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 i 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 ii 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 iii 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 iv 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 v 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 vi 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 vii 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. viii