generally suitable and adequately functioning, though
some portions of the action area exhibit mild or moderate impairment. Shellfish culturing and
harvesting activities result in measurable, temporary impacts to water quality. Where these
temporary impacts to water quality are concerned, our primary focus is on four biologically and
behaviorally relevant water quality parameters: turbidity, DO, BOD, and nutrients (e.g., nitrogen
and ammonium). ENVIRON International Corp. (2011, p. 41) has observed that water quality
conditions typically reflect the pervasive influence of oceanic conditions, residence time, and
other human activities in these same nearshore environments and watersheds. Forrest et al.
2009, p. 5) have observed, “…the potential for adverse water quality-related effects … is low,
which is perhaps not surprising considering that intertidal farm sites are substantially or
completely flushed on every tidal cycle.” Shellfish activities result in temporary effects to water
quality that are localized, limited in physical extent, and low intensity.
During 2008, the Service evaluated the effects of commercial geoduck harvest. That review
indicated minor and small-scale effects resulting from elevated turbidity and sedimentation
during harvest activities. The described impacts to designated bull trout critical habitat included
temporary elevation of sediment levels (USFWS 2009b, p. 134).
Bivalves and other filter-feeding shellfish, whether occurring naturally or in farmed/cultured
settings, provide important benefits in the form of ecosystem services. The Service expects that
shellfish activities will generally, and in the majority of cases, provide long-term benefits in the
form of improved water quality and sequestration of carbon and nutrients. These ecosystem
services may be important as a means to control and prevent the effects of excess nutrient
additions occurring elsewhere in the contributing watersheds and may lessen or counteract the
potential for climate-induced ocean acidification and hypoxia.
Ecological carrying capacity is a useful concept for thinking about the possible erosion or loss of
ecosystem services, and resulting consequences, under a scenario of pervasive and extremely
high shellfish culturing densities. While we do not deny the role or significance of social
carrying capacity and public acceptance, those aspects are beyond the scope of the Service’s
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considerations, and therefore we limit our consideration of carrying capacity to the physical and
ecological elements. Available information leads us to conclude it is unlikely that the projected
20-year future growth of the industry will approach or exceed ecological carrying capacity
within the action area.
The Service concludes that the proposed action, consisting of the issuance of Corps permits and
permit verifications for continuing and proposed, new shellfish activities and farms, will not
degrade PCE #8. The proposed action will result in temporary impacts to water quality, but
these effects will be limited in physical extent, intensity, and duration, and are not likely to
measurably impair the current function of PCE #8. The proposed action will provide significant,
measurable long-term benefits in the form of improved water quality and sequestration of carbon
and nutrients. The Service expects no measurable adverse effects to the function of PCE #8.
Within the action area this PCE will retain its current level of function (generally suitable and
adequately functioning).
Summary
The proposed action will have measurable adverse effects to PCE #3 (food base, including
marine forage fish) and PCE #4 (complex marine shoreline aquatic environments and
processes). The Service expects that any permanent adverse effects to PCE #4 will be limited in
scale. The Service concludes that the proposed action, consisting of the issuance of Corps
permits and permit verifications for continuing and proposed, new shellfish activities and farms,
will not prevent designated nearshore marine critical habitat from functioning as intended.
CUMULATIVE EFFECTS
Cumulative effects include the effects of future State, tribal, local, or private actions that are
reasonably certain to occur in the action area considered in this Opinion. Future federal actions
that are unrelated to the proposed action are not considered in this section because they require
separate consultation pursuant to section 7 of the ESA.
Ongoing non-federal actions in the action area include implementation of State shellfish and
angling regulations, State hatchery programs, and State, tribal, local, and private habitat
restoration programs (i.e., those not supported by federal funds). Future local actions will
include planned growth, development, and re-development consistent with land use and growth
management plans. Future State and local actions may include implementation of TMDLs and
watershed-scale water quality improvement programs. Taken as a whole, the foreseeable future
State, tribal, local, and private actions may have both beneficial effects and adverse effects to the
marbled murrelet, bull trout, and designated bull trout critical habitat.
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The State’s programs implementing shellfish and angling regulations provide for sustainable,
fish- and wildlife-related recreational and commercial opportunities, while also ensuring long-
term protection and enhancement of marine and estuarine resources. Related to these programs,
the State administers more than two dozen marine protected areas in Puget Sound (conservation
areas, marine preserves, and exclusion zones) for the protection and preservation of sensitive
species and their habitats.
The State’s hatchery programs produce fish for harvest and support large and regionally
important recreational fisheries. Hatchery programs also support wild stock research and
conservation. The State is currently working with federal, tribal, and private managers and
scientists to examine hatchery operations and determine what structural and operational changes
are necessary to ensure that hatchery programs can continue to meet these dual objectives. Key
issues include genetic introgression, competition, and disease transmission between hatchery-
reared and wild stocks.
Ongoing non-federal actions also include State, tribal, local, and private habitat restoration
programs. These programs are directed at protecting, enhancing, and restoring marine and
estuarine habitats and the native fish and wildlife populations they support. Habitat restoration
programs also provide for the advancement of marine and estuarine science, refinement of
applied techniques, and public participation and education.
Future local actions will include planned growth, development, and re-development consistent
with land use and growth management plans. Additional urban and suburban residential,
commercial, and industrial development (or redevelopment) is certain to occur in the action area.
Over the long-term, planned growth consistent with land use and growth management plans will
result in additional effects to watershed conditions and functions, water and sediment quality,
and nearshore marine and estuarine habitat conditions. However, with effective implementation
of Shoreline Management Programs and Critical Area Ordinances, and in conjunction with State
and local (city, county) environmental permit requirements (including those requirements
established for the protection of wetlands and for the regulation of private and municipal
stormwater discharges), effects to ecological functions should be reduced. Future State and local
actions may also include implementation of TMDLs and watershed-scale water quality
improvement programs.
Taken as a whole, the foreseeable future State, tribal, local, and private actions may have both
beneficial effects and adverse effects to the marbled murrelet, bull trout, and designated bull
trout critical habitat. Some of these actions (e.g., effective implementation of land use and
growth management plans, TMDL clean-up plans, and habitat restoration programs) will be
essential, and must be successful, to ensure that the action area will continue to provide for the
conservation and recovery of the bull trout and marbled murrelet.
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INTEGRATION AND SYNTHESIS OF EFFECTS (BULL TROUT)
The Integration and Synthesis section is the final step in assessing the risk posed to species and
critical habitat as a result of implementing the proposed action. In this section, we add the
effects of the action and cumulative effects to the status of the species and critical habitat, and
the environmental baseline, to formulate our Opinion as to whether the proposed action is likely
to: (1) appreciably reduce the likelihood of both survival and recovery of the species in the wild
by reducing its numbers, reproduction, or distribution; or (2) reduce the value of designated
critical habitat for the conservation of the species.
Shellfish culturing and harvesting activities result in measurable, temporary impacts to water
quality. Where these temporary impacts to water quality are concerned, our primary focus is on
four biologically and behaviorally relevant water quality parameters: turbidity, DO, BOD, and
nutrients (e.g., nitrogen and ammonium). Shellfish activities result in temporary impacts that are
localized, limited in physical extent, and low intensity.
Shellfish provide important benefits in the form of ecosystem services. The Service expects that
shellfish activities will, in the majority of cases, provide significant long-term benefits in the
form of improved water quality and sequestration of carbon and nutrients. These ecosystem
services may be important as a means to control and prevent the effects of excess nutrient
additions occurring elsewhere in the contributing watersheds. These ecosystem services may
also lessen or counteract the potential for climate-induced ocean acidification and hypoxia.
Bull trout, their habitat, and prey resources will be exposed to shellfish activities, including
foreseeable temporary and long-term impacts to water and sediment quality. However, with
successful implementation of the included conservation measures, we conclude that shellfish
activities will not have adverse effects to water or sediment quality, and related direct and
indirect effects to bull trout and designated bull trout critical habitat will be insignificant, or
measurable and beneficial.
Shellfish culturing and harvesting activities result in temporary impacts to the sound and visual
environment. Most effects are temporal and limited in both physical extent and duration.
Taking into consideration both the geographic setting (i.e., an open water marine environment),
and the intensity and duration of exposures, we conclude that temporary impacts to the sound
and visual environment will not significantly disrupt normal bull trout behaviors (i.e., the ability
to successfully feed, move, and/or shelter), and are therefore considered insignificant.
Shellfish activities frequently involve or require placement of culturing equipment and materials
on and over the bed (e.g., nets, bags, racks, stakes, longlines, and tubes). These materials are not
generally an impediment to movement. To our knowledge, there have been no reported
instances of bull trout becoming entrapped or entangled in shellfish culturing equipment. To our
knowledge, there have been no reported instances of bull trout becoming stranded behind berms
or dikes, or within pools impounded by or around shellfish culturing equipment.
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Considering the size and mobility of subadult and adult anadromous bull trout, the Service
believes that the incidence rate of entanglement, entrapment, and/or stranding must be very low
across the whole of the industry. However, shellfish farms occupy tens of thousands of
nearshore marine acres in Washington State, and overlap significantly with habitats that are
regularly used by anadromous bull trout (e.g., approximately 12,000 acres of designated bull
trout critical habitat). Therefore, the Service concludes with reasonable certainty that there will
be limited instances of individual bull trout injury or mortality over the 20-year term of the
programmatic (2016 to 2036). We expect that instances of bull trout injury or mortality will
occur more frequently in the north Puget Sound, where anadromous bull trout are relatively more
abundant, and will occur less frequently in the other four geographic sub-areas (Willapa Bay,
Grays Harbor, Hood Canal, and south Puget Sound). The Service expects that a maximum of six
6) subadult or adult bull trout will be injured or killed in the north Puget Sound over the 20-year
term of the programmatic. We expect that a maximum of two (2) subadult or adult bull trout will
be injured or killed in each of the other four geographic sub-areas (Willapa Bay, Grays Harbor,
Hood Canal, and south Puget Sound) over the 20-year term of the programmatic (2016 to 2036).
Shellfish culturing and harvesting activities have direct and indirect effects to nearshore marine
habitat structure, function, and productivity. These effects may have significance for how well
these habitats support the essential behaviors and needs of listed species, including bull trout that
forage in the marine environment. The Service expects there will be measurable losses of native
eelgrass and rooted kelp production. We expect that there will be measurable losses of
associated ecosystem services, including habitat functions and prey production that are important
to bull trout. The Service expects there will be measurable, temporal losses of marine forage fish
spawning habitat and production.
However, the Service also expects that most of these impacts and measurable losses will be
temporary. In most cases, and in most settings, we expect that much of the lost production and
function will be recovered over time. The weight of available evidence suggests and leads the
Service to conclude that permanent losses of submerged aquatic vegetation, production, and
function will not be typical of most outcomes.
The weight of available evidence suggests and leads the Service to conclude that permanent
losses of marine forage fish spawning habitat and production will be uncommon, and not typical
of most outcomes. The Service does not expect that permanent losses attributable to shellfish
activities will be measurable at the scale of the five geographic sub-areas (Willapa Bay, Grays
Harbor, Hood Canal, south and north Puget Sound), at the scale of any whole waterbody (e.g.,
Willapa Bay), or sub-basin (e.g., Totten Inlet, Samish Bay). We expect that these temporal
losses will rarely, if ever, occur at a scale, or with a duration or severity, sufficient to measurably
reduce the quality or availability of bull trout prey resources in any portion of the action area.
Ecological carrying capacity is a useful concept for thinking about the possible erosion or loss of
ecosystem services, and resulting consequences, under a scenario of pervasive and extremely
high shellfish culturing densities. While we do not deny the role or significance of social
carrying capacity and public acceptance, those aspects are beyond the scope of the Service’s
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considerations. Available information leads us to conclude it is unlikely that the projected
20-year future growth of the industry will approach or exceed ecological carrying capacity
within the action area.
Bull trout will be exposed to the measurable, persistent and long-term effects of regulated
shellfish activities. The Service expects that persistent and long-term stressors and exposures
resulting directly and indirectly from continuing and proposed, new shellfish activities and farms
will in some instances have adverse effects to bull trout. However, we are not able to
demonstrate that exposures are reasonably certain to result in a significant disruption of normal
bull trout behaviors (i.e., the ability to successfully feed, move, and/or shelter). The best
available information is currently insuffcient to demonstrate that persistent and long-term
stressors and exposures are reasonably certain to result in measurable adverse effects to
energetics, growth, fitness, or long-term survival (injury or mortality).
The Service concludes that the proposed action, consisting of the issuance of Corps permits and
permit verifications for continuing and proposed, new shellfish activities and farms, will not
appreciably reduce or diminish the current, known distribution of anadromous bull trout in
Washington’s inland marine waters, and will not appreciably reduce or diminish bull trout
numbers (abundance) or reproduction (productivity) at the scale of the local populations, core
areas, or coterminous range. The anticipated direct and indirect effects of the action, combined
with the effects of interrelated and interdependent actions, and the cumulative effects associated
with future State, tribal, local, and private actions will not appreciably reduce the likelihood of
survival and recovery of the species. The anticipated direct and indirect effects of the action
permanent and temporary) will not measurably reduce bull trout reproduction, numbers, or
distribution at the scale of the core areas or Coastal Recovery Unit. The anticipated direct and
indirect effects of the action will not alter the status of the bull trout at the scale of the Coastal
Recovery Unit or coterminous range.
The proposed action will have measurable direct and indirect effects to the PCEs of designated
bull trout critical habitat. The proposed action will have measurable, temporary adverse effects
to PCE #3 (food base, including marine forage fish) and PCE #4 (complex marine shoreline
aquatic environments and processes). The Service does not expect permanent adverse effects to
any of the PCEs. The Service concludes that the proposed action, consisting of the issuance of
Corps permits and permit verifications for continuing and proposed, new shellfish activities and
farms, will not prevent designated nearshore marine critical habitat from functioning as intended.
Within the action area, the PCEs of designated bull trout critical habitat will remain functional,
and designated critical habitat will continue to serve its intended conservation role. The
anticipated direct and indirect effects of the action, combined with the effects of interrelated and
interdependent actions, and the cumulative effects associated with future State, tribal, local, and
private actions will not prevent the PCEs of critical habitat from being maintained, and will not
degrade the current ability to establish functioning PCEs at the scale of the action area. Critical
habitat within the action area will continue to serve the intended conservation role for the species
at the scale of the core areas, Coastal Recovery Unit, and coterminous range.
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INTEGRATION AND SYNTHESIS OF EFFECTS (MARBLED MURRELET)
The Integration and Synthesis section is the final step in assessing the risk posed to species and
critical habitat as a result of implementing the proposed action. In this section, we add the
effects of the action and cumulative effects to the status of the species and critical habitat, and
the environmental baseline, to formulate our Opinion as to whether the proposed action is likely
to: (1) appreciably reduce the likelihood of both survival and recovery of the species in the wild
by reducing its numbers, reproduction, or distribution; or (2) reduce the value of designated
critical habitat for the conservation of the species.
Shellfish culturing and harvesting activities result in measurable, temporary impacts to water
quality. Where these temporary impacts to water quality are concerned, our primary focus is on
four biologically and behaviorally relevant water quality parameters: turbidity, DO, BOD, and
nutrients (e.g., nitrogen and ammonium). Shellfish activities result in temporary impacts that are
localized, limited in physical extent, and low intensity.
Shellfish provide important benefits in the form of ecosystem services. The Service expects that
shellfish activities will, in the majority of cases, provide significant long-term benefits in the
form of improved water quality and sequestration of carbon and nutrients. These ecosystem
services may be important as a means to control and prevent the effects of excess nutrient
additions occurring elsewhere in the contributing watersheds. These ecosystem services may
also lessen or counteract the potential for climate-induced ocean acidification and hypoxia.
Marbled murrelets, their habitat, and prey resources will be exposed to shellfish activities,
including foreseeable temporary and long-term impacts to water and sediment quality. However,
with successful implementation of the included conservation measures, we conclude that
shellfish activities will not have adverse effects to water or sediment quality, and related direct
and indirect effects to marbled murrelets will be insignificant, or measurable and beneficial.
Shellfish culturing and harvesting activities result in impacts to the sound and visual
environment. Most effects are temporal and limited in both physical extent and duration.
Taking into consideration both the geographic setting (i.e., an open water marine environment),
and the intensity and duration of exposures, temporary sound and visual disturbance resulting
from shellfish activities is unlikely to significantly disrupt normal marbled murrelet behaviors
i.e., the ability to successfully feed, move, and/or shelter). The Service concludes that these
temporary exposures will not result in direct injury or mortality, a significant disruption of
normal behaviors (i.e., the ability to successfully feed, move, and/or shelter), or measurable
adverse effects to energetics, growth, fitness, or long-term survival. However, these general
conclusions regarding shellfish activities do not extend to the practice of intentionally hazing
wildlife. Growers and farm operators who engage in intentional wildlife hazing should educate
themselves and understand their liabilities under the Migratory Bird Treaty Act, Bald and Golden
Eagle Protection Act, and ESA (see Temporary Stressors, Resulting Exposures, and Effects,
Intentional Hazing of Wildlife).
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Shellfish activities frequently involve or require placement of culturing equipment and materials
on and over the bed (e.g., nets, bags, racks, stakes, longlines, and tubes). These materials are not
generally an impediment to movement. To our knowledge, there have been no reported
instances of marbled murrelets becoming entrapped or entangled in shellfish culturing
equipment. Available information suggests that exposure of marbled murrelets is likely to occur
very infrequently, if at all. We conclude that exposures are not discountable (“extremely
unlikely”). However, the Service is not able to demonstrate that potential exposures are
reasonably certain to result in a significant disruption of normal marbled murrelet behaviors (i.e.,
the ability to successfully feed, move, and/or shelter) or instances of direct injury or mortality.
Shellfish culturing and harvesting activities have direct and indirect effects to nearshore marine
habitat structure, function, and productivity. These effects may have significance for how well
these habitats support the essential behaviors and needs of listed species, including marbled
murrelets. The Service expects there will be measurable losses of native eelgrass and rooted kelp
production. We expect that there will be measurable losses of associated ecosystem services,
including habitat functions and prey production that are important to bull trout. The Service
expects there will be measurable, temporal losses of marine forage fish spawning habitat and
production.
However, the Service also expects that most of these impacts and measurable losses will be
temporary. In most cases, and in most settings, we expect that much of the lost production and
function will be recovered over time. The weight of available evidence suggests and leads the
Service to conclude that permanent losses of submerged aquatic vegetation, production, and
function will not be typical of most outcomes.
The weight of available evidence suggests and leads the Service to conclude that permanent
losses of marine forage fish spawning habitat and production will be uncommon, and not typical
of most outcomes. The Service does not expect that permanent losses attributable to shellfish
activities will be measurable at the scale of the five geographic sub-areas (Willapa Bay, Grays
Harbor, Hood Canal, south and north Puget Sound), at the scale of any whole waterbody (e.g.,
Willapa Bay), or sub-basin (e.g., Totten Inlet, Samish Bay). We expect that these temporal
losses will rarely, if ever, occur at a scale, or with a duration or severity, sufficient to measurably
reduce the quality or availability of marbled murrelet prey resources in any portion of the action
area.
Ecological carrying capacity is a useful concept for thinking about the possible erosion or loss of
ecosystem services, and resulting consequences, under a scenario of pervasive and extremely
high shellfish culturing densities. While we do not deny the role or significance of social
carrying capacity and public acceptance, those aspects are beyond the scope of the Service’s
considerations. Available information leads us to conclude it is unlikely that the projected 20-
year future growth of the industry will approach or exceed ecological carrying capacity within
the action area.
Marbled murrelets will be exposed to the measurable, persistent and long-term effects of
regulated shellfish activities. The Service expects that persistent and long-term stressors and
exposures resulting directly and indirectly from continuing and proposed, new shellfish activities
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and farms will in some instances have adverse effects to marbled murrelets. However, we are
not able to demonstrate that exposures are reasonably certain to result in a significant disruption
of normal marbled murrelet behaviors (i.e., the ability to successfully feed, move, and/or shelter).
The best available information is currently insufficient to demonstrate that persistent and long-
term stressors and exposures are reasonably certain to result in measurable adverse effects to
energetics, growth, fitness, or long-term survival (injury or mortality).
The Service concludes that the proposed action, consisting of the issuance of Corps permits and
permit verifications for continuing and proposed, new shellfish activities and farms, will not
appreciably reduce or diminish the current, known distribution of the marbled murrelet in
Washington’s inland marine waters, and will not appreciably reduce or diminish marbled
murrelet numbers (abundance) or reproduction (productivity) at the scale of the action area,
Conservation Zones 1 (Puget Sound) and 2 (Western Washington Coast Range), or rangewide.
The anticipated direct and indirect effects of the action, combined with the effects of interrelated
and interdependent actions, and the cumulative effects associated with future State, tribal, local,
and private actions will not appreciably reduce the likelihood of survival and recovery of the
species. The anticipated direct and indirect effects of the action (permanent and temporary) will
not measurably reduce marbled murrelet reproduction, numbers, or distribution at the scale of
action area, Conservation Zone 1, or Conservation Zone 2. The anticipated direct and indirect
effects of the action will not alter the status of the marbled murrelet at the scale of Conservation
Zone 1, Conservation Zone 2, or rangewide.
CONCLUSION (BULL TROUT AND DESIGNATED CRITICAL HABITAT)
The Service has reviewed the current rangewide status of the bull trout, the environmental
baseline for the action area, the direct and indirect effects of the proposed action, the effects of
interrelated and interdependent actions, and the cumulative effects that are reasonably certain to
occur in the action area. It is the Service’s Biological Opinion that the action, as proposed, will
not appreciably reduce the likelihood of survival and recovery of the bull trout in the wild. The
action, as proposed, is not likely to jeopardize the continued existence of the bull trout. It is the
Service’s Biological Opinion that the action, as proposed, will not destroy or adversely modify
designated bull trout critical habitat.
CONCLUSION (MARBLED MURRELET)
The Service has reviewed the current rangewide status of the marbled murrelet, the
environmental baseline for the action area, the direct and indirect effects of the proposed action,
the effects of interrelated and interdependent actions, and the cumulative effects that are
reasonably certain to occur in the action area. It is the Service’s Biological Opinion that the
action, as proposed, will not appreciably reduce the likelihood of survival and recovery of the
marbled murrelet in the wild. The action, as proposed, is not likely to jeopardize the continued
existence of the marbled murrelet.
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INCIDENTAL TAKE STATEMENT
Section 9 of the ESA and federal regulation pursuant to section 4(d) of the ESA prohibit the take
of endangered and threatened species, respectively, without special exemption. Take is defined
as to harass, harm, pursue, hunt, shoot, wound, kill, trap, capture, or collect, or to attempt to
engage in any such conduct. Harm is defined by the Service as an act which actually kills or
injures wildlife. Such an act may include significant habitat modification or degradation where it
actually kills or injures wildlife by significantly impairing essential behavior patterns, including
breeding, feeding, or sheltering (50 CFR 17.3). Harass is defined by the Service as an
intentional or negligent act or omission which creates the likelihood of injury to wildlife by
annoying it to such an extent as to significantly disrupt normal behavioral patterns which
include, but are not limited to, breeding, feeding, or sheltering (50 CFR 17.3). Incidental take is
defined as take that is incidental to, and not the purpose of, the carrying out of an otherwise
lawful activity. Under the terms of section 7(b)(4) and section 7(o)(2), taking that is incidental to
and not intended as part of the agency action is not considered to be prohibited taking under the
ESA provided that such taking is in compliance with the terms and conditions of this Incidental
Take Statement.
The measures described below are non-discretionary, and must be undertaken by the Corps so
that they become binding conditions of any grant or permit issued to Corps permit applicants, as
appropriate, for the exemption in section 7(o)(2) to apply. The Corps has a continuing duty to
regulate the activity covered by this Incidental Take Statement. If the agency 1) fails to assume
and implement the terms and conditions, or 2) fails to require applicants to adhere to the terms
and conditions of the Incidental Take Statement through enforceable terms that are added to the
permit or grant document, the protective coverage of section 7(o)(2) may lapse. In order to
monitor the impact of incidental take, the Corps must report the progress of the action and its
impact on the species as specified in this Incidental Take Statement [50 CFR 402.14(i)(3)].
The Service does not anticipate that the proposed action will incidentally take marbled murrelets.
The Service must provide a reasoned basis for a likelihood of take in order to anticipate and
exempt it. Since no marbled murrelet take is anticipated or exempted, no related reasonable and
prudent measures or terms and conditions are provided below. If take of marbled murrelets is
detected during implementation of the proposed action, reinitiation of formal consultation should
be requested, and any operations causing such take must cease pending the outcome of the
reinitiated consultation.
AMOUNT OR EXTENT OF TAKE
The Service expects that take of anadromous subadult and adult bull trout, in the form of harm,
will result from the proposed action. The Service expects take in each of the five geographic
sub-areas (Willapa Bay, Grays Harbor, Hood Canal, south and north Puget Sound). Anadromous
bull trout from any of the Puget Sound and coastal Washington core areas may be taken (Puget
Sound: Nooksack, Lower Skagit, Stillaguamish, Snohomish-Skykomish, Puyallup, Skokomish,
Dungeness, and Elwha River bull trout core areas; Coastal Washington: Hoh, Queets, and
Quinault River bull trout core areas).
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The Service expects that incidental take of bull trout will be difficult to detect or quantify for the
following reasons: 1) the low likelihood of finding dead or injured adults or subadults; 2)
delayed mortality; and, 3) losses may be masked by seasonal fluctuations in numbers.
1. Incidental take of subadult and adult bull trout, in the form of harm (injury or mortality),
as a direct effect of entrapment or entanglement in shellfish culturing equipment,
stranding behind berms or dikes, and/or stranding within pools impounded by or around
shellfish culturing equipment.
a. A maximum of six (6) subadult or adult bull trout will be harmed in the north Puget
Sound geographic sub-area over the 20-year term of the programmatic (2016 to
2036).
b. A maximum of two (2) subadult or adult bull trout will be harmed in each of the other
four geographic sub-areas (Willapa Bay, Grays Harbor, Hood Canal, and south Puget
Sound) over the 20-year term of the programmatic (2016 to 2036); a total of eight (8)
subadult or adult bull trout.
EFFECT OF THE TAKE
In the accompanying Opinion, the Service determined that the level of anticipated take is not
likely to result in jeopardy to the species (bull trout) or destruction or adverse modification of
critical habitat (designated bull trout critical habitat).
REASONABLE AND PRUDENT MEASURES
1. Minimize and monitor incidental take caused by entrapment or entanglement in shellfish
culturing equipment, stranding behind berms or dikes, and/or stranding within pools
impounded by or around shellfish culturing equipment.
The proposed action incorporates conservation measures which we expect will avoid and
minimize the direct loss of bull trout individuals. We expect that the Corps will fully implement
the conservation measures, and therefore they have not been identified as terms and conditions.
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TERMS AND CONDITIONS
1. The Corps shall include permit language requiring that all growers/farm operators, when
performing other activities on-site, shall inspect for and document any salmonids that are
entrapped or entangled in shellfish culturing equipment, stranded behind berms or dikes,
or stranded within pools impounded by or around shellfish culturing equipment. The
permit language shall provide for immediate notification (within 24 hours) to the Corps,
NMFS, and the Service. The permit language shall require a written and photographic
record of the event, including dates, species identification, number of individuals, and
final disposition.
2. The Corps shall compile information annually and submit a report to the Service
Washington Fish and Wildlife Office, Consultation and Conservation Planning Division,
Attn: Federal Activities Branch Manager) by March 1 each year.
3. The Corps shall obtain, compile, and submit to the Service by March 1, 2017,
information to describe the ongoing use and prevalence of berms or dikes on the upper
intertidal bed: number of current, authorized berms or dikes; permittee, grower or farm
operator, name and location; position, length, and current condition of the berm(s) or
dike(s). Alternatively, the Corps shall collect this information from applicants during
pending permit reauthorizations and shall provide this information in a report to the
Service (Washington Fish and Wildlife Office, Consultation and Conservation Planning
Division, Attn: Federal Activities Branch Manager) by March 1 each year.
The Service is to be notified within 24 hours upon locating a dead, injured, or sick endangered or
threatened species specimen. Initial notification must be made to the nearest U.S. Fish and
Wildlife Service Law Enforcement Office. Notification must include the date, time, precise
location of the injured animal or carcass, and any other pertinent information. Care should be
taken in handling sick or injured specimens to preserve biological materials in the best possible
state for later analysis of cause of death, if that occurs. In conjunction with the care of sick or
injured endangered or threatened species or preservation of biological materials from a dead
animal, the finder has the responsibility to ensure that evidence associated with the specimen is
not unnecessarily disturbed. Contact the U.S. Fish and Wildlife Service Law Enforcement
Office at (425) 883-8122, or the Service’s Washington Fish and Wildlife Office at (360) 753-
9440.
CONSERVATION RECOMMENDATIONS
Section 7(a)(1) of the ESA directs federal agencies to utilize their authorities to further the
purposes of the ESA by carrying out conservation programs for the benefit of endangered and
threatened species. Conservation recommendations are discretionary agency activities to
minimize or avoid adverse effects of a proposed action on listed species or critical habitat, to
help implement recovery plans, or to develop information.
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The Corps has included conservation measures as elements of their proposed action (Corps 2015,
pp. 49-53). Permits and permit verifications issued by the Corps will incorporate these
conservation measures as enforceable permit conditions. Permits and permit verifications issued
by the Corps will include permit conditions addressing security of culturing equipment used on
the tidelands, spill prevention and containment, avoidance of native eelgrass and rooted kelp,
performance of marine forage fish spawn surveys, and other related restrictions designed to
protect fish and wildlife, aquatic resources, and water quality.
If a Corps permit applicant or group of applicants cannot or will not commit to fully
implementing the conservation measures, the issuance of that permit or permit verification
cannot be covered under the programmatic consultation, and case-by-case consideration and
individual section 7 ESA consultations will be required. Growers and farm operators who seek
coverage under the programmatic consultation, but who also fail to fully comply with these
conservation measures (where applicable), will not satisfy the requirements of their Corps permit
and are potentially liable under provisions of the ESA.
The Corps has excluded 14 specific activities from programmatic coverage (Corps 2015, p. 39).
The Corps has indicated that the following activity is specifically excluded from coverage under
the programmatic consultation (Corps 2015, p. 39): Any form of chemical application to control
undesired species (e.g., non-native eelgrass, Zostera japonica; ghost shrimp, Neotrypaea
californiensis; mud shrimp, Upogebia pugettensis).
Service Comment and/or Recommendation – The Service assumes and expects that the Corps
will actively solicit information from their applicants about all of the excluded activities,
including chemical applications, prior to approving coverage under the programmatic
consultation, and before issuing permits or permit verifications. Growers and farm operators
who seek coverage under the programmatic consultation, but who also engage in any of the
excluded activities (including chemical application to control undesired species), will not satisfy
the requirements of their Corps permit and are potentially liable under the provisions of the ESA.
In the event that a Corps applicant or group of applicants has been issued a valid State permit(s)
to engage in application of herbicides or pesticides to the bed or waters, the Service expects that
the Corps will confirm compliance with the procedural requirements of the ESA before issuing a
permit or permit verification under this programmatic. We recommend that the Corps include
relevant language to collect this information in the Programmatic ESA Consultation Specific
Project Information Form. The Corps has a continuing obligation to implement the
programmatic and will only do so successfully if the Corps acts on good information to
effectively exclude each and all of the prohibited activities.
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REINITIATION NOTICE
This concludes formal consultation on the action(s) outlined in the Corps’ request. As provided
in 50 CFR 402.16, reinitiation of formal consultation is required where discretionary federal
agency involvement or control over the action has been retained (or is authorized by law) and if:
1) the amount or extent of incidental take is exceeded; 2) new information reveals effects of the
agency action that may affect listed species or critical habitat in a manner or to an extent not
considered in this opinion; 3) the agency action is subsequently modified in a manner that causes
an effect to the listed species or critical habitat not considered in this opinion; or 4) a new species
is listed or critical habitat designated that may be affected by the action. In instances where the
amount or extent of incidental take is exceeded, any operations causing such take must cease
pending reinitiation.
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