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THE MICROBIOME of the EASTERN OYSTER, Crassostrea

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THE MICROBIOME of the EASTERN OYSTER, Crassostrea THE MICROBIOME OF THE EASTERN OYSTER, Crassostrea virginica, IN HEALTH AND DISEASE by Eric G. Sakowski A dissertation submitted to the Faculty of the University of Delaware in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biological Sciences Fall 2015 © 2015 Eric G. Sakowski All Rights Reserved ProQuest Number: 10014741 All rights reserved INFORMATION TO ALL USERS The quality of this reproduction is dependent upon the quality of the copy submitted. In the unlikely event that the author did not send a complete manuscript and there are missing pages, these will be noted. Also, if material had to be removed, a note will indicate the deletion. ProQuest 10014741 Published by ProQuest LLC (2016). Copyright of the Dissertation is held by the Author. All rights reserved. This work is protected against unauthorized copying under Title 17, United States Code Microform Edition © ProQuest LLC. ProQuest LLC. 789 East Eisenhower Parkway P.O. Box 1346 Ann Arbor, MI 48106 - 1346 THE MICROBIOME OF THE EASTERN OYSTER, Crassostrea virginica, IN HEALTH AND DISEASE by Eric G. Sakowski Approved: __________________________________________________________ Robin W. Morgan, Ph.D. Chair of the Department of Biological Sciences Approved: __________________________________________________________ George H. Watson, Ph.D. Dean of the College of Arts and Sciences Approved: __________________________________________________________ Ann L. Ardis, Ph.D. Interim Vice Provost for Graduate and Professional Education I certify that I have read this dissertation and that in my opinion it meets the academic and professional standard required by the University as a dissertation for the degree of Doctor of Philosophy. Signed: __________________________________________________________ K. Eric Wommack, Ph.D. Professor in charge of dissertation I certify that I have read this dissertation and that in my opinion it meets the academic and professional standard required by the University as a dissertation for the degree of Doctor of Philosophy. Signed: __________________________________________________________ Shawn W. Polson, Ph.D. Professor in charge of dissertation I certify that I have read this dissertation and that in my opinion it meets the academic and professional standard required by the University as a dissertation for the degree of Doctor of Philosophy. Signed: __________________________________________________________ E. Fidelma Boyd, Ph.D. Member of dissertation committee I certify that I have read this dissertation and that in my opinion it meets the academic and professional standard required by the University as a dissertation for the degree of Doctor of Philosophy. Signed: __________________________________________________________ John R. Jungck, Ph.D. Member of dissertation committee I certify that I have read this dissertation and that in my opinion it meets the academic and professional standard required by the University as a dissertation for the degree of Doctor of Philosophy. Signed: __________________________________________________________ M. Ramona Neunuebel, Ph.D. Member of dissertation committee I certify that I have read this dissertation and that in my opinion it meets the academic and professional standard required by the University as a dissertation for the degree of Doctor of Philosophy. Signed: __________________________________________________________ Carl J. Schmidt, Ph.D. Member of dissertation committee ACKNOWLEDGMENTS There are many people I need to thank, without whom this would not have been possible. I must begin by thanking my advisors, Dr. Eric Wommack and Dr. Shawn Polson. They have been a constant source of support and guidance. Eric has an infectious enthusiasm for viral ecology that has not diminished since we first met. His enthusiasm did not waiver even when the rest of ours did during those late nights on the research cruises. Eric has always encouraged me to think ambitiously and push boundaries, for which I am extremely grateful. I wish him the best of luck as he takes on new challenges as deputy dean. Shawn has been an invaluable source of knowledge on a seemingly inexhaustible number of topics (seriously, is there anything he doesn’t have at least a passing knowledge of?). No matter how busy he is – and he is always busy – his door has always been open. I truly appreciate the many thought-provoking impromptu conversations we shared. I must also thank my committee members who have been there to help guide me along the way. Dr. Fidelma Boyd has been a part of this journey through nearly every major milestone, beginning with my Preliminary exam. I thank her for her guidance and insights. Thank you to Dr. Diane Herson, who was always encouraging. I wish her all the best as she prepares for a well-deserved retirement. I must also thank Dr. John Jungck and Dr. Ramona Neunuebel who both graciously agreed to join my committee last minute. Their support is greatly appreciated. Thank you to Dr. Carl Schmidt, whose novel perspective has led me to answer questions I had not thought to v ask. Finally, I must thank Dr. David Smith, who was always teaching whether he was inside a classroom or outside of it. I hope he is enjoying his retirement. There are several members of the community to whom I am grateful. Eric Weissberger and Carol McCollough of the Maryland Dept. of Natural Resources were instrumental in getting this project started. They were there to aid in sample collection early in the morning every month and helped put me in contact with the wider oyster community. I must also thank Mitch Tarnowski and David White of the Maryland Dept. of Natural Resources for allowing me to tag along the annual MD fall oyster survey and collect my own samples. Thank you, as well, to John Ewart of the Delaware Aquaculture Resource Center, E.J. Chalabala of the DE Center for the Inland Bays, and Jeff Harrison for their aid with sample collection. I must also express my gratitude to current and past members of the Wommack Lab. This would not have been possible without the aid of undergraduate interns and graduate students alike, and their support helped me to persevere when it seemed like there was no light at the end of the tunnel. For this I am truly grateful. Finally, I must thank my friends and family for their love and support. They were unwavering through the good times and bad and never once complained that I was talking about grad school AGAIN. vi To my loving wife, Lauren. For everything. vii TABLE OF CONTENTS LIST OF TABLES ......................................................................................................xiii LIST OF FIGURES...................................................................................................... xv ABSTRACT ................................................................................................................xix Chapter 1 INTRODUCTION.............................................................................................. 1 1.1 General Biology of Crassostrea virginica ................................................ 1 1.2 Ecological Impacts of C. virginica............................................................ 2 1.3 Threats to Current and Future C. virginica Populations ........................... 5 1.3.1 Habitat degradation ....................................................................... 5 1.3.2 Temperature and pH...................................................................... 6 1.3.3 Bacterial pathogens ....................................................................... 8 1.3.4 Viral pathogens............................................................................ 10 1.3.5 Protozoan pathogens.................................................................... 11 1.4 The Oyster Microbiome .......................................................................... 14 1.4.1 Microbiomes and host health....................................................... 14 1.4.2 Commensal bacteria in oysters.................................................... 16 1.4.3 The oyster microbiome and bacterial pathogens......................... 19 1.4.4 Protozoan-bacterial interactions .................................................. 20 1.5 Natural Viral Assemblages in Oysters .................................................... 21 2 SEASONALLY DYNAMIC AND DIFFERENTIALLY REGULATED BACTERIAL COMMUNITIES IN OYSTER EXTRAPALLIAL FLUID MAY PLAY A ROLE IN SHELL FORMATION........................................... 25 2.1 Abstract ................................................................................................... 25 2.2 Introduction ............................................................................................. 26 2.3 Materials and Methods ............................................................................ 29 2.3.1 Annual survey sample collection................................................. 29 2.3.2 Bacterial abundance and correlations.......................................... 30 2.3.3 Bacterial DNA isolation .............................................................. 31 viii 2.3.4 16S amplification, barcoding, and sequencing............................ 31 2.3.5 Denoising and taxonomic assignment......................................... 32 2.3.6 Rarefaction of oyster and water samples..................................... 32 2.3.7 Bacterial community composition of oyster and water samples. 33 2.3.8 Bacterial abundance correlations with environmental parameters...................................................................................
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