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Sources and Composition of Particulate Organic Matter in the Sacramento-San Joaquin River Delta, California

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Sources and Composition of Particulate Organic Matter in the Sacramento-San Joaquin River Delta, California W&M ScholarWorks Dissertations, Theses, and Masters Projects Theses, Dissertations, & Master Projects 2006 Sources and composition of particulate organic matter in the Sacramento-San Joaquin River Delta, California Vicki Pilon College of William and Mary - Virginia Institute of Marine Science Follow this and additional works at: https://scholarworks.wm.edu/etd Part of the Environmental Sciences Commons, and the Oceanography Commons Recommended Citation Pilon, Vicki, "Sources and composition of particulate organic matter in the Sacramento-San Joaquin River Delta, California" (2006). Dissertations, Theses, and Masters Projects. Paper 1539616811. https://dx.doi.org/doi:10.25773/v5-1gyc-vn38 This Dissertation is brought to you for free and open access by the Theses, Dissertations, & Master Projects at W&M ScholarWorks. It has been accepted for inclusion in Dissertations, Theses, and Masters Projects by an authorized administrator of W&M ScholarWorks. For more information, please contact [email protected]. SOURCES AND COMPOSITION OF PARTICULATE ORGANIC MATTER IN THE SACRAMENTO-SAN JOAQUIN RIVER DELTA, CA A Dissertation Presented to the Faculty of the School of Marine Science of the College of William and Mary in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy by Vicki L. Pilon January 2006 Reproduced with permission of the copyright owner. Further reproduction prohibited without permission. APPROVAL SHEET This dissertation is submitted in partial fulfillment o f the requirements for the degree of Doctor of Philosophy Vicki L. Pilon Approved, January 2006 Elji^abeth A. Canuel, Ph.D. Committee Chairperson/Advisor imes E.flBauer, Ph.D. c /X . Iris C. Anderson, Ph.D. \o Jj Robert J. Orth, Pn.D. /illiam V. Sobczak, Ph.D. Department of Biology, College of the Holy Cross Worchester, MA Reproduced with permission of the copyright owner. Further reproduction prohibited without permission. DEDICATION This dissertation is dedicated to my husband Frankie Gross and my sister Nancy. To Frankie, whom I met and married during my tenure at VIMS, for his continued support and love over the course of my Ph.D., and to Nancy, who was my greatest champion when I was young, but passed away before this dream could be realized. Reproduced with permission of the copyright owner. Further reproduction prohibited without permission. TABLE OF CONTENTS ACKNOWLEDGMENTS................................................................................................................. v LIST OF TABLES.............................................................................................................................vii LIST OF FIGURES..........................................................................................................................viii ABSTRACT...........................................................................................................................;............x CHAPTER 1......................................................................................................................................... 2 Introduction CHAPTER 2 ........................................................................................................................................13 Spatial and temporal variations in organic carbon dynamics o f the Sacramento and San Joaquin Rivers, CA CHAPTER 3 ....................................................................................................................................... 75 Particulate organic matter composition in three shallow-water habitats o f the Sacramento-San Joaquin River Delta, CA CHAPTER 4 ..................................................................................................................................... 116 Sources of particulate and sediment organic matter in shallow-water habitats of the Sacramento-San Joaquin River Delta, CA CHAPTER 5 ..................................................................................................................................... 162 Spatial variability in amino acid composition and organic matter degradation of suspended particles and sediments in the Sacramento-San Joaquin River Delta, CA CHAPTER 6 .....................................................................................................................................210 Summary and conclusions APPENDICES................................................................................................................................. 232 Appendix A. Sterol concentrations in suspended particles, 1998-2000 ............. 233 Appendix B. Fatty acid concentrations in suspended particles, 1998-2000 ......244 Appendix C. Sterol concentrations in surface sediments, 1998-2000 .................257 Appendix D. Fatty acid concentrations in surface sediments, 1998-2000 ..........259 Appendix E. Water content of surface sediment, sampling season 1999-2000.261 Appendix F. Biochemical concentrations of suspended particles, 1998-2000..262 Appendix G. Biochemical concentrations of surface sediments, 1998-2000.. .265 Appendix H. Amino acid composition of suspended particles, 1998-2000 ......266 Appendix I. Amino acid composition of surface sediments, 1998-2000 ...........271 VITA...................................................................................................................................................274 Reproduced with permission of the copyright owner. Further reproduction prohibited without permission. ACKNOWLEDGMENTS My greatest praise is reserved for my advisor, Dr. Elizabeth Canuel. Through both good and tough times, she has been instrumental in guiding me and pushing me to develop the best possible dissertation. Her INFINITE patience and encouragement kept me moving forward (sometimes very slowly), and made me believe that an end was in sight!!! To say that she is a gifted scientist, teacher and mentor would not do her justice. She is truly the best. I also want to thank my committee members. To Dr. Iris Anderson, for her roles as scientific guide, Graduate Dean, and reference provider! To Dr. Jim Bauer, thank you for both scientific guidance as well as use o f lab equipment and time for my amino acid analyses. To Dr. Robert Orth, I thank you for always providing the biological point of view to my research. Finally, I want to thank Dr. William Sobczak, whose insight and encouragement allowed me to always see hope in the research, and reminded me that the Delta really is a cool place to do research. I want to thank others outside o f VIMS that made the completion o f my research possible. The crew (Byron Richards and Scott Conard) of the R/V Polaris, for always providing our research team with everything we needed. I would like to thank fellow researchers Dr. James Cloem, Brian Cole, Andrew Amsberg, Tara Schraga, Jody Edmunds, Dr. Anke Miiller-Solger, Francis Parchaso and Ken Forshay for field assistance and providing ancillary data from the cruises. I would also like to thank Dr. Antonio Mannino, Kip Gardner and Dr. David Burdige for providing assistance in developing the carbohydrate protocol I used. Dr. David Burdige also provided lab space, supplies, and assistance for my amino acid analyses. Dr. Reno Nguyen provided protocol assistance and guidance for the total protein analyses. My labmates have been a pivotal part o f my great experience at VIMS, so I would like to thank Beth Waterson, Melissa Ederington-Hagy, Dr. Krisa Arzayus, and Dr. Andrew Zimmerman. Thanks to Cathy Mingee and Courtney Graves, who were my F.I.R.S.T. students, so to speak, and aided in the analyses of the total proteins samples as part o f their student proj ects. Every member of the VEMS staff should be commended for their dedication to m aking VIMS a world-class institute, and a home for graduate students. In particular, I would like to thank Sue Presson and Fonda Powell for keeping my paperwork on track. To Cynthia Harris, Cindy Hornsby and Beth Marshall for their assistance on everything from travel reimbursement to getting my paycheck to me. To ITNS for addressing all my software needs and issues. To the entire library staff who always got my articles from obscure journals to me, and the staff at Publications for always making my slides and posters look perfect, I thank you all. To Vicki Clark, thank you for Seafood Seminars, they were always great fun! Finally, to Susan Haynes, for making the Outlook on Ocean Science Program a fun experience, and one that whet my appetite to continue outreach efforts in the future. Reproduced with permission of the copyright owner. Further reproduction prohibited without permission. vi VIMS friends can not be forgotten: Christine, Jennifer, Sara, David, and my incoming class in 1998, thanks for making the experience at VIMS a memorable one. A wonderful experience that I was able to participate in while a student at VIMS was the Knauss Sea Grant Marine Policy Fellowship, working at the EPA in Washington D.C. for a year. I would like to thank all employees o f the Wetlands Division, in particular Stan Austin, my branch chief, Donna, Doreen, Connie, Lori, Kathleen, Rebecca, Tracie, and Palmer for their camaraderie and guidance. To fellow Fellows in the Wetlands Division and other EPA offices: Chris, Eric, Jordan and Rachel, Laura, Rachel and Jennifer, thanks for your friendship and support. My coworkers at The Office o f Pollution Prevention and Monitoring for The Ocean Conservancy in Virginia Beach also provided invaluable support during the time I was finishing the dissertation. My director,
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