W&M ScholarWorks Dissertations, Theses, and Masters Projects Theses, Dissertations, & Master Projects 2013 Abundance, structure and function of zooplankton-associated bacterial communities within the York River, VA Samantha L. Bickel College of William and Mary - Virginia Institute of Marine Science Follow this and additional works at: https://scholarworks.wm.edu/etd Part of the Ecology and Evolutionary Biology Commons, Marine Biology Commons, and the Microbiology Commons Recommended Citation Bickel, Samantha L., "Abundance, structure and function of zooplankton-associated bacterial communities within the York River, VA" (2013). Dissertations, Theses, and Masters Projects. Paper 1539616567. https://dx.doi.org/doi:10.25773/v5-mrzd-mq81 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]. ABUNDANCE, STRUCTURE AND FUNCTION OF ZOOPLANKTON- ASSOCIATED BACTERIAL COMMUNITIES WITHIN THE YORK RIVER, VA A Dissertation Presented to The Faculty of the School of Marine Science The College of William and Mary In Partial Fulfillment Of the Requirements for the Degree of Doctor of Philosophy by Samantha Lynn Bickel 2013 APPROVAL SHEET This dissertation is submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy '/ Samantha L. Bickel Approved by the Committee July, 2013 f Kam W. Tarig, Ph.D. Committee Chaiirnan/ Advisor Vladk J. Brush, Ph.D. J. Emmett Duffy, Ph.D. J Kimberly S. Reece, Ph.D. JsA cOu Fred C. Dobbs, Ph.D. Old Dominion University Norfolk, VA TABLE OF CONTENTS Page ACKNOWLEDGEMENTS........................................................................................................ vi LIST OF TABLES...................................................................................................................... vii LIST OF FIGURES..................................................................................................................... ix ABSTRACT.................................................................................................................................. xi AUTHOR’S NOTE..................................................................................................................... xii CHAPTER 1 Introduction to the Dissertation ...................................................................................................2 INTRODUCTION..................................................................................................................... 3 STRUCTURE OF DISSERTATION......................................................................................6 REFERENCES...........................................................................................................................9 CHAPTER 2 Zooplankton-associated and free-living bacteria in the York River, Chesapeake Bay: Comparison of temporal variations and controlling factors..................................................12 ABSTRACT............................................................................................................................. 13 INTRODUCTION................................................................................................................... 14 MATERIALS & METHODS.................................................................................................17 RESULTS.................................................................................................................................25 DISCUSSION..........................................................................................................................30 REFERENCES........................................................................................................................ 39 CHAPTER 3 Structure and function of zooplankton-associated bacterial communities in a temperate estuary change more with time than zooplankton species .....................................................55 ABSTRACT.............................................................................................................................56 INTRODUCTION...................................................................................................................57 MATERIALS & METHODS.................................................................................................61 RESULTS..................................................................................................................................67 DISCUSSION..........................................................................................................................72 REFERENCES.........................................................................................................................82 CHAPTER 4 Carbon substrate usage by aerobic and facultative anaerobic bacteria associated with estuarine zooplankton ............................................................................................................... 103 ABSTRACT........................................................................................................................... 104 INTRODUCTION................................................................................................................. 105 MATERIALS AND METHODS........................................................................................ 109 RESULTS................................................................................................................................114 DISCUSSION........................................................................................................................118 LITERATURE CITED.........................................................................................................127 CHAPTER 5 Conclusions and Future Research ............................................................................................149 Zooplankton-associated bacteria in Estuarine Systems ................................................... 150 Future Research Directions ..................................................................................................153 REFERENCES.......................................................................................................................157 APPENDIX I Fluorescence in situ Hybridization with bacterial group specific probes .......................... 161 MATERIALS & METHODS...............................................................................................162 RESULTS & DISCUSSION................................................................................................165 REFERENCES.......................................................................................................................166 APPENDIX II Alternative Multiple Regression Models Assessed by AIC 168 APPENDIX III Zooplankton Community Composition VITA ACKNOWLEDGEMENTS There are a number of people who generously shared their time, knowledge and resources with me during my time at VIMS. Without them, this dissertation would not have been possible. First and foremost, I would like to thank my advisor and mentor, Kam Tang. I truly appreciate his generosity with his time, and exceptional guidance and patience when things didn’t go quite as planned. He constantly challenged me to think critically and helped me become a better scientist. I am grateful for all members of the Tang lab, past and present who helped with experiments or were available for conversations, including David Elliott, Haley Garrison, Yuan Dong, Sikai Peng and Jami Ivory. I would also like to thank my committee members, Drs. Fred Dobbs, Kim Reece, Mark Brush and Emmett Duffy for their advice and interest in my research. Funding for this research was provided by NSF grant OCE-0814558, NSF GK-12 program (Division of Graduate Education 0840804), a VIMS Dean’s fellowship and a Leibniz Institute for Freshwater Ecology and Inland Fisheries (IGB) visiting PhD student fellowship. Thank you to the entire MiBi group at IGB including Hans-Peter Grossart, Kirsten Pohlmann, Claudia Dziallas, Solvig Pinnow, Ivette Salka, Franzi Leunert, Stefan Rosel, Katrin Attermeyer and Katharina Frindte, for welcoming me and making me feel at home during my time in Germany in addition to sharing your knowledge of microbial ecology. I want to thank a number of people at VIMS for sharing data and equipment, processing samples, helping with procedures and trouble shooting, and just being helpful in general: Steven Baer, Quinn Roberts, Steve Kaattari, Ryan Carnegie, Alanna MacIntyre, Gail Scott, Bill Jones, Nancy Stokes, Gina Burrell, Maxine Butler and Fonda Powell. Also, a huge thank you to all the people that gave the opportunity to participate in the GK-12 program: Kam Tang, Iris Anderson, Carol Hopper-Brill, Vicki Clark, Pat McGrath, Amy Holtschneider and all the students at Chesapeake Bay Governor’s School and York High School. Even when I was in the throes of data analysis and dissertation writing, your enthusiasm made me remember how much fun science can be and why I wanted to be a scientist in the first place. To all my friends, I don’t think I can ever repay you for the kindness, generosity, encouragement and support you have offered me throughout the years. Thank you for your willingness to help in the lab and field at the strangest hours, but more