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Effects of Nitrogen-Fixing Symbiotic Cyanobacteria on the Microbial Ecology of the Coral, Montastraea Cavernosa

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Effects of Nitrogen-Fixing Symbiotic Cyanobacteria on the Microbial Ecology of the Coral, Montastraea Cavernosa University of New Hampshire University of New Hampshire Scholars' Repository Doctoral Dissertations Student Scholarship Spring 2012 Effects of nitrogen-fixing symbiotic cyanobacteria on the microbial ecology of the coral, Montastraea cavernosa Jessica K. Jarett University of New Hampshire, Durham Follow this and additional works at: https://scholars.unh.edu/dissertation Recommended Citation Jarett, Jessica K., "Effects of nitrogen-fixing symbiotic cyanobacteria on the microbial ecology of the coral, Montastraea cavernosa" (2012). Doctoral Dissertations. 652. https://scholars.unh.edu/dissertation/652 This Dissertation is brought to you for free and open access by the Student Scholarship at University of New Hampshire Scholars' Repository. It has been accepted for inclusion in Doctoral Dissertations by an authorized administrator of University of New Hampshire Scholars' Repository. For more information, please contact [email protected]. EFFECTS OF NITROGEN-FIXING SYMBIOTIC CYANOBACTERIA ON THE MICROBIAL ECOLOGY OF THE CORAL, MONTASTRAEA CAVERNOSA BY JESSICA KJARETT BS, Southampton College, 2005 DISSERTATION Submitted to the University of New Hampshire in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy in Microbiology May, 2012 UMI Number: 3525060 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. OiSi«Wior» Ftattlisttlfl UMI 3525060 Published by ProQuest LLC 2012. Copyright in the Dissertation held by the Author. Microform Edition © ProQuest LLC. All rights reserved. This work is protected against unauthorized copying under Title 17, United States Code. ProQuest LLC 789 East Eisenhower Parkway P.O. Box 1346 Ann Arbor, Ml 48106-1346 This dissertation has been examined and approved. Dissertation Director^Dr. Michael P. Lesser Research Professor, Microbiowgy and Marine Sciences Dr. Marianne Litvaitis Professor, Biology, Environmental Conservation Sciences, and Marine Sciences Dr. Louis S. Tisa Professor, Microbiology and Genetics Dr. Marc Slattery Professor, Pharmacognosy, Univej^tty^TMississippt Dr. Ruth Gates Research Professor, Zoology and Oceanography, University of Hawai'i at Manoa Hn<ojt7- Date ACKNOWLEDGEMENTS This Ph.D. has been the most challenging and rewarding undertaking of my life so far, and I have been very fortunate to have a great number of people who have helped me in this journey. First and foremost, my advisor Michael Lesser. I am grateful to him for his patience, guidance, support, and encouragement over these last five years, and for always being in my corner. Thank you for starting me on this project and trusting me enough to let me take some new approaches. I know we haven't always seen eye to eye but I think we've come to understand each other! I respect him tremendously and I have grown so much as a scientist under his guidance. I would like to thank my committee members, Marc Slattery, Ruth Gates, Lou Tisa, and Marian Litvaitis for their guidance and expertise. Special thanks to Marc Slattery from the University of Mississippi for help with experiments and collections in the field and our many edifying conversations. Ruth Gates from the University of Hawaii made me think more deeply about symbiosis and many of my underlying assumptions, which has certainly improved my writing and my work. Lou Tisa has brought to the table his truly encyclopedic knowledge of prokaryotic biology and physiology. Marian Litvaitis's expertise in invertebrate biology was invaluable. Many people at the University of New Hampshire Genome Center have helped me with the bioinformatic aspects of this project. I gleaned a great deal of invaluable information and insight from conversations with Kelley Thomas and Holly Bik. I am very grateful to Holly for helpful advice and assistance with 454 sequencing and data analysis, and for teaching me how to use ARB and QIIME. Many hours were spent in the iii computer room at Gregg Hall with Linda van Diepen and Kazu Okamoto, both of whom were always willing to talk over problems and give help. Steve Vollmer at Northeastern performed the differential expression analysis for the metatranscriptomic data, I am looking forward to our continued collaboration with him and his graduate student Stefan Kaluziak. I am indebted to Anne Cohen and Kathryn Rose at the Woods Hole Oceanographic Institution, who scanned the coral cores and instructed me in the complex process of measuring growth from CT scans. Dan Brazeau at the University of New England performed the AFLP analysis and helped me interpret the results. He also enabled Cara Fiore and I to be trained on the new 454 GS Junior pyrosequencer at UNE, and very graciously opened his home to us while we were there. Ruth Gates and Hollie Putnam kindly provided a curated database of Symbiodinium ITS2 sequences that saved me a great deal of time and effort. I am grateful to Bill Fitt at the University of Georgia for allowing me and my lab mates to work out of his small field station on Key Largo, and Dustin Kemp for his assistance with boating, diving, and coring while we were there. Marc Slattery, Deb Gochfeld, Liz Kintzing, Erica Hunkin, Cole Easson, and Sly Lee were all willing to offer excellent advice and a helping hand when needed, whether it be with diving, boating, experiments in the wet lab, or just generally making things work on a small island. Liz Kintzing deserves a special commendation for tolerating my whining with admirable grace while I was earning my scientific diver certification in cold, cold New Hampshire waters. Thanks also the Aquarius aquanauts, including Cara Fiore, Marc Slattery, and Cole Easson, who collected some of my samples from Florida, and to the topside crew iv who processed them. I thank the staff and interns at the Caribbean Marine Research Center on Lee Stocking Island, and the Little Cayman Research Centre on Little Cayman Island for logistical support. Miss Emily at LCRC earned my undying gratitude by taking excellent care of me when I was very sick during one field trip there. I am extremely grateful for the financial support of the National Science Foundation Graduate Research Fellowship Program, a luxury that enabled me to focus full-time on my research for three years. The University of New Hampshire generously provided travel funding, the COLSA summer fellowship, a summer teaching assistant fellowship, and most importantly the Dissertation Year Fellowship that gave me the freedom to write without worrying about other commitments. The UNH Marine Program, the PADI Foundation, and a Lerner-Gray Marine Research Grant from the American Museum of Natural History helped to fund my research. In the Microbiology program at UNH, I must thank Bob Mooney who was always happy to help with any number of odd and obscure tasks. Dan Merselis and Seana Fraser worked in the Lesser lab as undergraduates and helped with several aspects of this project. It was a pleasure getting to know both of them and I wish them all the best in their future endeavors. Cara Fiore and Nate Olson joined the Lesser lab in my second year and we quickly became fast friends. Nate's meticulousness encouraged me to improve my laboratory technique and I greatly miss my thought-provoking conversations with him. Cara has been my lab mate, dive buddy, field trip comrade, voice of reason, shoulder to cry on, and all around awesome friend. She has helped me out countless times and I don't think I would have made it this far without her. Cara, I quadrat you. v Special thanks to Elissa Ford and the Ford family, my "foster family" here in New England. Crystal Ellis, Brian Schuster, Christine Chapman, Cintia Felix, and Lauren Petersen are some of the best friends anyone could ask for and helped me stay more or less sane for the past five years. The NHSPCA and all the wonderful staff and volunteers there were my second home on Saturday afternoons, and took great care of my cat Squishy while she was there. My deepest gratitude to all of my family for all their love, patience, support and understanding. Mom, you've encouraged me and cheered for me every step of the way. Every day I am thankful that I get to have you as a mom. I love you and I hope I've made you proud. vi TABLE OF CONTENTS ACKNOWLEDGEMENTS iii LIST OF TABLES ix LIST OF FIGURES x ABSTRACT xii CHAPTER PAGE INTRODUCTION 1 I. NITROGEN FIXING SYMBIOTIC ASSOCATIONS IN THE MARINE ENVIRONMENT 6 Introduction 6 Marine Nitrogen-Fixing Symbioses 19 Evolution and Ecology of Marine Nitrogen-Fixing Symbiosis 35 II. METAGENETIC ANALYSIS OF THE PROKARYOTIC COMMUNITIES ASSOCIATED WITH BROWN AND ORANGE COLONIES OF THE CORAL MONTASTRAEA CAVERNOSA 39 Introduction 39 Methods and Materials 51 Results 59 Discussion 67 III. METATRANSCRIPTOMIC ANALYSIS OF MONTASTRAEA CAVERNOSA HOLOBIONTS 101 Introduction 101 Methods and Materials 111 Results 114 Discussion 119 IV. EFFECTS OF SYMBIOTIC NITROGEN-FIXING CYANOBACTERIA ON FITNESS OF THE HOST CORAL MONTASTRAEA CAVERNOSA 153 vii Introduction 153 Methods and Materials 182 Results 197 Discussion 202 CONCLUSIONS 231 LIST OF REFERENCES 237 APPENDIX 277 viii LIST OF TABLES TABLE 2.1 78 TABLE 2.2 79 TABLE 2.3 80 TABLE 2.4 82 TABLE 2.5 83 TABLE 2.6 84 TABLE 3.1 131 TABLE 3.2 132 TABLE 4.1 213 TABLE 4.2 214 TABLE 4.3 215 TABLE 4.4 216 ix LIST OF FIGURES FIGURE 2.1 85 FIGURE
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