Food web impacts of geoduck clam aquaculture practices in Puget Sound, Washington Kathleen C ...

180 Pages·2013·4.24 MB·English

Food web impacts of geoduck clam aquaculture practices in Puget Sound, Washington

Kathleen C. McPeek

A thesis submitted in partial fulfillment of the requirements for the degree of

Master of Science

University of Washington

2013

Committee:

Glenn R. VanBlaricom

David A. Beauchamp

P. Sean McDonald

Program Authorized to Offer Degree:

School of Aquatic and Fishery Sciences
©Copyright 2013
Kathleen C. McPeek
TABLE OF CONTENTS

LIST OF FIGURES ....................................................................................................................... iii
LIST OF TABLES ......................................................................................................................... vi
PREFACE .................................................................................................................................... viii
ACKNOWLEDGEMENTS ........................................................................................................... ix
PROLOGUE ................................................................................................................................... 1
CHAPTER 1 ................................................................................................................................... 9
Diet and trophic ecology of Pacific staghorn sculpin (Leptocottus armatus Girard, 1854) at
geoduck aquaculture farms and nearby reference areas ................................................................. 9
INTRODUCTION ....................................................................................................................... 9
MATERIALS AND METHODS .............................................................................................. 16
Study Area and Design .......................................................................................................... 16
Data Analysis ......................................................................................................................... 17
Mark-Recapture ..................................................................................................................... 17
Stomach Content Analysis..................................................................................................... 18
Stomach Content Data Analysis ............................................................................................ 19
Stable Isotope Sample Collection .......................................................................................... 20
Stable Isotope Processing and Analysis ................................................................................ 22
Stable Isotope Data Analysis ................................................................................................. 22
Stable Isotope Mixing Model ................................................................................................ 25
Fitness Metrics Analyses ....................................................................................................... 26
RESULTS.................................................................................................................................. 27
Mark-Recapture ..................................................................................................................... 27
Stomach Content Analysis..................................................................................................... 28
Stable Isotope Analysis ......................................................................................................... 29
Stable Isotope Mixing Model ................................................................................................ 30
Fitness Metrics Analyses ....................................................................................................... 31
DISCUSSION ........................................................................................................................... 32

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CHAPTER 2 ................................................................................................................................. 80
Bioenergetics of Pacific staghorn sculpin (Leptocottus armatus Girard, 1854) consumption and
growth at geoduck aquaculture farms and nearby reference areas ............................................... 80
INTRODUCTION ..................................................................................................................... 80
MATERIALS AND METHODS .............................................................................................. 85
Study Area and Design .......................................................................................................... 85
Model Parameterization ......................................................................................................... 86
Model Application ................................................................................................................. 87
Temperature/Thermal Experience ..................................................................................... 87
Growth ............................................................................................................................... 88
Diet Composition ............................................................................................................... 89
Feeding Rates and Individual Growth and Consumption .................................................. 90
Population Consumption .................................................................................................... 93
Biomass of Prey ................................................................................................................. 94
RESULTS.................................................................................................................................. 96
Mark-Recapture ..................................................................................................................... 96
Feeding Rates and Individual Growth and Consumption ...................................................... 97
Population Consumption and Biomass of Prey ..................................................................... 99
DISCUSSION ......................................................................................................................... 101
REFERENCES ........................................................................................................................... 157

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LIST OF FIGURES

Figure Number Page
Figure 1.1. Nets and tubes at a geoduck aquaculture site 55
Figure 1.2. Location of research sites 56
Figure 1.3. Pumping device used to sample epibenthos 57
Figure 1.4. Proportion of each prey group from sculpin stomach contents 58
Figure 1.5. Relative abundances of all fish captured during seining events 59
Figure 1.6. NMDS plot of sculpin stomach contents in May 60
Figure 1.7. NMDS plot of sculpin stomach contents in June 61
Figure 1.8. NMDS plot of sculpin stomach contents in July 62
Figure 1.9. NMDS plot of sculpin stomach contents in August 63
Figure 1.10. NMDS plot of sculpin stomach contents in September 64
Figure 1.11. NMDS plot of sculpin stomach contents for cultured plots in
May and September 65
Figure 1.12. NMDS plot of sculpin stomach contents for reference plots in
May and September 66
Figure 1.13. Stable isotope biplot for April prey groups and May sculpin 67
Figure 1.14. Stable isotope biplot for June prey groups and July sculpin 68
Figure 1.15. Stable isotope biplot for August prey groups and September sculpin 69
Figure 1.16. Stable isotope biplot for sculpin 70
Figure 1.17. Stable isotope biplot for non-corophium amphipods 71
Figure 1.18. Stable isotope biplot for corophium amphipods 72
Figure 1.19. Stable isotope biplot for crabs 73
Figure 1.20. Stable isotope biplot for filter-feeding polychaetes 74
Figure 1.21. Stable isotope biplot for predatory polychaetes 75
Figure 1.22. Stable isotope biplot for shrimp 76
Figure 1.23. Median proportions of each prey group from the mixing model 77

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Figure 1.24. Boxplot of the ratio of sculpin mass to the mass of the gut contents 78
Figure 1.25. Boxplot of the ratio of sculpin length to sculpin mass 79
Figure 2.1. Nets and tubes at a geoduck aquaculture site 128
Figure 2.2. Location of research sites 129
Figure 2.3a. Sculpin length and diet contribution of the amphipod prey group 130
Figure 2.3b. Sculpin length and diet contribution of the corophium prey group 131
Figure 2.3c. Sculpin length and diet contribution of the crab prey group 132
Figure 2.3d. Sculpin length and diet contribution of the isopod prey group 133
Figure 2.3e. Sculpin length and diet contribution of the shrimp prey group 134
Figure 2.4. Average densities of sculpin from seining data 135
Figure 2.5. Pumping device for sampling epibenthos 136
Figure 2.6. Relative abundances of all fish captured during seining events 137
Figure 2.7. P-values for sculpin recaptures at Foss in 2011 138
Figure 2.8. P-values for sculpin recaptures at Foss and Manke in 2012 139
Figure 2.9. Model projections for sculpin growth at Foss in 2011 140
Figure 2.10. Model projections for sculpin growth efficiency at Foss in 2011 141
Figure 2.11. Model projections for sculpin consumption at Foss in 2011 142
Figure 2.12. Model projections for sculpin growth at Foss in 2012 143
Figure 2.13. Model projections for sculpin growth efficiency at Foss in 2012 144
Figure 2.14. Model projections for sculpin consumption at Foss in 2012 145
Figure 2.15. Model projections for sculpin growth at Manke in 2012 146
Figure 2.16. Model projections for sculpin growth efficiency at Manke in 2012 147
Figure 2.17. Model projections for sculpin consumption at Manke in 2012 148
Figure 2.18. Model projections for sculpin growth at Rolfs in 2012 149
Figure 2.19. Model projections for sculpin growth efficiency at Rolfs in 2012 150
Figure 2.20. Model projections for sculpin consumption at Rolfs in 2012 151
Figure 2.21. Sculpin population consumption and prey biomass at Foss in 2011 152
Figure 2.22. Sculpin population consumption and prey biomass at Foss in 2012 153

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Figure 2.23. Sculpin population consumption and prey biomass at Manke in 2012 154
Figure 2.24. Sculpin population consumption and prey biomass at Rolfs in 2012 155
Figure 2.25. Sculpin population consumption and prey biomass at all sites 156

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LIST OF TABLES

Table Number Page
Table 1.1. Field site descriptions 41
Table 1.2. Diet composition of sculpin stomach contents 42
Table 1.3. Diet proportions used in the mixing model 43
Table 1.4. Numbers of tagged and recaptured sculpin 44
Table 1.5. ANOSIM results for sculpin stomach content data between plots 45
Table 1.6. ANOSIM results for sculpin stomach content data between months 46
Table 1.7. Mean δ13C and δ15N values for all organisms 47
Table 1.8. Candidate models for δ13C and Akaike weights 48
Table 1.9. Model averaged parameter weights for δ13C 49
Table 1.10. Candidate models for δ15N and Akaike weights 50
Table 1.11. Model averaged parameter weights for δ15N 51
Table 1.12. Mixing model results 52
Table 1.13. ANOVA table for the ratio of sculpin mass to the mass of the gut contents 53
Table 1.14. ANOVA table for the ratio of sculpin length to sculpin mass 54
Table 2.1. Field site descriptions 107
Table 2.2. Physiological parameters and equations used in the bioenergetics model 108
Table 2.3. Mean daily temperatures at each site and plot in 2011 and 2012 109
Table 2.4. Sculpin diet composition and energy densities 110
Table 2.5. Sculpin prey groups and energy densities used in the bioenergetics model 111
Table 2.6. Total numbers of sculpin captured 112
Table 2.7. Biomass of sculpin prey groups in 2011 at Foss 113
Table 2.8. Biomass of sculpin prey groups in 2012 at Foss 114
Table 2.9. Biomass of sculpin prey groups in 2012 at Manke 115
Table 2.10. Biomass of sculpin prey groups in 2012 at Rolfs 116
Table 2.11. Numbers of tagged and recaptured sculpin 117

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Table 2.12. P-values for sculpin recaptures from the bioenergetics model 118
Table 2.13. Average P-values of sculpin recaptures 119
Table 2.14. Candidate models for 2011 P-values from sculpin recaptures 120
Table 2.15. Model averaged parameter weights for 2011 P-values 121
Table 2.16. Candidate models for 2012 P-values from sculpin recaptures 122
Table 2.17. Model averaged parameter weights for 2012 P-values 123
Table 2.18. Total biomass of prey compared to sculpin population consumption 124
Table 2.19. Sculpin population consumption at Foss 125
Table 2.20. Sculpin population consumption at Manke 126
Table 2.21. Sculpin population consumption at Rolfs 127

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PREFACE
Subsequent chapters of the thesis are formatted with the intent of eventual submission for
publication in the appropriate peer-reviewed technical literature. Much of the introductory
material for both chapters is contained within the following prologue, parts of which are repeated
in the introductions of each chapter to facilitate fully informative stand-alone status. Sample
collection for both chapters occurred concurrently, resulting in additional repetition between
chapters in some of the methods, figures and tables.

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