Fish Assemblages in South Puget Sound Z. Marina

Item

Title

Eng Fish Assemblages in South Puget Sound Z. Marina

Date

2018

Creator

Eng McCormick, Kyle

Subject

Eng Environmental Studies

extracted text

FISH ASSEMBLAGES IN SOUTH PUGET SOUND Z. MARINA

BY
KYLE MCCORMICK

A Thesis
Submitted in partial fulfillment
of the requirements for the degree
Master of Environmental Studies
The Evergreen State College
June 2018

©2018 by Kyle McCormick. All rights reserved.

This Thesis for the Master of Environmental Studies Degree
by
Kyle McCormick

has been approved for
The Evergreen State College
by

________________________
John Withey, Ph. D.
Member of the Faculty

________________________
Date

ABSTRACT
Fish Assemblages in South Puget Sound Z. marina
Kyle McCormick

Seagrass is a marine flowering plant that is an important indicator of ecosystem health by
providing vital habitat for fish in marine ecosystems. Unfortunately, seagrass is currently
experiencing a worldwide decline due to multiple stressors including shoreline development and
pollution. Eelgrass (Zostera marina), a seagrass species native to the Salish Sea, provides vital
habitat for important commercial fishes including herring (Clupea pallasii) and salmon
(Oncorhynchus spp.). A loss of eelgrass coverage could potentially harm these vital food fish
stocks. Washington Department of Natural Resources (DNR) manages approximately 500 m2 of
transplanted eelgrass at Joemma State Park (JSP) in South Puget Sound as part of their goal to
increase total eelgrass coverage in Puget Sound 20% by 2020. To observe fish abundance and
diversity at a transplanted eelgrass site, video data was collected to compare fish assemblages at
JSP and a natural eelgrass bed at Dupont Warf. Unbaited underwater video cameras were
deployed biweekly from June to August 2017. A two-minute video was recorded every ten
minutes after initial camera deployment at low tide. Video was recorded for 24 hours, but
footage after sunset was discarded due to low light. The data were analyzed to quantify fish
abundance and diversity at each site. Of the 12 fish groups identified, 2 were not present at either
JSP site (spiny dogfish and striped surfperch). Bay pipefish were the only fish group
significantly associated with transplanted eelgrass, while shiner perch, gunnels, tube-snout,
striped surfperch, and spiny dogfish were significantly associated with the natural eelgrass. The
remaining 5 groups (salmonids, forage fishes, pacific snake prickleback, pacific stag sculpin, and
pile perch) had no significant association with a site type. Despite the lack of a significant
association between site and 5 fish groups, each of these fishes has been shown to associate with
eelgrass in previous studies. This research can be treated as a pilot study for using non-invasive
video recording to assess fish assemblages in South Puget Sound eelgrass beds.

Table of Contents
List of Figures ................................................................................................................................ vi
List of Tables ................................................................................................................................ vii
Acknowledgements ...................................................................................................................... viii
Introduction ..................................................................................................................................... 1
Literature Review............................................................................................................................ 5
Overview of Seagrasses .............................................................................................................. 5
Nursery/Shelter ........................................................................................................................ 6
Sedimentation .......................................................................................................................... 7
Carbon Sequestration .............................................................................................................. 7
Global Seagrass Decline ......................................................................................................... 8
Restoration of Seagrass ........................................................................................................... 9
Z. marina and Puget Sound ....................................................................................................... 10
Z. marina Coverage in Puget Sound ...................................................................................... 14
Z. marina Decline in Puget Sound ......................................................................................... 14
Z. marina Restoration ............................................................................................................ 17
Fishes in Puget Sound ............................................................................................................... 18
Assemblage Theory and Seagrass ............................................................................................. 20
Methods......................................................................................................................................... 25
Study Area ................................................................................................................................. 25
Joemma State Park ................................................................................................................ 25
Dupont Warf .......................................................................................................................... 26
Grid Creation ............................................................................................................................. 27
Camera Setup ............................................................................................................................ 29
Camera Deployment .................................................................................................................. 31
Measuring visibility ............................................................................................................... 33
Camera Programming ............................................................................................................... 33
Camera Retrieval ....................................................................................................................... 34
Data Analysis ............................................................................................................................ 34
Results ........................................................................................................................................... 36
iv

Abundance Based on Site Type ................................................................................................ 37
Natural Z. marina .................................................................................................................. 37
Transplanted Z. marina ......................................................................................................... 40
Bare Sediment ........................................................................................................................ 41
No Observable Relationship .................................................................................................. 41
Abundance Based on Time of Day ........................................................................................... 44
Discussion ..................................................................................................................................... 46
Limitations of the Study Design................................................................................................ 51
Future Improvements ................................................................................................................ 54
Conclusion................................................................................................................................. 55
Bibliography ................................................................................................................................. 56
Appendix A. Camera/PVC rig setup ............................................................................................. 78
Appendix B. Fish abundance based on time of day ...................................................................... 80

v

List of Figures
Figure 1. Seagrass anatomy ............................................................................................................ 5
Figure 2. Fauna associated with Z. marina ................................................................................... 13
Figure 3. Mean (±SE) fish species richness per tow at four Puget Sound .................................... 20
Figure 4. Model representing different predator/prey interactions at various scales .................... 23
Figure 5. Aerial image of Joemma State Park Z. marina restoration site ..................................... 25
Figure 6. Aerial shot of Dupont Warf ........................................................................................... 27
Figure 7. Example of T3 and T4 grid created to randomize camera placement ........................... 29
Figure 8. Camera setup for JSP at transplanted Z. marina site. .................................................... 30
Figure 9. Diagram representing camera setup at Dupont natural Z. marina site. ......................... 31
Figure 10. Location of both study sites in Puget Sound ............................................................... 32
Figure 11. Shiner perch abundance based on site type ................................................................. 38
Figure 12. Gunnel abundance based on site type .......................................................................... 38
Figure 13. Tube-snout abundance based on site type ................................................................... 39
Figure 14. Striped surfperch abundance based on site type .......................................................... 39
Figure 15. Spiny dogfish abundance based on site type ............................................................... 40
Figure 16. Bay pipefish abundance based on site type ................................................................. 40
Figure 17. Flatfish abundance based on site type ......................................................................... 41
Figure 18. Pacific snake prickleback abundance based on site type............................................. 42
Figure 19. Forage fish abundance based on site type ................................................................... 42
Figure 20. Pacific staghorn sculpin abundance based on site type ............................................... 43
Figure 21. Pile perch abundance based on site type ..................................................................... 43
Figure 22. Salmonid abundance based on site type ...................................................................... 44
Figure 23. Example of difficulties when identifying fish species ................................................ 54

vi

List of Tables

Table 1. Median Fish Count/Hour for each Fish Species or Group.............................................. 37

vii

Acknowledgements

First and foremost, I’d like to thank my advisor Dr. John Withey for his guidance and
support throughout the entire thesis process. His patience with my myriad of revisions did not go
unnoticed. I’d also like to thank Dr. Erin Martin for her help with my initial thesis study design.
I’d also like to thank the Washington Department of Natural Resources, in particular Dr.
Jeff Gaeckle and Dr. Bart Christiaen for their mentorship and assistance during field excursions
and with any questions I had about research design. I’d also like to thank Casey Pruitt for lending
me the equipment necessary to complete my experiment. This study could not have happened
without all of your support.
I’d like to thank my good friends Ben Leonard for going out of his way on numerous
occasions to help me develop my statistics for this thesis, and Joe Wheeler for lending me his
wetsuit, which made my field work an enjoyable (and warm) experience. In addition, I want to
thank my family for always supporting me throughout my academic endeavors, and loving me
unconditionally as I navigate across the country for my academic career.
Finally, I dedicate this thesis to Chez Puget. An Olympia icon, gross punk house, host of
my bidet, and my loving home.

viii

Introduction
Puget Sound is a temperate estuarine system spanning over one thousand square miles
along the inland waters of Washington State. The Puget Sound is a diverse ecosystem containing
211 fish species among its marine waters and 19 river drainage basins (Washington State
Department of Ecology, 2016). Fishes in Puget Sound range from small gobies and blennies to
larger salmonids and cod. Fish communities in Puget Sound can vary based on seasonal patterns,
with certain fishes like salmonids transitioning from streams to open ocean at different life stages
(Simenstad et al., 1982). Fish habitat in Puget Sound includes oyster mudflats, tidal floodplains,
and kelp beds. Puget Sound’s development and pollution has caused fish populations to decline
due to loss of habitat (Toft et al., 2007). Adequate habitat is essential for fishes to survive
predation, as well as find sources of food. One critically important habitat for fishes in Puget
Sound is seagrass.
Seagrass is an important marine macrophyte that is considered an indicator of ecosystem
health (Macreadie et al., 2017), and provides habitat, nursery and shelter habitat for a variety of
fishes. Among the thousands of miles of marine waters in Puget Sound are patches of eelgrass
(Zostera marina L.), a species of seagrass, which can range from a few square meters of
hundreds of meters in both intertidal and subtidal areas of the Sound. Z. marina can inhabit
depths between +1.4 and -11 meters relative to mean lower low water, and is commonly found in
fringe or tideflat habitats (Christiaen et al., 2017). The abundance and diversity of fishes found in
Z. marina is extensive, supporting fishes like salmonids and herring (Phillips, 1984; Simenstad et
al., 1982), making it a critical habitat for preserving biodiversity in Puget Sound. Unfortunately,

1

seagrasses populations are declining globally due to a suite of anthropogenic factors (Duarte,
2002). Restoration efforts of global seagrass populations have met mixed results, but advances in
technology and habitat modeling have proven to be successful in recent restoration efforts
(Fonseca, 1998). In Puget Sound, the local species of seagrass, eelgrass, plays important roles in
the nearshore environment ranging from binding sediment to carbon sequestration (Bos et al.,
2007; Duarte et al., 2005).
Z. marina populations face many of the same anthropogenic stressors that seagrasses face
globally, along with increased development along Puget Sound’s shoreline (Li et al., 2007). With
declining Z. marina coverage comes declining ecosystem services that benefit marine fauna and
humans alike. Reduced Z. marina coverage also means less biodiversity in Puget Sound, as there
are fish species that depend on the habitat for specific parts of their lives or the entirety of their
lives (Phillips, 1984). Restoration of Z. marina throughout the United States is mixed in terms of
success in creating large seagrass beds that are resilient over time; issues stem from similar
problems that global seagrass restoration efforts have faced, including large die-offs of Z. marina
populations (Robblee et al., 1991; Short, Muehlstein, & Porter, 1987) and an inability to recruit
seagrass at restoration sites (Bell et al., 2008; Fonseca, 1998). However, trends of growth and
restoration efforts in Puget Sound have been positive within the past five to ten years based on
overall stable populations and successful small-scale restorations (Christiaen et al., 2017). The
restoration of Z. marina is a critical component of ensuring nearshore ecosystems do not lose
important habitat. An important component of seagrass restoration activities is looking at how
seagrasses are used by fishes.
Examining fish abundance and diversity, also known as fish assemblages, in relation to
seagrasses, helps scientists determine what ecosystem services seagrasses are providing for
2

marine fauna. Research on fish assemblages in Z. marina in the Pacific Northwest found that fish
assemblages varied based on time of day and season (Garwood et al., 2013; Obaza et al., 2015;
Robinson et al., 2013). In addition, research comparing fish assemblages in transplanted seagrass
to natural seagrass has been observed throughout the country with a variety of seagrass types
(Brown-Peterson et al., 1993; Sheridan, 2004). However, a combination of these two bodies of
work (fish assemblages in the Pacific Northwest and comparing fish assemblages between
restored and natural seagrass) is lacking.
The Washington Department of Natural Resources (DNR) manages approximately 500
m2 of transplanted Z. marina at Joemma State Park (JSP), on Case Inlet in South Puget Sound.
The DNR transplanted Z. marina to JSP with the hopes of creating new beds to provide
ecosystem services and functions for the nearshore environment. Understanding what fish are
present in Z. marina in South Puget Sound is one important measure of how well transplanted Z.
marina is providing ecosystem services in relation to natural seagrass, a term known as
“functional equivalency” (Fonseca, 1998). Determining if transplanted seagrass provides
ecosystem services for the local environment can dictate future restoration efforts within Puget
Sound, and provide future restoration efforts with important data on fish assemblages in recently
transplanted seagrass. Ensuring that restored Z. marina beds provide ecosystem services is
critical because of the alarming rate that Z. marina, and seagrasses all over the world, are losing
coverage (Waycott et al., 2009). Restoring seagrass communities is crucial to prevent further loss
of this important marine fauna, their habitat, and the ecosystem services that seagrasses,
including Z. marina, provides.
To assess the diversity and abundance of fishes present in transplanted seagrasses, studies
on fish assemblages were conducted in South Puget Sound (SPS). The use of unbaited
3

underwater video to study fish assemblages is a common technique in coral reefs and seagrasses
(Smith et al., 2011; Watson et al., 2005). Studies using underwater video collect continuous
footage ranging from periods of 15 minutes to 90 minutes to examine fish assemblages, although
there is no standard methodology for underwater video census. Other conventional methods of
sampling fish assemblages (seine nets and baited underwater video cameras) have raised
concerns about unbiased results or potential damage to seagrass. Although unbaited underwater
video to study fish assemblages has been used for coral reef and seagrass fish assemblages in the
past, its use for fish assemblages of restored Z. marina, specifically in Puget Sound, is lacking.
Therefore, this fieldwork will passively collect data on fish use of transplanted Z. marina that
will add to the knowledge of fish communities in SPS and the potential uses of transplanted Z.
marina for said communities.
The results of this study will provide information on fish abundance and diversity at
transplanted Z. marina sites at JSP, bare sediment sites at JSP, and natural Z. marina sites at
Dupont. Evidence of fish presence in transplanted Z. marina at JSP can elucidate the ecosystem
services the restored Z. marina is providing at JSP for fishes. Video footage showing fish
abundance and diversity at bare sediment and natural Z. marina sites will provide data on fish
use of both habitats. The results of this thesis will help determine if transplanted Z. marina at JSP
is providing ecosystem services like natural Z. marina, by being used by fishes commonly found
in SPS. Data from fieldwork will aggregate hours of collective footage, showing which fish are
present in transplanted Z. marina in relation to nearby natural Z. marina.

4

Literature Review
Overview of Seagrasses

Seagrasses are aquatic flowering plants consisting of 70 differing species found in marine
and estuary environments on every continent except Antarctica (Green, 2003). Found in both
intertidal and subtidal environments, seagrass (which are taxonomically distinct from seaweed an
alga), has an aboveground portion that consists of leaves connected to a sheath and a
belowground portion that the sheath connects to the root/rhizome complex (Figure 1). Seagrasses
can form large underwater meadows capable of altering the surrounding water current, nutrient
dynamics, and sediment level (Bos et al., 2007; Heiss et al., 2000), and can even filter bacterial
pathogens from the water column (Lamb et al., 2017). These meadows are also home to a myriad
of aquatic vertebrates and invertebrates that use seagrass as shelter and nursery habitat
(McDevitt-Irwin et al., 2016; Ruso & Bayle-Sempere, 2006). Seagrass also an important food
source for large vertebrates including black brant geese (Wilson & Atkinson, 1995), dugong
(Yamamuro & Chirapart, 2005), and sea turtles (Bjorndal, 1979).

Figure 1. Seagrass anatomy. Modified from (Collier, 2004)
5

Nursery/Shelter

Seagrasses provide essential nursery habitat for many juvenile and larval stages of
important commercial and recreational fishes and shellfishes (Bertelli & Unsworth, 2014; Short
et al., 2011). Multiple meta-analyses conclude the aboveground biomass of seagrass meadows
provides complex habitat that provides better shelter when compared to bare sediment (Heck Jr.
et al., 2003; McDevitt-Irwin et al., 2016; Whitfield, 2017). Marine organisms use seagrass blades
as refuge from predators, which have reduced maneuverability and visual acuity for prey hiding
in seagrass blades, increasing the likelihood of survival for juvenile or residential organisms
(Horinouchi et al., 2009). Seagrass blades also provide surface area for sessile organisms like
encrusting algae to attach, which utilize the blade tips as a means of having better access to
sunlight (Trautman & Borowitzka, 1999). Alga attached to seagrass also provide a source of food
for invertebrate mesograzers that inhabit seagrass beds (Ebrahim et al., 2014), while sessile
organisms and invertebrate mesograzers in seagrass beds also provide fishes with a source of
food (Horinouchi et al., 2012; Kwak et al., 2015). In addition, epiphytic algae attached to
seagrass blades provide further structural complexity in seagrass beds by creating additional
housing for microcrustaceans and vertebrates (Adams et al., 2004; Corona et al., 2000). Seagrass
also provides an important connecting habitat between other marine habitats like mangroves and
coral reefs. The distance between seagrass, mangroves, or coral reefs can dictate fish abundance
and diversity based on availability of shelter from predation, nursery habitat, and migration
distance (Dorenbosch et al., 2007; Unsworth et al., 2008).

6

Sedimentation

The seagrass canopy is capable of reducing wave action, in turn filtering particles out of
the water current that drop into the seagrass bed, promoting sediment accretion (Bos et al.,
2007). Removing particles from the water current can reduces erosion risk (Potouroglou et al.,
2017) while also reducing opacity, effectively filtering the water (Fonseca et al., 1998). The
canopy can further prevent erosion by reducing the likelihood of sediment resuspension. By
attenuating waves, the seagrass canopy prevents upwelling of deposited sediments within its
meadow (Ros et al., 2014; Terrados & Duarte, 2000). Seagrass meadows create a positive
feedback loop i.e. promoting sediment accumulation that allows more seagrass to grow in the
surrounding environment that otherwise would be unable to do so, which in turn promotes more
sediment accumulation (Heide et al., 2011). This ability to reduce coastal erosion is not only
based on aboveground canopy length, but can be promoted via the root/rhizome system’s ability
to hold sediment in place (Christianen et al., 2013).
Carbon Sequestration

The filtration of particulate from the water column not only promotes sedimentation, but
also the burial of organic carbon within seagrass beds. The carbon stored in seagrass biomass and
soil is referred to as “blue carbon” (Howard et al., 2014). Despite only occupying less than 0.2%
of the world’s oceans, it’s estimated that the global seagrass biomass contains 75.5 – 151 TgC,
while the top meter of global seagrass soils contains between 4.2 and 8.4 PgC (Fourqurean et al.,
2012). Seagrasses are responsible for 20% of global carbon sequestration in marine sediments
(Duarte et al., 2013). Reduced flow of water within seagrass canopies causes detritus, seston, and
other allochonous carbon to drop out of the water current and deposit within the meadow
7

(Greiner et al., 2013; Kennedy et al., 2010). Organic carbon that settles in seagrass meadows is
retained for centuries to a millennium due to multiple mechanisms including poor metabolism in
sediments due anaerobic conditions and dissipation of wave action due to seagrass canopy
reducing resuspension (Duarte et al., 2013). However, seagrasses also play an important role in
spreading carbon throughout the ocean. Seagrass exports a large amount of carbon to both
nearshore and deep ocean environments (Duarte & Krause-Jensen, 2017), indicating a significant
role in carbon burial throughout aquatic environments.
Global Seagrass Decline

Despite the critical ecosystem services that seagrasses provide, seagrasses are currently
facing a global decline. A review by Waycott et al. (2009) revealed alarming values in seagrass
loss, including a rate of decline at 110 km per year since 1980, with 1.5% of mean seagrass area
per year disappearing. This rate is comparable to the loss of mangroves (1.8% mean area per
year) and even faster than tropical forest loss per year (0.5% mean area per year). The same
study found that the rate of loss increased from 0.9% per year in 1940 to 7% per year in 1990.
Overall, 80-100% of seagrass species are in decline (Green, 2003), with at least 10 species at an
elevated risk of extinction (Short et al., 2011). Declining seagrass coverage has a slew of
detrimental environmental affects, ranging from increased carbon returning to the oceanatmosphere system (between 11.3 and 22.7 TgC per year) (Fourqurean et al., 2012), increased
resuspension of sediment, and reduced biodiversity (Duarte, 2002). Loss of seagrass also affects
the organisms that inhabit it, including 115 IUCN Red List species of marine invertebrates,
fishes, sea turtles, and mammals that rely on seagrass (Short et al., 2011).

8

Causes of seagrass decline range from anthropogenic factors including coastal pollution
and dredging to environmental issues including sea level rise and wasting disease (Duarte, 2002;
Waycott et al., 2009). Seagrass decline has been linked to lower fishery production in multiple
cases (Gillanders, 2006; McArthur & Boland, 2006; Tuya et al., 2014), indicating an economic
stake in preserving seagrass ecosystems. The decline of seagrass can have immediate effects on
smaller communities that rely on artisanal fisheries for sustenance (de la Torre-Castro &
Rönnbäck, 2004). In addition, the nursery function that seagrasses provide for commercial fishes
means seagrasses are an important source for future fisheries as much as current ones (Tuya et
al., 2014). Seagrass ecosystem services for fisheries is valued at $34,000/ha per year (in 2010
USD) (Short et al., 2011), making their loss not only an environmental issue, but an economic
one too. Other estimates of the economic savings seagrass provide humans includes up to 13.7
billion per year collectively in carbon sequestration (Pendleton et al., 2012).
Restoration of Seagrass

Restoration of seagrasses is critical to preserving the myriad of ecosystem services it
provides for animals and humans alike. It has been shown that restored seagrass can improve the
surrounding environment, including storing more carbon, nitrogen, and sediment compared to
unvegetated areas. Restoration not only has benefits for ecosystem services, but tangible
monetary benefits for modern efforts to store carbon and nitrogen. A restored Z. marina bed in
Virginia Coast Reserve Long Term Ecological Research site was estimated to store
approximately $4.10 (in 2011 USD) per hectare per year of carbon (Greiner et al., 2013).
However, improvements from restoration are not immediate, as the same study found in their
experiment showing restored seagrass beds 4 years old were not as good at storing carbon and
sediment as 10-year-old seagrass beds. Their experiment shows that seagrass restoration efforts
9

are an ongoing process that requires habitual monitoring to determine successful restoration of
ecosystem services. The definition of “success” for seagrass restoration commonly focuses on
increased coverage of seagrass, but often overlooks the importance of seeing if restored
seagrasses are providing the ecosystem services for organisms that natural seagrass does
(Lefcheck et al., 2017). Investigating the effectiveness of restored seagrass sites at providing
ecosystem services similar to natural seagrass, a term known as “functional equivalency”
(Fonseca et al., 1998).
Z. marina and Puget Sound

Z. marina is the dominant biomass found on the Pacific Coast of North America between
Baja California and Alaska’s Yukon Delta; in addition, Z. marina is found throughout the world
including the east coast of the United States, Japan, and the Wadden Sea (Green, 2003). Puget
Sound’s seagrass population is predominately Z. marina, but has populations of the introduced
Japanese eelgrass (Zostera japonica) as well (Christiaen et al., 2016). Phillips' (1984) ecological
profile on the Pacific Northwest provides a thorough description of Z. marina’s features. Found
in muddy or mixed sand/mud substrate, Z. marina, a perennial seagrass, is characterized by
having between two and five round-tipped and strap-like leaves per shoot, depending on the
environment. In addition, Z. marina has thin mesh of rhizome commonly buried between 3 and 4
cm below the sediment surface. Z. marina is capable of both vegetative (rhizomatic expansion)
and reproductive (flowering and pollination) growth. Z. japonica, although similar in
appearance, is discernable from Z. marina by its smaller sized leaves and shallow rhizome (no
deeper than 3 cm).

10

The Washington State Department of Fish and Wildlife (WDFW) has classified seagrass
beds as habitats of special concern (WAC 220-110-250) when dealing with hydraulic projects
(RCW 77.55.021), while the Washington Department of Ecology lists seagrass as a critical
habitat in its Shoreline Management Act (RCW 90.58), making seagrass beds federally protected
within the state of Washington (Christiaen et al., 2016). Monetizing the importance of Z. marina
for Puget Sound rests on one study by Batker et al. (2008), which valued Z. marina’s nutrient
cycling in Puget Sound at $5 - $15 million (in 2006 USD) . However, the economic value of Z.
marina consists of a slew of other ecosystem services that are not quantified in their evaluation.
The importance of Z. marina has been acknowledged long before colonization of the Pacific
Coast by Europeans. Z. marina had significant cultural value to coastal native groups including
the Haida and Kwakwaka’wakw peoples, which used eelgrass as a food source and a material for
basket weaving (Wyllie-Echeverria et al., 1994).
The Z. marina ecosystem of Puget Sound is an intricate and complex system connecting
zooplankton to fishes to black brant geese (Figure 2). Z. marina provides important commercial
food fishes like Pacific herring (Clupea pallasii) and Chinook salmon (Oncorhynchus
tshawytscha) with habitat used for nursery and shelter. Pacific herring use Z. marina blades as a
substrate to attach eggs, with up to 20,000 eggs being deposited on blades by a single female
pacific herring. Pacific herring are a valuable commercial food fish as well as an important
forage fish within Puget Sound (Phillips, 1984). Salmonids use Z. marina as a migration corridor
as well as a refuge from predators during juvenile stages (Simenstad et al., 1982). However, the
association between juvenile salmon and Z. marina is contested by Murphy (2000), who claims
that direct evidence is lacking to make such a claim. Instead, he found that juvenile salmon likely
have been found in Z. marina not because of the Z. marina itself, but the reduced exposure to
11

currents and waves within the beds. However, seagrasses are known to reduce wave action
through blade attenuation (Fonseca & Cahalan, 1992), which provides a service to juvenile
salmonids. The effectiveness of Z. marina as a source of denitrification has been observed as
well (Zarnoch et al., 2017). Top down predation by fishes that frequent Z. marina is also an
important controlling factor in reducing potentially harmful mesograzers from consuming Z.
marina biomass, reducing coverage and production (Lewis & Anderson, 2012).

12

1. Zooplankton
2. Larval crab
3. Salmon
4. Herring
5. Epiphytic macroalgae
6. Epiphytic microalgae,
Hydozoa, and bryozoa
7. Sea cucumber
8. Dungeness crab
9. Octopus
10. Sand dollars
11. Clams and cockles
12. Pacific spiny
Lumpsucker
13. Caprellid amphipod

14. Stalked jellyfish
15. Eelgrass isopod
16. Juvenile salmon
17. Bubble shell
18. Opalescent nudibranch
19. Perch
20. Juvenile kelp crab
21. Alabaster nudibranch
22. Scallop
23. Gunnel
24. Bay pipefish
25. Sea urchin
26. Juvenile sculpin
27. Decorator crab
28. Juvenile clams

29. Juvenile flounder
And sole
30. Juvenile crab
31. Geoduck
32. Sediment microfauna
33. Snail and snail eggs
34. Juvenile cod, tomcod
And wall-eyed pollock
35. Herring eggs
36. Jellyfish
37. Larval fish
38. Melibae-hooded
nudibranch
39. Tubesnout
40. Shrimp

41. Brooding anemone
42. Prickleback
43. Sculpin
44. Bacteria on detritus
45. Moonsnail
46. Sunflower seastar
47. Sea pen
48. Red rock crab
49. Hermit crab
50. Worms
51. Ghost shrimp
52. Sand lance
53. Black Brant
54. Canada Goose
55. Bufflehead

Figure 2. Fauna associated with Z. marina (Mumford Jr, 2007)

13

Z. marina Coverage in Puget Sound

It is difficult to ascertain the exact acreage of Z. marina historically present in Puget
Sound due a lack of reliable information regarding potential or historic coverage; estimates of
historic coverage between 45,000 and 50,000 hectares have issues with methodology and
conflicting data from more recent analysis (Dowty et al., 2010). A lack of reliable historic Z.
marina population information is further exacerbated by the fact that it is unknown if south
Puget Sound ever had a historic presence of Z. marina (Thom et al., 2011). Defining seagrass as
“natural” can become an issue when a historical presence is not known. In 2000, Washington’s
Department of Natural Resources (DNR) created the submerged vegetation monitoring program
in order to address spatial and temporal trends in Z. marina (Berry et al., 2003). As of 2014, the
total Puget Sound eelgrass coverage was 24,300 ha (Christiaen et al., 2016). The depth
distribution of Puget Sound’s Z. marina can range from +1.4 m to -12.4 m in relation to the mean
lower low water tide (Thom et al., 2014). The size and density of patches can have differing
effects on community assemblages, with larger, contiguous beds capable of housing more
permanent, residential species (Hensgen et al., 2014). Despite being smaller in size, fringe Z.
marina beds play an important role in connecting habitats for migrating fishes like salmon;
fringe habitat accounts for approximately 50% of Z. marina in Puget Sound while the other half
is larger tidal flat sites (Christiaen et al., 2016).
Z. marina Decline in Puget Sound
Although a majority of seagrasses are in decline worldwide, Puget Sound’s seagrass
population remains stable at the large scale (100s of kms), despite a shift in coverage at a smaller
scale (10s of kms) (Shelton et al., 2016). This stability should not create the assumption that
14

there is no need for restoration, as small-scale changes in seagrass coverage could create
unknown shifts in ecosystem productivity and sediment transport. Furthermore, evidence in
contemporary monitoring shows a larger amount of Z. marina sites with declining populations
than sites with increasing populations (Dowty et al., 2010).
Z. marina populations in Puget Sound are declining from factors common among all
seagrass declining populations (Duarte, 2002; Walker et al., 2007); however, local loss of Z.
marina coverage in Puget Sound is attributed to indirect changes in water quality including
increased sediment and nutrient inputs into Puget Sound (Li et al., 2007; Orth et al., 2006) and
limited light due to overhanging structures (Rehr et al., 2014). Seagrass are photosynthetic
organisms dependent on adequate amounts of light to survive (Thom et al., 2008), making
overhanging structures detrimental for seagrasses. Nightingale & Simenstad's (2001b) review
found the construction of overhanging structures like docks and ferry terminals can reduce the
amount of light in the water column to a point that effectively kills off Z. marina. In addition,
direct disturbances include dredging (Nightingale & Simenstad, 2001a), and aquaculture reduce
Z. marina populations in Puget Sound. Seagrass restoration in Puget Sound is in direct contact
with the shellfish aquaculture.
The shellfish industry brought in over 50 million dollars in South Puget Sound alone
(Washington Sea Grant, 2015); however, the practices of shellfish growing/harvest can have
negative effects on seagrass beds. Dumbauld et al. (2009) provides a review of shellfish
aquaculture’s effects on Z. marina including boat anchor scars, dredging and filling. Their
review also cites the negative effects of hard clam harvest methods like “clam kicking” and hand
digging have on eelgrass; furthermore, his review shows clam harvest with shovels was found to
reduce eelgrass coverage and biomass in the short term. However, a recent study of oyster
15

aquaculture effects on eelgrass in Willapa Bay showed no long-term negative effects on eelgrass
coverage, and could potentially enhance their presences on larger scales (Dumbauld & McCoy,
2015).
Population growth and associated development in the Puget Sound region is another
factor that puts Z. marina at risk of decline. Coastal populations are predicted to increase
throughout Puget Sound, with projected increases in the counties surrounding South Puget Sound
(Thurston, Pierce, and Mason counties) ranging from 34% to 52% between 2000 and 2025
(Puget Sound Action Team, 2007). Increased populations can have negative effects on Z.
marina, as the increase in coastal infrastructure due to booming populations have been cited as a
critical threat to Z. marina (Grech et al., 2012). This increasing coastal population leads to an
increase in coastal development, which can take the form of shoreline armoring. Puget Sound has
approximately 27% of its coast armored, about 13 million feet (Thom et al., 2011). Shoreline
armoring can change the sediment regime, starving beaches of sediments required to promote Z.
marina colonization/growth (Simenstad et al., 2008). Poor seedling survival due to increased
hydrogen sulfide levels (Dooley et al., 2013; Thom et al., 2011) and wasting disease (Groner et
al., 2014; Short et al., 1987) have also reduced Z. marina populations in Puget Sound.
Climate change is predicted to increase Z. marina losses due to higher water levels
reducing the amount of light able to penetrate the water column and reach seagrass blades
(Stevens & Lacy, 2012). The predicted increase in oceanic temperatures due to climate change
will also create additional stressors for seagrass, as Z. marina production is optimal in a narrow
range of 5-8 degrees Celsius, with die off more apparent at temperatures 15 degrees Celsius or
higher (Thom et al., 2001). However, changes in climate can potentially benefit Z. marina, as La
Niña and El Niño events have already proven to drastically increase production of Z. marina in
16

Washington state (Thom et al., 2003); the same study found that climate-induced changes in sealevel can potentially affect Z. marina coverage. Rising sea levels can potentially open new areas
to Z. marina colonization by inundating upper tidelands, where desiccation was once a limiting
of a factor (Duarte, 2002). Links between changes in climate and Z. marina abundance have been
observed in areas including Sequim bay during El Niño conditions, with Z. marina growth lower
during colder years and growing faster at the beginning of the 1997 El Niño, one of the strongest
in the 20th century (Puget Sound Action Team, 2007).
Z. marina Restoration

Efforts to restore global Z. marina populations have met mixed success. Common
methods employed to restore Z. marina globally include conventional seagrass restoration
methods like staples (Davis & Short, 1997; Park & Lee, 2007) and nutrient enrichment (Orth et
al., 2006), as well as alternative methods like seed dispersal (Busch et al., 2010; Orth et al.,
2006) and “Transplanting Eelgrass Remotely with Frame Systems,” known as TERFS (Short et
al., 2002). Issues with success in restoration of Z. marina populations predominately focus on
flaws in the methodology itself or stochastic environmental factors. Despite roadblocks with
previous restoration attempts, there are efforts underway to restore Z. marina populations in
South Puget Sound. The Washington DNR has a goal to increase eelgrass coverage by 20%,
approximately 4,000 hectares, by 2020 (Thom et al., 2014). The 4,000-hectare restoration criteria
is based on baseline Z. marina coverage documented in 2000 and 2008. A transplant suitability
model was created in 2014 to establish specific locations in Puget Sound where large-scale
restoration plantings would succeed. This suitability model was based on a combination of
biophysical factors, historical presence of seagrass, and results from test plantings (Thom et al.,
2014). It was concluded that Joemma Beach State Park (JSP) was a suitable site for large-scale
17

seagrass restoration. Currently, approximately 500 m2 of Z. marina is present at JSP (J. Gaeckle,
pers. comm.).
Fishes in Puget Sound

Puget Sound is home to a wide array of marine life. Phillips (1984) summarized the
communities found in the Pacific Northwest’s Z. marina into four categories: 1) permanent
residents (syngnathids, gobies, blennies, etc.) 2) seasonal residents consisting of either juveniles
(sea bass, rock fishes, greenlings, etc.) or residents during spawning seasons (squid, portunid
crabs, some shrimps) 3) transient species (puffers) and 4) casual species (undefined). Puget
Sound is also home to important migratory fishes including salmonid species like Chinook
salmon (Rice et al., 2011; Rice et al., 2012) and Pacific herring (Penttila, 2007; Phillips, 1984).
Information on fish stocks within Puget Sound are mixed, with forage fish stocks including sand
lance and pacific herring documented throughout the Sound (Penttila, 2007) as well as salmon
(Rice et al., 2012). Common fishes found in South Puget Sound (SPS) that use eelgrass during
the summer include surf smelt (Hypomesus pretiosus), sand lance (Ammodytes hexapterus),
Pacific herring, and juvenile salmonids including Chum (Oncorhynchus keta) and Chinook
(Oncorhynchus tshawytscha) salmon (Rice et al., 2012). Each of these fishes utilizes eelgrass as
a means of shelter, migration corridor, or nursery habitat during one or all of their life stages
(Phillips, 1984).
Common practices of observing fish assemblages involve active data collection methods
including seine netting and baited underwater video cameras. Seine nets are the preferred method
of net-based seagrass fish assemblage collection (Guest et al., 2003), especially when waters are
too turbid to use visual census or fishes sampled are small enough to pass through the seine net

18

mesh (Nagelkerken et al., 2001). Studies using underwater video collect continuous footage
ranging from periods of 15 minutes to 90 minutes to examine fish assemblages, although there is
no standard methodology for underwater video census. Baited cameras, although effective at
attracting fish to the field of view of the camera, can potentially bias results by attracting
scavenger fish to the experiment site that normally might not be present (Harvey et al., 2007;
Murphy & Jenkins, 2010) and can potentially attract fish from greater distances, creating bias in
fish assemblage data at the experiment site. Information on fish assemblages in South Puget
Sound are sparse, with Rice et al. (2012) being one of the first studies to document pelagic fishes
and jellyfish in Puget Sound. Their study found South Puget Sound dominated by jellyfish in the
southern sampling sites (Main basin and South Sound) while pelagic fish i.e. salmonids, herring,
flatfish, etc. were the dominant sample in the northern sampling sites (Whidbey and Rosario
basins). Species richness in South Sound was found to be highest between June and July,
although the species richness was much lower than richness during most months of sampling in
the Rosario and Whidbey basins (Figure 3). An important note in this study is that although
published in 2012, the sampling occurred in 2003, which indicates if it is one of the first studies
to assess forage fish and jellyfish in Puget Sound, there is a decade plus gap in sampling.
Differences in fish assemblages between night and day has also been observed for fish
assemblages in eelgrass (Thedinga et al., 2011) and seagrasses globally (Kopp et al., 2007;
Robertson, 1980; Unsworth et al., 2007). Abundance of fish can stay the same during day and
night, but diversity of fishes can be found to alter depending on the time of day (Thedinga et al.,
2011). Investigating differences in fish assemblages based on time of day can elucidate other
important ecosystem services seagrasses provide marine life at different times of day. Fish
assemblages in relation to Z. marina in parts of the greater pacific northwest such as California

19

(Garwood et al., 2013; Obaza et al., 2015), Oregon (Ferraro & Cole, 2010), and Alaska (Murphy,
2000) are recorded as well.

Figure 3. Mean (±SE) fish species richness per tow at four Puget Sound locations (Rice et al.,
2012)

Assemblage Theory and Seagrass

Understanding why and how areas are colonized by species requires examining the
theory behind assemblage formation and understanding the relationship between colonizing
organisms and their environment. Two prominent assemblage-based theories are neutral theory,
also known as universal neutral theory (UNT), and niche theory.
Neutral theory assumes all ecological communities of similar trophic levels are structured
by stochastic events like ecological drift, random migration, and random speciation; organisms
are identical in every other way i.e. they all have the same chances of reproduction and death
20

regardless of their species (Hubbell, 2001). Macarthur and Wilson’s island biogeography theory
is a type of neutral theory, according to Hubbell. His work was based on their island
biogeography and species area relationship work (MacArthur & Wilson, 1963). Neutral theory is
not universally accepted, sparking a widespread debate on the logistics of treating all organisms
as equal in terms of reproductive success, which some argue is too simplified of a notion that
cannot work at every spatial scale (McGill et al., 2006).
Niche theory is a group of theories that assert the importance of competition between
species as a defining factor in species distribution (Bruno et al., 2003). Niche theory, according
to Chase (2003), can be divided into two main components, the Grinnellian component,
consisting of the requirements of a species for survival in an environment (Grinnell, 1917), and
the Eltonian component, how a species affects its surrounding environment (Elton, 1927). Local
processes like environmental filtering, biotic interactions, and interspecific tradeoffs are
considered the determining factors in local assemblages (Chase & Myers, 2011). Niche theory
makes multiple assumptions to work, as summarized by Weiher et al. (2011): 1) Functional traits
are the currency of assemblages 2) species traits are fixed due to trait evolution being slower than
community assembly, and speciation takes much longer than competitive exclusion. Aspects
from both theories are important to structuring communities, as stochastic and deterministic
forces both play parts in structuring communities at various scales (Chase & Myers, 2011).
Assemblage theory in relation to seagrass and the fauna that inhabit it can be used to
examine issues of genetic resilience in relation to connectivity of beds in the wake of
disturbances like climate change (Chust et al., 2013). Unlike animals, seagrass, a plant, is not
capable of rapid expansion through movement; spreading genetic material involves pollination or
clonal reproduction (Hemminga & Duarte, 2000). The lack of physical movement makes aquatic
21

plants reliant on ocean currents for connections to other macrophyte populations for reproduction
or colonization (Filipe et al., 2011; Coleman et al., 2011). Connectivity between habitats, for
both macrophytes and the fauna that inhabit them, is critical for promoting genetic diversity and
resilience. This can prove problematic when looking at conservation of seagrass, as dispersal
limitation makes sudden habitat loss potentially critical for seagrass populations (Chust et al.,
2013). Incorporating assemblage theory into seagrass conservation can help shareholders
examine how seagrass will respond to disturbances.
Using assemblage theory to investigate fish assemblages within seagrass is based on
similar principles to seagrass assemblage theory (reliance on currents for some dispersal,
importance of genetic resilience etc.), but fishes that inhabit seagrass are not always permanent
residents. Only certain fishes spending the entirety of their lives within beds, while some fishes
spend specific life stages in seagrass beds (Phillips, 1984). Stochastic forces like ocean currents
are important for larval distribution of fishes (Cowen & Sponaugle, 2009), while patch size, edge
effects, and proximity to other environments (seagrass, mangroves, mudflats, etc.) can affect
competition and predation of fish assemblages in seagrasses (Figure 4).

22

Figure 4. Model representing different predator/prey interactions at various scales in seagrass
beds (Heck Jr. & Orth, 2007)

Seagrasses provide nearshore environments with a variety of ecosystem services that are
essential to the health of global marine waters. They are capable of absorbing and holding onto
large amounts of carbon (Duarte et al., 2013), help support nearshore sedimentation (Fonseca &
Cahalan, 1992), and provide fishes with complex habitat that translates to food sources for both
higher and lower trophic levels (Mumford Jr, 2007). Puget Sound’s resident species of seagrass,
Z. marina, is a vital component of the nearshore ecosystem, providing Puget Sound’s important
commercial fishes with critical habitat. Seagrasses are facing a global decline, and local Z.
marina populations are not exempt. Restoration efforts of Z. marina are underway in Puget
Sound, and one way to examine the effectiveness of restored sites is by examining fishes present.
Fish assemblages are an indicator of how restored seagrasses are potentially being used, and the
use of underwater video is a non-invasive way of examining what fishes are present in seagrass.
23

By looking at fish assemblages in seagrasses, stakeholders can assess if restoration efforts are
providing nearshore ecosystem services. Restoration efforts of Z. marina at Joemma State Park
are currently underway to assess if transplanted Z. marina is providing habitat functions for
fishes in a manner like other parts of Puget Sound.

24

Methods
Study Area

Joemma State Park

Joemma State Park (JSP), located at southeast Key Peninsula, is a popular destination for
camping, boating, and shellfish harvesting. A local shellfish farm uses a section of the tidelands
for aquaculture. As of 2017, approximately 500 m2 of Z. marina has been transplanted at
Joemma State Park by the Washington Department of Natural Resources (DNR). The focus of
this thesis is on two specific sites at JSP: 1) two rectangular strips of Z. marina transplanted in
2015 (Figure 5), referred to as transects three and four (T3 and T4) and 2) two bare sediment
transects of similar proportion to T3 and T4. “Bare” is defined as an unvegetated tide flat.

Figure 5. Aerial image of Joemma State Park Z. marina restoration site. Green transects lines
(not drawn to scale) labeled T3 and T4 represent approximate location of transplanted Z. marina
transects three and four. Red transects lines (not drawn to scale) represent approximate location
of bare sediment transects three and four (labeled BS3 and BS4). Red arrow indicates North
(Image courtesy of Department of Ecology, 2016).
25

Dupont Warf
The city of Dupont is home to a large (300+ m2) naturally occurring Z. marina bed at
Dupont Warf, located at the end of Sequalitchew creek (Figure 6). The continuous Z. marina bed
is large enough where it is impossible to measure its full size on foot. Notable environmental
features of the area include the freshwater input from the Sequalitchew creek (red circle in
Figure 6) and human presence due to being a scenic destination at the end of the Sequalitchew
creek hiking trail. The two locations of the fieldwork, JSP and Dupont, are 48 miles apart. The
purpose of collecting data at Dupont’s natural Z. marina bed was to provide summary
information on fish diversity and abundance at a different location with a natural Z. marina bed.
Dupont’s information was studied in relation to JSP’s data to assess any similarities or
differences in fish assemblages between the two sites. Dupont and JSP’s fish assemblages were
compared per four-day tide series, as comparison of assemblages per day was not possible due to
the inability to deploy cameras at the same time at each location (see below).

26

Figure 6. Aerial shot of Dupont Warf. Red circle indicates freshwater input from Sequalitchew
creek. Green line represents approximate area of thesis fieldwork camera deployment. Red arrow
indicates North (Image courtesy of Department of Ecology, 2016)

Grid Creation
Using a 100m transect tape, the dimensions of the two rectangular strips of the DNR’s
transplanted seagrass were measured (T3: 20 m x 1.75 m, T4: 25 m x 2.25 m). To establish the
location for each camera along the edge of the transplanted and bare sediment sites at JSP, a grid
was created with 9 cells (numbered 1-9), each representing a square 5 meters long (Figure 7).
Each cell of the grid represented a potential location for one camera, to be placed at the midpoint
of the length of the cell. Camera placement at a grid cell would be along the outer edge of the
cell (blue line in Figure 7), facing towards the inner substrate, i.e. seagrass (green color in Figure
7) or bare sediment. Each cell was assigned a number (1-9) and, using www.random.org, the
placement of each camera was randomized based on the number selected (the first 5 numbers
chosen are the assigned locations for the 5 cameras at the site). An identical grid was used to

27

randomly assign camera deployment in a measured bare sediment area at JSP, referred to as BS3
and BS4. BS3 and BS4 were parallel strips (to imitate the shape of T3 and T4) and were 13.7
meters apart based on the top left corner of BS3 to the bottom left corner of BS4, which was also
based on an approximate distance T3 and T4 were spaced apart. BS3 and BS4 were both west of
T3 and T4.
The direction each camera faced (towards the shore or away from the shore) was
randomized as well, assigned either a 1 or a 2 on random.org. A ‘1’ represented placing the
camera at the edge of the transect so that it faced the shore (West), while ‘2’ represented placing
the camera at the edge so it faces out towards the open water (East). Cameras were never
deployed in the same cell to ensure duplication of footage did not occur.
At the natural seagrass site at Dupont, creating a transect of the natural Z. marina bed was
not possible due to the large size of the bed. Therefore, each of the 5 GoPro cameras were placed
5 meters apart along one edge of the Z. marina bed. The screw anchors were left in the sediment
at Dupont for the duration of the fieldwork to ensure camera deployment was in the same spots.

28

Figure 7. Example of T3 and T4 grid created to randomize camera placement. Red circle
indicates screw anchor placement, where transect line was measured from. arrow indicates
approximate cardinal direction.

Camera Setup

A GoPro Hero 3+ camera with a programmable time-lapse intervalometers (CamDo
Solutions) in waterproof housing was used for each camera/PVC rig. Cameras were secured on
top of a 55 cm long ¾’’ PVC pipe. A 0.4 cm diameter hole was drilled 0.5 cm from the top
portion of the PVC to allow the fastening of a black plastic zip tie through the PVC and
underwater housing to secure the camera to the PVC (Appendix A.1, A.2). An angle grinder was
used to remove a portion of the top of the PVC to allow the GoPro underwater housing and
camera lens to be level (Appendix A.3). The bottom of the PVC was cut at an angle to fashion a
needle-like point to allow insertion of the PVC into sediment to be easier (Figure 8). Due to large
rocks in Dupont’s sediment, the simple insertion of the PVC rig used at JSP was not feasible.
Instead, each camera was attached to a garden screw anchor (see Figure 9) using three black
29

plastic zip ties to secure the camera in the sediment. The total length of the PVC was shorter (30
cm) to have the cameras at each location sit at the same height above the sediment (30 cm)
without inserting the PVC directly into the rocky sediment. A yellow tag with the DNR’s contact
information was attached to each camera’s PVC tubing by drilling a 0.4 cm diameter hole
approximately 5.5 cm from the top. A black plastic zip tie was used to secure the tag to the PVC.

Figure 8. Camera setup for JSP at transplanted Z. marina site.

30

Figure 9. Diagram representing camera setup at Dupont natural Z. marina site.

Camera Deployment
A total of 15 GoPro Hero 3+ cameras, each installed with a CamDoTM intervalometer and
encased in a waterproof housing were deployed. At JSP, five cameras were placed in the
randomized grid at T3 and T4 while 5 cameras were placed in the randomized grid at BS3 and
BS4. During each deployment, a 100m transect tape was secured to the screw anchor on the
southern end of the Z. marina strip, and the tape was stretched across the strip to create the
length of the grid on site. Camera placement was determined prior to deployment based on
randomization.
The natural seagrass bed at Dupont was too far away from JSP to deploy cameras the
same day as the JSP site (Figure 10), so cameras were deployed within two days of camera
deployment at JSP to collect data during the same tide series.
31

Figure 10. Location of both study sites in Puget Sound Green marker indicates JSP, yellow
marker indicates Dupont (Image courtesy of Google Maps, 2018).

The five cameras at Dupont were secured to the screw anchors using three black plastic
zip ties securing the PVC around the stem of the screw anchor. Due to the rocky sediment, the
camera’s PVC was unable to penetrate the rock; instead, the bottom of the PVC was placed on
the sediment surface. Camera placement was not randomized like at JSP, instead, the 5 screw
anchors remained at the location to ensure repetition with each camera deployment. The lack of
randomization was due to a lack of enough edge/shallow enough Z. marina edge to warrant
randomizing the deployment of the cameras every time.
Each camera was placed 30 cm away from the edge of the bed at all three sites, with the
lens of the camera facing towards the bed. 30 cm was chosen as the ideal distance from the Z.
marina bed to view a majority of the bed (within the cameras viewpoint) and minimize wasted
32

recording of bare sediment areas outside of transects. At both sites, the PVC was inserted 25 cm
deep at JSP, putting the camera approximately 30 cm above the sediment. Camera deployment
occurred during low tide. At the time of deployment, the time of each camera’s deployment was
recorded, as well as weather and temperature.
Measuring visibility

Visibility was measured after camera deployment. A printed/laminated secchi disk (35
cm diameter) was held at camera height (30 cm above sediment) and moved away from a Go-Pro
Hero 3+ camera installed with a CamDoTM intervalometer (not one of the cameras used during
deployments) at 0.5-meter increments until the 4 or 5-meter mark. The intervalometer was
programmed so it would not activate, letting the camera record continuous video footage.
Distance away from the camera was determined by holding a measuring tape and walking away
from the camera holding the secchi disk at the approximate height of the camera. The location
for determining visibility was at a bare sediment location at least 30 meters away from deployed
cameras.
Camera Programming

A 2-minute video was recorded every 10 minutes on each camera once cameras were
deployed in the field. The Cam-DoTM intervalometer attached to the back of each Go-Pro camera
was programmed to turn on the camera every 10 minutes, while a coding script on the SD
memory card was programmed to auto-record the first 2 minutes of video once the camera was
turned on via the intervalometer. 2-minute clips were recorded for 24 hours after deployment.

33

Camera Retrieval

Cameras were retrieved approximately 24 hours after deployment during low tide. At the
time of retrieval, average canopy height of the square meter approximately one meter away from
the camera measured at each retrieval. Average canopy height was measured by averaging the
tallest blade (leaf) measurement of three different seagrass shoots and taking 80% of that value
per Washington DNR protocol (J. Gaeckle, pers. comm.). After average canopy height was
measured at each camera’s deployment location, the camera was removed. Zip ties fastening the
cameras to the PVC were cut to access the camera’s memory cards. Cameras (in underwater
housing) and PVC were rinsed with fresh water after retrieval to prevent salt water damage.
Data Analysis

Footage after nightfall was discarded due to lack of visibility. In addition, clips became
increasingly shorter as time went on due to reduced battery life but clips shorter than 30 seconds
were discarded. Clips with 1/4th of the screen obstructed by sea lettuce (Ulva lactuca) for 20 or
more seconds were discarded. Every fish present within the field of observation was identified to
species (if possible) or to one of four groupings (flatfishes, forage fishes, gunnels, and
salmonids). The number of fish that enter the field of view was counted, with fish that left the
field of view and returned within 10 seconds being considered the same fish, and not recounted.
The dependent variables measured were fish abundance, fish diversity, vertical location
of fishes (pelagic, above seagrass, within seagrass, benthic), and foraging behavior based on
buccal expansion and/or lunging (yes/no). This thesis presented results based on fish abundance
and diversity, but not on vertical location or foraging behavior. Independent variables measured
34

at each deployment included canopy height, tidal current (rising, high, falling, or low), and
weather at time of deployment (cloud coverage, temperature), and major environmental issues
(large presence of algae, etc.).
Fish groupings were created based on ability to identify down to species. If species
identification was not possible, fish were identified to groups based on body type (flatfishes,
salmonids, etc). Fish count data was converted into count/hour data to reduce the number of
zeros. Count/hour data was analyzed using a Kruskal-Wallis test with a Dunn’s test for pairwise
differences to determine abundance associations based on site type. Count data was also
analyzed for abundance in relation to time of day. Graphs showing abundance in relation to time
of day were selected based on data having a majority of non-zero values (Appendix B). Fish
species/groups that were not recorded at a site during majority of the research period (example:
spiny dogfish abundance at JSP was zero for entire research period) are not presented. Graphs
were evaluated qualitatively for patterns relating abundance to time of day or tidal period. Serial
correlation between time and abundance was examined by calculating a correlogram in R
statistical software (R Core Team 2018). Shiner perch was the only fish group examined using
the serial correlation because the it had the largest amount of count data of all the fish groupings.

35

Results
A total of 78,963 fish were counted over a total of 2,276 clips. 705 clips were from the
natural site, 753 from bare sediment, and 818 from the transplanted site. The majority of the clips
(92.3%) lasted two minutes, only 176 (7.7%) of all clips had a recording time of less than two
minutes. 12 fish species or groups were recorded that included most of fishes seen between all
three sites. Eight species could be reliably identified (shiner perch, pacific snake prickleback,
pacific staghorn sculpin, bay pipefish, tube-snout, pile perch, striped surfperch, and spiny
dogfish, see Table 1 for scientific names) while an additional four groups were identified by their
body shape (flatfishes, gunnels, forage fishes, and salmonids). Shiner perch were the most
abundance fish across all three sites, while bay pipefish and tube-snout were the least common
species seen between all three sites (Table 1). Of the 12 species or groups, only spiny dogfish
and striped surfperch were not viewed in any clips at JSP (transplanted and bare sediment sites);
all 12 species or groups were viewed at the natural site.

36

Table 1. Median Fish Count/Hour for each Fish Species or Group
Fish
Bare Sediment Transplanted
Natural
Fish Identified to Species
302.17
278.51
1632.75
Shiner Perch (Cymatogaster aggregata)
2.83
0.64
0.25
Pacific Snake Prickleback (Lumpenus sagitta)
0.45
0.73
1.25
Pacific Staghorn Sculpin (Leptocottus armatus)
0.00
1.00
0.00
Bay Pipefish (Syngnathus leptorhyncus)*
0.00
0.00
2.25
Tube-snout (Aulorhynchus flavidus)*
0.22
0.22
2.25
Pile Perch (Rhacochilus vacca)
0.00
0.00
2.39
Striped Surfperch (Embiotoca lateralis)
0.00
0.00
0.32
Spiny Dogfish (Squalus acanthias)
Fish Identified to Body Type
14.13
6.85
207.27
Forage Fishes
18.7
4.16
2.89
Flatfishes
1.19
0.43
5.96
Salmonids
0.23
0.14
4.81
Gunnels
* For the bay pipefish and tube-snout, a zero median count/hour does not mean a complete
absence of that species in that site. There was one tube-snout observed at the transplanted site
and one at the bare sediment site, and one bay pipefish observed at the natural and bare
sediment sites.

Abundance Based on Site Type

Natural Z. marina

Five fish species or groups (shiner perch, gunnels, tube-snout, striped surfperch, and
spiny dogfish) had varying abundance across the three sites (Figures 11-15). Abundance of
shiner perch and gunnels was higher in natural than transplanted Z. marina (Shiner perch:
Kruskal-Wallis χ2(2) = 6.74, P = 0.034, Dunn test Z = -2.33, P = 0.059. Gunnels: Kruskal-Wallis
χ2(2) = 6.72, P = 0.035, Dunn test Z = -2.51, P = 0.036). Abundance of tube-snouts, striped
surfperch and spiny dogfish was higher in the natural site compared to the bare sediment and
transplanted sites (Tube-snout: Kruskal-Wallis χ2(2) = 10.19, P = 0.0061, transplanted and natural
site Dunn test Z = -2.76, P = 0.017, natural and bare sediment site Dunn test Z = 2.61, P = 0.027.
37

Striped surfperch: Kruskal-Wallis χ2(2) = 9.88, P = 0.0071, transplanted and natural site Dunn test
Z = -2.63, P = 0.026, natural and bare sediment Dunn test Z = 2.63, P = 0.026. Spiny dogfish:
Kruskal-Wallis χ2(2) = 13.29, P = 0.0013, transplanted and natural site Dunn test Z = -3.07, P =
0.0064, natural and bare sediment site Dunn test Z = 3.07, P = 0.0064).

a*
ab

b*

Figure 11. Shiner Perch abundance based on site type. Different letters indicate a significant
difference based on Dunn’s test at *P < 0.05, or 0.05 < P < 0.10.

a*

ab

b*

Figure 12. Gunnel abundance based on site type. Different letters indicate a significant difference
based on Dunn’s test at *P < 0.05, or 0.05 < P < 0.10.

38

a*

b*

b*

Figure 13. Tube-snout abundance based on site type. Different letters indicate a significant
difference based on Dunn’s test at *P < 0.05, or 0.05 < P < 0.10.

a*

b*

b*

Figure 14. Striped surfperch abundance based on site type. Different letters indicate a significant
difference based on Dunn’s test at *P < 0.05, or 0.05 < P < 0.10.

39

a**

b**

b**

Figure 15. Spiny dogfish abundance based on site type. Different letters indicate a significant
difference based on Dunn’s test at **P < 0.05, or 0.05 < P < 0.10.
Transplanted Z. marina
The abundance of bay pipefishes varied across the three sites (Figure 16, Kruskal-Wallis
χ2(2) = 8.42, P = 0.015). The abundance of bay pipefishes was higher in transplanted seagrass
compared to the natural seagrass (Dunn test Z = 2.68, P = 0.022).

b*

ab
a*

Figure 16. Bay pipefish abundance based on site type. Different letters indicate a significant
difference based on Dunn’s test at *P < 0.05, or 0.05 < P < 0.10.

40

Bare Sediment
The abundance of flatfishes varied across the three sites (Figure 17, Kruskal-Wallis χ2(2) =
10.22, P = 0.0060). The abundance of flatfishes was lower in natural seagrass compared to the
bare sediment (Dunn test Z = -3.04, P = 0.0071).

a**

ab
b**

Figure 17. Flatfish abundance based on site type. Different letters indicate a significant
difference based on Dunn’s test at **P < 0.05, or 0.05 < P < 0.10.

No Observable Relationship

Five fish species or groups (pacific snake prickleback, forage fishes, pacific staghorn
sculpin, pile perch, and salmonids) had no variation across the three sites. These five groups
(Figures 18-22) also had no pairwise differences in abundances between the three sites (Pacific
Snake Prickleback Kruskal-Wallis χ2(2) = 4.94, P = 0.085. Forage fish Kruskal-Wallis χ2(2) =
2.39, P = 0.30. Pacific Staghorn Sculpin Kruskal-Wallis χ2(2) = 2.66, P = 0.26. Pile perch
Kruskal-Wallis χ2(2) = 4.50, P = 0.11. Salmonid Kruskal-Wallis χ2(2) = 3.39, P = 0.18.

41

Figure 18. Pacific Snake Prickleback abundance based on site type. Different letters indicate a
significant difference based on Dunn’s test at *P < 0.05, or 0.05 < P < 0.10.

Figure 19. Forage fish abundance based on site type. Different letters indicate a significant
difference based on Dunn’s test at *P < 0.05, or 0.05 < P < 0.10.

42

Figure 20. Pacific staghorn sculpin abundance based on site type. Different letters indicate a
significant difference based on Dunn’s test at *P < 0.05, or 0.05 < P < 0.10.

Figure 21. Pile perch abundance based on site type. Different letters indicate a significant
difference based on Dunn’s test at *P < 0.05, or 0.05 < P < 0.10.

43

Figure 22. Salmonid abundance based on site type. Different letters indicate a significant
difference based on Dunn’s test at *P < 0.05, or 0.05 < P < 0.10.

Abundance Based on Time of Day

The abundance of fish over the course of a single day did not have statistically significant
autocorrelation for any species x day combination, with one exception (shiner perch on
7/22/2017 at the transplanted eelgrass site, see Appendix B). Therefore, the following summary
should be taken as a qualitative description based on the plots alone (Appendix B). Nine fishes
(shiner perch, flatfishes, pacific snake prickleback, forage fishes, gunnels, pipefish, pile perch,
striped surfperch, spiny dogfish) at the natural site had a majority (3 or more of the 5 research
days) of their peak count/efforts (abundance) between low and high tides, with a decline in
abundance generally after the peak value; flatfishes at the bare sediment site also had a peak
abundance between tides that generally decreased afterwards. Similarities between JSP and
Dupont in terms of abundance in relation to time of day were not apparent. Peak abundance was
earlier in the day (closer to low tide) for shiner perch (JSP transplanted), flatfish (both sites JSP),
and tubenose (natural site) with a decline in abundance throughout the day. Peaks in abundance
around specific hours of the day were apparent for a majority of pacific snake prickleback days
44

(close to 7 PM at natural site) and forage fishes days of observation (close to 6 or 7 PM at natural
site). Other noticeable relationships between abundance peaks and time of day were an
increasing abundance past the high tide period for flatfishes at the transplanted site; in addition,
pacific staghorn sculpin had an early peak in abundance and then a decline throughout the
observation period for most of the research days.

45

Discussion
Out of the 12 fish species or groups observed in this study, two species (striped surfperch
and spiny dogfish) were not observed Joemma State Park (JSP) sites (bare sediment and
transplanted Z. marina). All 12 fish species or groups were observed at the natural eelgrass site at
Dupont Warf. Shiner perch was the most abundant fish observed throughout the study. Shiner
perch abundance at the natural site was significantly greater than in transplanted seagrass. These
results concur with previous studies that have shown a relationship between shiner perch and Z.
marina when investigating fish assemblages in Z. marina (Obaza et al., 2015; Robinson &
Yakimishyn, 2013). Gunnels, striped surfperch, and tube-snout had significantly higher
abundances with the natural Z. marina when compared to transplanted Z. marina; bay pipefishes
had a significantly higher abundance in transplanted Z. marina when compared with natural Z.
marina. Each of these fishes have been observed to inhabit Z. marina and prefer said habitat to
unvegetated areas elsewhere on the west coast of the United States (Hosack et al., 2006; Johnson
et al., 2003; Johnson et al., 2010). Together these results may indicate a preference for vegetated
habitat over unvegetated habitat.
Z. marina provides a source of refuge and nursery habitat for fishes (Bertelli &
Unsworth, 2014; Lazzari, 2015), as well as a food source from the macroinvertebrates and other
epifauna that inhabit Z. marina (Reum & Essington, 2008). The role of a nursery, refuge, and a
location that prey inhabit are all potential explanations for the association of these fishes with the
Z. marina recorded during this study. Preference for natural or transplanted Z. marina in this
study compared to bare sediment could be dictated by food availability (Macreadie et al., 2010),
edge effects, predation, or patch scale variables (size of Z. marina patch, closeness to other
environments i.e. other Z. marina patches, algae, bare sediment (see Gillanders, 2007 for
46

review), all of which have been shown to influence fish abundance and diversity within seagrass
beds. Fish assemblages have also been observed to be influenced by seagrass shoot density and
blade length (McCloskey & Unsworth, 2015), as well as predation that can change based on the
scale of observation (Heck Jr. & Orth, 2007). Macroinvertebrate abundance in relation to
seagrass can also be influenced by shoot density (Attrill et al., 2000) and blade surface area (De
Troch et al., 2005), in addition to patch dynamics and edge effects (Dorenbosch et al., 2007;
Hensgen et al., 2014). A mix of these factors could be influencing the associations of the 12 fish
species/groupings between the three site types, but this study was not designed to assess which
factors specifically affected fish assemblages.
Flatfishes were found in greater abundance at the bare sediment site when compared to
the natural eelgrass site. Flatfishes are benthic fishes, predominately resting on the sediment
surface. Flatfishes are also cryptic, making use of their flat body shape and crypsis to hide on the
sediment surface, often burying themselves within the sediment to avoid predation (Ryer et al.,
2008; Ryer et al., 2004). Observing fewer flatfish in Z. marina compared to bare sediment could
be due to the flatfishes’ commonly being found in sandy and muddy substrate, which it uses for
camouflage and protection (Gibson et al., 2014). However, juvenile flatfishes have been
observed to prefer vegetation like Z. marina as habitat, likely to avoid predation by hiding in the
vegetation (Murphy, 2000). Flatfishes in the Pacific Northwest are known to have preferences
for certain sand types and grain size (Moles & Norcross, 1995; Rooper et al., 2003), however,
habitat structures like shells and sponges can also affect flatfish habitat preference (Ryer et al.,
2004). Sediment preference of certain Pacific Northwest flatfishes, including Lepidopsetta
polyxystra and Platichthys stellatus (the latter of which was identified as one of the flatfishes in
the flatfish grouping) can shift during their first year of development (Moles & Norcross, 1995;
47

Ryer et al., 2004). Open sediment, i.e. bare sediment with no structural complexity, can benefit
flatfishes by having higher foraging opportunity, but also increase predation risk (Ryer et al.,
2004). The life stage of the flatfishes identified in this study was not determined, so it’s difficult
to know whether any differences in abundances observed were due to differences in their stage
of development.
Salmonids did not have a significant association with any site type; however, salmonids
were observed at all three sites. Salmonids were also the third most abundant fish out of the 12
groups and species. Although it has been shown that juvenile salmonids use seagrass for feeding
and shelter (Simenstad et al., 1982), and salmonid association with Z. marina has been observed
in other studies (Harris et al., 2008), there was no association between salmonid abundance and a
site type in our study. Salmonids are highly mobile predator has been noted to use Z. marina
beds. Juvenile chinook salmon travel through estuaries from April through July (Healey, 1982)
while coho, sockeye, and some chinook travel through estuaries from April through June (Duffy
et al., 2005). These months coincide with the time frame of our study, and evidence of salmonids
traveling through Z. marina beds during recordings aligns with those months as well. The age of
salmonids recorded on video was not possible, as they were moving too fast past cameras to
assess potential age based on image alone.
Spiny dogfish were found to have higher abundance in natural Z. marina at Dupont
Warf, in comparison to both transplanted seagrass and bare sediment at JSP. Spiny dogfish have
been observed in Puget Sound during summer months (Reum & Essington, 2008), explaining
their presence for the duration of this study. Spiny dogfish are a higher trophic level than the
other fish groupings recorded, all of which can be considered lower mesopredators. Spiny
dogfish feed on pacific herring (Harvey et al., 2012; Jones & Geen, 1977; Tanasichuk et al.,
48

1991), a fish that uses Z. marina beds for spawning habitat in Puget Sound (Phillips, 1984). In
addition, they have been caught in/near Z. marina beds in other parts of Puget Sound, and are
considered as a part of the Z. marina food web (Penaluna & Bodensteiner, 2015). Spiny
dogfish’s presence at the natural seagrass could have been dictated by a larger presence of its
food source at that site. Although pacific herring was not one of the fish identified in the fish
groupings, other forage fishes were observed in larger numbers at the natural site, indicating a
possibility that pacific herring, a forage fish, would also have been in larger numbers at that site.
There were no significant associations between fish and site type for pacific snake
pricklebacks, forage fishes, pacific staghorn sculpin, and pile perch. These fish are all mobile
mesopredators, and the use of non-baited video cameras to record fish assemblages means it is
inevitable that some fishes were not recorded, or those fish that were recorded were not
representative of the entire population. Evidence of these fishes and their association with Z.
marina for habitat has been observed in other studies (Johnson et al., 2003; Johnson et al., 2010;
Murphy, 2000; Robinson & Yakimishyn, 2013), so the lack of evidence from this study should
not be taken to mean that these fishes do not in fact have a significant association with Z. marina.
Fish assemblages in seagrass have been previously observed to change in abundance in
relation to time of day. A change in tides changes the amount of water above seagrass beds:
higher tides mean more room for fishes to move around seagrass beds, which can be beneficial
for fishes feeding on pelagic invertebrates or predator fishes maneuvering through seagrass beds
for prey. Lower tides can often leave seagrass exposed, as was the case for the first two sampling
days in this research, preventing fishes from inhabiting seagrass beds. Lower tides also make it
harder for larger predator fish to maneuver through seagrass beds, giving smaller prey fish a
better chance at survival.
49

Changes in seagrass fish assemblages based on time of day can also be caused by fish
migrations to/from seagrass beds from nearby habitats. Fishes have been observed to migrate
from coral reefs and mangroves to/from seagrass beds at night, suggesting diel changes in
assemblages based on nearby habitats (Kopp et al., 2007; Unsworth et al., 2007). The change in
habitat selection could be due to differences in protection from predators (Thedinga et al., 2011)
and/or differing food availability based on time of day (Unsworth et al., 2007). Fishes in tropical
regions have been observed to migrate to seagrass beds to feed at specific times of the day based
on prey availability (Robblee & Zieman, 1984; Unsworth et al., 2007). Diel changes in
assemblages can also be caused by trophic dynamics, with the presence/absence of a few select
species of fishes affecting the assemblages in seagrass (Thedinga et al., 2011). Migration can
also take place within vertical water column above seagrass beds, traveling vertically based on
food availability and protection from predators (Ruso & Bayle-Sempere, 2006).
The presence of a peak in abundance between low and high tide for mesopredator fishes
(shiner perch, flatfishes, pacific snake prickleback, forage fishes, gunnels, pipefish, pile perch,
and striped surfperch) could be dictated by food availability and/or protection from predators.
Incoming and outgoing tides could affect the presence of pelagic zooplankton and small
invertebrates that these mesopredators feed on. Incoming tides could bring more nekton and
seston from deeper waters, increasing food availability which could cause increased abundance
due to feeding. Differences in fish groups/species peaks based on time of day could be due to
different peaks in food availability as well, as the diets of these mesopredators are not necessarily
identical and could consist of invertebrates that have higher abundances based on different times
of day. Another potential factor in mesopredator abundance could be the amount of water above
the Z. marina. More water above Z. marina as the tide heightens means larger predator fishes
50

(spiny dogfish, salmonids, etc.) can move through the beds to hunt mesopredator fishes. The
explanation for the rise to a peak mesopredator abundance then a decline afterwards could be the
time of day trade-off mesopredator fishes make between foraging in Z. marina and being
vulnerable to predation. Spiny dogfish peak abundance between tides could also be related to
diel changes in prey abundance at the study sites, but peak abundance was scattered between low
and high tide, making it difficult to ascertain if their abundance was in relation to peaks or
declines in abundance for other fishes examined in this study. It is not possible to determine if
nearby habitat affected fish assemblages at the study sites, as various sized patches of Z. marina,
bare sediment, and drifting algae were present at each study site but were not examined in the
scope of this research. In addition, diel changes in assemblages based on trophic could not be
examined due to the inability to record at night.
Limitations of the Study Design

The lack of replication limits the ability to draw conclusions about differences in
abundance across sites. Any differences cannot be directly attributed to the presence or absence
of Z. marina, due to the lack of replicates in the research design. More replicates (sites) would
create a more robust picture of fish assemblages in each site. However, due to limited resources
and time this study was not able to examine multiple sites.
In addition, the lack of a bare sediment site at the natural eelgrass site (Dupont) to serve
as a comparison was another design flaw. With only one bare sediment site at JSP, it is difficult
to draw robust conclusions about fish assemblages between both JSP and Dupont’s seagrass sites
without a baseline bare sediment site to reference for Dupont. The bare sediment site at JSP had
statistically significant differences in fish counts/hour for flatfishes, so having a bare sediment

51

site at the natural seagrass site would have been beneficial to compare the two bare sediment
sites for flatfish significance. Adding a bare sediment site at the natural seagrass site would have
also provided more information about fish assemblages present near said seagrass at Dupont.
In this study it was not possible to mimic the dimensions of the transplanted bed with the
natural bed surveyed, which meant any differences in fish activity/presence could be due to size
of the eelgrass bed alone. The large amount of seagrass edge habitat present at the transplanted
site was not matched at the natural site section used for the study. It is well documented that fish
have different uses of edge vs bed habitat, with edges providing different habitat for
predator/prey interactions (Bologna, 2006; Bologna & Heck, 2002; Moore & Hovel, 2010). The
position of a fish within a seagrass patch and the location of said seagrass patch in relation to
other patches has been observed to affect predation, as predation at seagrass edges is greater than
other locations in some seagrass beds (Smith et al., 2011). The larger amount of continuous Z.
marina at the natural site could have potentially created different predator/prey interactions
compared to the transplanted site, which could bias the assemblages.
Fish are influenced by the complexity of their environment, and it became apparent that
there was a noticeably larger amount of Ulva lactuca and Laminaria was present at the natural
site. Algae can provide additional habitat and food sources for fish and invertebrates (Adams et
al., 2004; Gartner et al., 2013), especially when compared with habitat lacking any type of
vegetation (Sogard & Able, 1991), which could potentially influence their presence in the area.
Gunnels were often recorded hiding within Ulva lactuca, which could explain their higher
abundance at the natural site compared to the other two sites. Ulva lactuca presence was
observed at all three sites, but was seen more at the natural site, while Laminaria was only
observed at the natural site.
52

The inability to deploy cameras at both JSP and Dupont on the same day makes it
difficult to ascertain any conclusions about time-related fish assemblages. Although cameras
often covered similar timeframes on different days, there are a myriad of possibilities that could
occur in a 24-hour period that could affect which fish are recorded, including weather events,
human presence, and other stochastic factors. Another issue with camera placement lies in the
fact that it is possible for double counting to have occurred. It is possible that fish counted during
one clip were present during the unrecorded 10-minute segments between recordings and
counted again for the following clip at any of the cameras at each site. The lack of
synchronization between cameras at all sites also means it is possible for fishes to have swum
between cameras during recordings, causing them to be counted multiple times as separate
fishes. Taking continuous footage between each camera was one way to solve the issue of double
counting, but it would have resulted in less overall footage due to constraints with battery life.
Completing this study in an open environment meant dealing with uncontrollable
environmental factors. Drifting algae was present at each site, often obstructing camera lenses.
Loss of footage related to Ulva lactuca covering camera lenses caused large portions of certain
days footage to be thrown out. Another issue with recording came from multiple cameras failing
to record entire days’ worth of clips in the first few deployments, likely an issue caused by
human error in programming the intervalometers. Issues were also apparent with fish
identification. Video quality was not fine enough to identify smaller species of fishes, or fishes
over 1.5 to 2 meters away from camera. Color patterns of fishes, often used for identification,
proved to be difficult to identify due to water coloration and camera grain (Figure 23).
Recordings after 7:00 PM often magnified these difficulties, as image quality significantly
deteriorated after sunset. Identification (to the species level) of small flatfishes, gunnels, and
53

salmonids proved to be the most difficult for these reasons. Smaller flatfishes and gunnels were
too small for the cameras to identify markings, while the salmonids often moved past cameras
too quickly to be able to identify. Cryptic fishes or fishes hiding within seagrass beds were also
difficult to identify, as viewing within the Z. marina benthos was not possible due from the angle
of the cameras. Cryptic species like flatfishes proved to be difficult to identify in the bare
sediment site due to their nature to blend into the surrounding sediment. Despite this array of
issues with fish identification, the 12 groupings of fish were based on fishes predominately seen
at each site, with unidentified species being a minority of the fishes observed.

Figure 23. Example of difficulties when identifying fish species due to time of day and color of
water.

Future Improvements

This thesis can be considered a pilot study in the use of non-invasive underwater video to
examine fish assemblages. However, there is room to improve the methodology. The addition of
a bare sediment site at the natural seagrass site would have made this study’s results more robust,
as comparisons could have been made between both Z. marina sites and both bare sediment sites.
54

In addition, it would have provided supplementary information on fishes present in Dupont’s
bare sediment. Fish assemblages could be quantitatively compared based on time of day between
each of the sites, as some fish are known to have diurnal patterns of behavior (Michael B.
Robblee & Zieman, 1984; Robertson, 1980; Thedinga et al., 2011). This data could help
determine if South Puget Sound fish assemblages are using seagrass differently between different
times of day. Temporal patterns in fish assemblages could also be investigated, as Z. marina fish
assemblages undergo changes based on season (Garwood et al., 2013). Investigating each of
these influences on fish assemblages would help create a better understanding of fish abundance
and diversity in Puget Sound’s Z. marina communities, which would contribute to the greater
understanding of how Z. marina, both natural and transplanted, supports fish communities.
Conclusion

Fish diversity was comparable between natural and transplanted Z. marina in south Puget
Sound, with only 2 of the 12 fish species or groupings not present in all three sites. Abundance of
fishes was significantly associated with natural Z. marina (Dupont Warf) or transplanted Z.
marina (JSP) for shiner perch, gunnels, pipefish, Tube-snout, Striped surfperch, and Spiny
dogfish. The lack of significant association between the other fish groupings (Pacific snake
prickleback, pacific staghorn sculpin, salmonids, forage fishes) could have been due to random
chance or lack of replicates, as each of these fishes have been observed to have associations with
Z. marina habitat as a means of refuge, food, or nursery. The significant association of flatfishes
with bare sediment habitat was potentially due to increased foraging potential in bare sediment
habitat as well as preference for specific types of sediment. Future efforts to examine fish
assemblages using a passive method could consider these results as a pilot study to guide
methodology for future research.
55

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Appendices

Appendix A. Camera/PVC rig setup: 1 & 2) GoPro underwater housing attachment to PVC. 3)
Top portion of PVC modified with angle grinder for underwater housing to sit level on PVC

Appendix A.1

Appendix A.2

78

Appendix A.3

79

Appendix B. Fish abundance based on time of day. Blue line indicates low tide, red line indicates high tide. Tide values are in Feet.
The asterisk on 7/22/2017 for shiner perch indicates significant autocorrelation at lag 1 (0.643), based on the correlogram.

-3.7

-3.5

14.9

14.7

-1.5

-3.2

13.8

14.6

-2.9

-1.4

14.7

13.9

-0.5

-1.8

11.9

14.0

-1.0

13.6

-0.9 13.7

*

80

Flatfish

-3.7

-3.5

14.9

14.7

-1.5

-3.2

13.8

14.6

-2.9

-1.4

14.7

13.9

-0.5

-1.8

11.9

14.0

-1.0

13.6

-0.9 13.7

81

Pacific Snake Prickleback

-3.7

-3.5

14.9

14.7

-1.5

-3.2

13.8

14.6

-2.9

-1.4

14.7

13.9

-0.5

11.9

-1.0

13.6

-1.8

14.0

-0.9 13.7

82

Forage Fishes

-3.7

-3.5

14.9

14.7

-1.5

-3.2

13.8

14.6

-2.9

-1.4

14.7

13.9

-0.5

11.9

-1.8

14.0

-1.0

13.6

-0.9 13.7

83

Pacific Staghorn Sculpin

-3.7

-3.5

14.9

14.7

-1.5

-3.2

13.8

14.6

-2.9

-1.4

14.7

13.9

-0.5

-1.8

11.9

14.0

-1.0

13.6

-0.9 13.7

84

Gunnels

-3.7

-3.5

14.9

14.7

-1.5

-3.2

13.8

14.6

-2.9

-1.4

14.7

13.9

-0.5

-1.8

11.9

14.0

-1.0

13.6

-0.9 13.7

85

Pipefish

-3.5

14.7

-3.2

14.6

-1.4

13.9

-1.8

14.0

-0.5

11.9

-0.9 13.7

Tube-snout

-3.7

14.9

-1.5

13.8

-2.9

14.7

-1.0

13.6

86

Pile Perch

-3.7

-3.5

14.9

14.7

-1.5

-3.2

13.8

14.6

-2.9

-1.4

14.7

13.9

-0.5

11.9

-1.0

13.6

-1.8

14.0

-0.9 13.7

87

Striped Surfperch

-3.7

14.9

-1.5

13.8

-2.9

14.7

-0.5

11.9

-1.0

13.6

14.9

-1.5

13.8

-2.9

14.7

-0.5

11.9

-1.0

13.6

Spiny Dogfish

-3.7

88

Salmonids

-3.7

-3.5

14.9

14.7

-1.5

-3.2

13.8

14.6

-2.9

-1.4

14.7

13.9

-0.5

-1.8

11.9

14.0

-1.0

13.6

-0.9 13.7

89

Media

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