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Biology and Long-Term Trends of Alien Hydromedusae and Striped Bass in a Brackish Tidal Marsh in the San Francisco Estuary

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Biology and Long-Term Trends of Alien Hydromedusae and Striped Bass in a Brackish Tidal Marsh in the San Francisco Estuary Biology and Long-Term Trends of Alien Hydromedusae and Striped Bass in a Brackish Tidal Marsh in the San Francisco Estuary By Robert Egon Schroeter B.S. (University of California, Davis) 1993 M.S. (University of Nevada, Reno) 1998 DISSERTATION Submitted in partial satisfaction of the requirements for the degree of DOCTOR OF PHILOSOPHY in Ecology in the OFFICE OF GRADUATE STUDIES of the UNIVERSITY OF CALIFORNIA DAVIS Committee in Charge 2008 UMI Number: 3350788 INFORMATION TO USERS The quality of this reproduction is dependent upon the quality of the copy submitted. Broken or indistinct print, colored or poor quality illustrations and photographs, print bleed-through, substandard margins, and improper alignment can adversely affect reproduction. In the unlikely event that the author did not send a complete manuscript and there are missing pages, these will be noted. Also, if unauthorized copyright material had to be removed, a note will indicate the deletion. ® UMI UMI Microform 3350788 Copyright 2009 by ProQuest LLC. All rights reserved. This microform edition is protected against unauthorized copying under Title 17, United States Code. ProQuest LLC 789 E. Eisenhower Parkway PO Box 1346 Ann Arbor, Ml 48106-1346 Copyright Robert Egon Schroeter December 2008 Ecology Biology and Long-Term Trends of Alien Hydromedusae and Striped Bass in a Brackish Tidal Marsh in the San Francisco Estuary ABSTRACT Pelagic fish declines and increased abundance of gelatinous zooplankton are increasingly common in physically and ecologically disturbed estuaries. This dissertation investigates the ecology and trends of three alien hydromedusae (Maeotias marginata, Blackfordia virginica, and Moerisia sp.) and striped bass Morone saxatilis in Suisun Marsh in the upper San Francisco Estuary. Chapter one examines the ecology and long term (1981-2005) trends of M. marginata medusae using by-catch data from an otter trawl survey. Maeotias marginata increased in abundance with its greatest spatial occurrence and abundance after 1992. Salinity and temperature were significant predictors of medusae abundance with moderate salinity and high temperature resulting in their highest abundance. Water transparency was related to medusae abundance, but had a smaller effect. Medusae fed primarily on pelagic invertebrates, although benthic / epibenthic prey and larval fishes were also found in the gut contents. Chapter two reports the environmental relationships and abundance of three hydromedusae from a two year (February 2004 to January 2006) plankton study. Moerisia was the most abundant species, followed by M. marginata and B. virginica. Salinity and temperature had the largest effect on predicted occurrence and abundance although turbidity and dissolved oxygen were significant at times. Maeotias marginata was captured at the lowest salinity and temperature and was the first and last species captured each year. Moerisia was captured in samples with slightly higher salinity, but similar temperatures as M. marginata. Blackfordia virginica was captured - ii - in moderate to high salinity. Chapter three investigates the seasonal trends in striped bass young-of-year (YOY) abundance (1980 to 2005) and their environmental relationships, habitat use, and prey relationships. Striped bass YOY declined in deep water sites, but not in shallow tidal marsh sites. Environmental conditions were poorly correlated with striped bass abundance in all seasons. Prey species declined similarly in all depth groups. The declining abundance of mysids and adult copepods were correlated with the YOY decline in deep water sites only. Increased mean YOY length and seasonal recruitment shifts after the decline of mysids, suggests additional affects of changing prey abundance. - iii - ACKNOWLEDGEMENTS Many people helped make this dissertation become a reality. Special thanks to my advisor, Peter Moyle, who provided the opportunity, encouragement, and full support from beginning to end. Peter's amazing knowledge and gestalt of fisheries and aquatic ecology was an invaluable resource and his foresight in striving for an all inclusive long term monitoring survey, including the blobs of jelly (i.e. Maeotias marginata), provided the basis for much of this work including the longest running survey of gelatinous zooplankton in the San Francisco Estuary. Thanks to my dissertation committee, Peter Moyle, Ted Grosholz, and Bill Bennett, who provided guidance and valuable comments throughout. Ted Grosholz provided valuable perspective in the discipline of invasion ecology and knowledge in estuarine ecology. Bill Bennett provided thoughtful feedback that challenged me to elevate the quality of the analyses and manuscripts. The fish ecology research group provided helpful comments and stimulating discussion on early drafts including Alpa Wintzer, Mariah Meek, Ron Yoshiyama, Jon Rosenfield, Joaquin Feliciano, and Filipe Ribeiro. Many thanks to the faculty and students in the Graduate Group in Ecology and special thanks to Silvia Hillyer for keeping me on track. Special thanks to the field/lab crew including Joe Heublein, Joe Sullivan, John Nogue, Jill Anderson, Katie Small, and Alphonse Leander-Ramos and countless other volunteers and assistants that toiled under the marsh sun, Suisun winds, and bone chilling winter cold to make sure one more month of sampling was done. Without your assistance, this long-term study would not be a success. Many thanks to the lab crew including Ninder Kandola and Fei Yian Yoong that soldiered through the countless vials and helped identify and enumerate the hydromedusae. Many thanks to lab manager Pat Crain for his help on all things, especially his being at the ready to join in on the field work with only a moment's notice. - iv - Funding for the long term fish monitoring project was provided by the California Department of Water Resources. Funding for the two year plankton survey was provided, in part, by the CALFED Ecosystem Restoration Program. I am especially thankful for the support of my family. My mother, Ursula who continuously keeps me up to date with all the recent environmental articles clipped out from local papers; my father, Bruno who bestowed upon me the stubbornness and mechanical ingenuity to get through even the most difficult situation, which seemed to arise pretty much every visit to the marsh; my brother Bruno, who gave me the energy to get around, at will, at least some of that stubbornness; and my sisters Karin and Sue who provided constant encouragement throughout. To my wife Angela, who has been my true inspiration, I thank you for your unending support, faith and most importantly your unbelievable patience! Finally, to my daughter and son Gabriella and Justin, thank you for letting me see the world through your eyes, as you have continuously reminded me that life should be cherished, and filled with curiosity, excitement, and just enough comic relief to get through the rough spots; traits that any field ecologist would find useful. DEDICATION I dedicate this dissertation to you Gabriella and Justin Schroeter. May you go forth and continue to explore all the world has to offer, with open hearts and minds. - v - TABLE OF CONTENTS Abstract ii Acknowledgements iv Dedication v Acronyms viii Introduction 1 Chapter 1. Ecology and Long Term Trends of the Invasive Gelatinous Zooplankton, Mateotiaa margtnata in the San Francisco Estuary 1.1 Introduction 4 1.1.1 Basic Biology of Maeotias Marginata 6 1.2 Methods 9 1.2.1 Study Area 10 1.2.2 Field Methods 12 1.2.3 Analyses 14 Population Patterns 14 Environmental Relationships 15 Environmental Changes and Relationships with Catch 19 Spatial and Temporal Overlap with Pelagic Fishes and Diet Analysis 20 1.3 Results 22 1.3.1 Population Patterns 22 1.3.2 Environmental Relationships 23 1.3.3 Environmental Changes and Relationship to Catch 27 1.3.4 Spatial and Temporal Overlap with Pelagic Fishes and Diet 29 1.4 Discussion 31 1.4.1 Population Patterns 31 1.4.2 Environmental Relationships 34 1.4.3 Environmental Changes and Relationship to Catch 39 1.4.4 Spatial and Temporal Overlap with Pelagic Fishes and Diet 40 1.5 Conclusion 44 1.5.1 Relationship to Worldwide Patterns 46 1.6 Literature Cited 51 1.7 Tables 59 1.8 Figures 66 1.9 Appendix A 75 1.10 Appendix B 77 Chapter 2. Biology and Habitat Use of a Brackish Tidal Marsh in the San Francisco Estuary by a Trio of Alien Hydromedusae 2.1 Introduction 80 2.1.1 Background 82 2.2 Methods 87 2.2.1 Study Area 87 2.2.2 Field Methods 89 2.2.3 Analyses 90 2.3 Results 98 2.3.1 Environmental Conditions by Year 100 - vi - TABLE OF CONTENTS cont. 2.3.2 Environmental Conditions by Area 101 2.3.3 Model Diagnostic Tests and Collinearity Checks 102 2.4 Discussion 113 2.5 Conclusion 130 2.6 Literature Cited 134 2.7 Tables 139 2.8 Figures 148 Chapter 3. The Importance of Shallow Water Habitat for Striped Bass Young-of-Year in the San Francisco Estuary 3.1 Introduction 160 3.1.1 Background 163 3.2 Methods 166 3.2.1 Field Methods 166 3.2.2 Analyses 168 3.3 Results 172 3.4 Discussion 181 3.5 Conclusion 195 3.6 Literature Cited 200 3.7 List of Tables 206 3.8 List of Figures 209 - Vll - ACRONYMS Akaike's Information Criteria AIC All Time Period ATP Contra Costa Water District CCWD California Department of Fish and Game CDFG California Department of Water Resources CDWR Central Valley Project CVP Fairfield-Solano Sewer District FSSD Dissolved Oxygen DO Generalized Linear Models GLM Goodness of Fit GIF Honest Significant Difference HSD Inter-agency Ecological Program for the San Francisco Estuary IEP Likelihood Ratio LR Negative Binomial NB San Francisco Estuary SFE State Water Project SWP Suisun March Salinity Control Gates SMSCG Variance Inflation Factor VIF Yellow Springs Instruments YSI Young-of-Year YOY - viii - 1 INTRODUCTION Estuarine communities are increasingly being affected by a number of disturbances that alter community composition, population abundances and system productivity (Caddy 1993; Cohen and Carlton 1998).
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