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The Eastern Oyster Microbiome and Its Implications in the Marine Nitrogen Cycle

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The Eastern Oyster Microbiome and Its Implications in the Marine Nitrogen Cycle W&M ScholarWorks Dissertations, Theses, and Masters Projects Theses, Dissertations, & Master Projects 2017 The Eastern Oyster Microbiome and its Implications in the Marine Nitrogen Cycle Ann Arfken College of William and Mary - Virginia Institute of Marine Science, [email protected] Follow this and additional works at: https://scholarworks.wm.edu/etd Part of the Aquaculture and Fisheries Commons, Marine Biology Commons, and the Microbiology Commons Recommended Citation Arfken, Ann, "The Eastern Oyster Microbiome and its Implications in the Marine Nitrogen Cycle" (2017). Dissertations, Theses, and Masters Projects. Paper 1516639592. http://dx.doi.org/doi:10.21220/V5QT7T 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]. The Eastern Oyster Microbiome and Its Implications in the Marine Nitrogen Cycle A Dissertation Presented to The Faculty of the School of Marine Science The College of William and Mary in Virginia In Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy by Ann M. Arfken January 2018 APPROVAL SHEET This dissertation is submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy Ann M. Arfken Approved by the Committee, December 2017 Bongkeun Song, Ph.D. Committee Chair / Advisor Iris C. Anderson, Ph.D. Ryan B. Carnegie, Ph.D. Lisa M. Kellogg, Ph.D. Michael F. Piehler, Ph.D. University of North Carolina at Chapel Hill Morehead City, North Carolina TABLE OF CONTENTS ACKNOWLEDGEMENTS ........................................................................................... v LIST OF TABLES ......................................................................................................... vii LIST OF FIGURES ....................................................................................................... x ABSTRACT ................................................................................................................... xiii CHAPTER 1 Introduction to the Dissertation ......................................................................... 2 References .......................................................................................................... 12 CHAPTER 2 Denitrification potential of the eastern oyster microbiome using a 16S rRNA gene based metabolic inference approach ........................................ 24 Abstract .............................................................................................................. 25 Introduction ........................................................................................................ 27 Materials and Methods ....................................................................................... 32 Results. ............................................................................................................... 40 Discussion .......................................................................................................... 45 Conclusions ........................................................................................................ 51 Acknowledgements ............................................................................................ 52 References .......................................................................................................... 53 CHAPTER 3 Seasonal effects on the eastern oyster (Crassostrea virginica) microbiome and associated denitrification activity in the Lynnhaven River, Virginia ................................................................................ 75 Abstract .............................................................................................................. 76 Introduction ........................................................................................................ 78 Materials and Methods ....................................................................................... 83 Results. ............................................................................................................... 91 Discussion .......................................................................................................... 101 Conclusions ........................................................................................................ 115 Acknowledgements ............................................................................................ 117 References .......................................................................................................... 118 iii" CHAPTER 4 Composition and diversity of the eastern oyster (Crassostrea virginica) microbiome and associated denitrifiers to spatial and temporal changes in the Chesapeake Bay, VA .................................................. 153 Abstract .............................................................................................................. 154 Introduction ........................................................................................................ 156 Materials and Methods ....................................................................................... 160 Results. ............................................................................................................... 168 Discussion .......................................................................................................... 182 Conclusions ........................................................................................................ 197 Acknowledgements ............................................................................................ 198 References .......................................................................................................... 199 CHAPTER 5 16S rRNA gene-based comparison of composition and diversity of development stages in the eastern oyster (Crassostrea virginica) larval microbiome .............................................................................................. 238 Abstract .............................................................................................................. 239 Introduction ........................................................................................................ 241 Materials and Methods ....................................................................................... 245 Results. ............................................................................................................... 251 Discussion .......................................................................................................... 257 Conclusions ........................................................................................................ 265 Acknowledgements ............................................................................................ 267 References .......................................................................................................... 268 CHAPTER 6 Conclusions ........................................................................................................ 293 APPENDICES Appendix I: Perkinsus marinus infection in oyster microbiomes ..................... 298 Appendix II: N2O production by oyster microbiomes ....................................... 302 VITA .............................................................................................................................. 304 iv" ACKNOWLEDGEMENTS I am grateful for the many people who have supported me along the way in the pursuit of my PhD. First and foremost, I must thank my advisor, Bongkeun Song for keeping me on track and providing me an endless supply of optimism and encouragement. I am truly appreciative for his guidance. I also thank my committee members Iris Anderson, Ryan Carnegie, Lisa Kellogg, and Mike Piehler for their contributions, much needed second opinions, and helpful feedback. Many thanks to the members of the Song lab past and present who have helped me tremendously with everything from locating missing samples to lugging dozens of 5lb carboys full of seawater back to VIMS. To Jess Lisa, for always offering support and being a true friend as we transitioned from UNCW to VIMS, to Miguel Semedo for his enthusiasm and keeping me sane, to Ken Czapla for his humor and dedication to field work despite eye injuries, Hunter Walker for his help piloting the boat and navigating the Anderson lab, to Ashley Smyth for keeping the MIMS happy, and to lab Raegan Bostic, Sam Fortin, Stephanie Wilson, Tavis Sparrer, Anjali Bhatnagar for their assistance with lab and field work. Thanks are also in order to VIMS community and all many friendships that have been made. A special thanks to Terry Mayo for always looking out for me, to Tony Nalovic for always getting me to see a different side of things, to Quang Huynand Fei Ye for our dinners at Peter Chang’s, and to Zoemma Warshafsky for being an awesome office mate. I am also thankful for my “special interest” group at VIMS, which has been a great escape from the rigors of academia. To Sarah Pease for being a great friend and a great support, to Lydia Bienlien for her encouragement and advice, to Seth West for helping with my computer issues and seemingly vast knowledge of everything, to Skyler West for his creativity and game mastery, to Robin Rennie for taking charge and making
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