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An Abstract of the Thesis Of AN ABSTRACT OF THE THESIS OF Kaitlin Mae McConnell, for the degree of Master of Science in Microbiology presented on September 6, 2019. Title: Reef Microbiomes of Mo’orea, French Polynesia, a Socio-Ecological Island System Abstract approved: ______________________________________________________ Andrew R. Thurber At a time of rapid global change, a socio-ecological system (SES) approach can provide a framework through which to quantify and communicate the risks and uncertainties of coupled human-natural systems. Islands, and tropical coral reef islands in particular, can be excellent models for SES research since they may be considered as both closed and open systems, where agents-- both human and non- human-- and their interactions, may be considered at a variety of spatial and temporal scales and with diverse levels of complexity. Bacteria and Archaea communities are the executants of biochemical cycling in systems, and alterations in the structure of microbial communities can provide indications of system-wide metabolic shifts driven by natural and human forces. In this thesis, I first present patterns of spatial and temporal variability in microbial communities across a tropical coral island reefscape, where I hypothesized: Microbiome host, habitat and sampling location will house distinct microbiomes (beta diversity) that differ between seasons. Microbiomes were primarily host specific, and host specificity varied with structural scale: microbiomes of reef sediment, seawater and corals were different from each other. Zooming in, the three species of corals examined also had distinct microbial communities associated with them. These host- specific microbiomes varied differentially across spatial scale, such as island side, reef habitat (fore, back and fringing reefs) and sampling locations. The structure of coral microbiomes supported evidence of a core microbiome with low species richness and a less-abundant but greatly richer resident microbiome or environmentally responsive community. Of 476 taxonomic families identified in our samples, sequences of the Family Endozoicamonaceae dominated all coral microbiomes, representing between 68-80% of the relative abundance of bacteria and archaea depending on species and varying less than 1% across reef habitats. Considering all coral species together, this meant that the bulk of coral microbiome richness made up less than 13% of the total microbiome. The top ten most relatively abundant families in each coral species across habitats and seasons showed that each host- and spatially distinct microbiome experienced seasonality differently. These shifts were contextualized within the scope of the Mo’orea Island Socio-Ecological system. Because coral microbiomes are sensitive to biophysical fluxes, coral microbiome diversity estimates (Chao1) were interpolated into an island- wide heatmap. By comparing and locating areas of anomalous microbiome diversity with locations of biophysical anomalies around the island, such as increased nitrogen concentrations, we found that locations of convergent anomalies were situated near to areas of increased human activity, although uncertainty exists as to at what extent and whether human activity is a directly causative effect. However, our maps do provide evidence for the integration of human and natural systems at local to microbial scales. ©Copyright by Kaitlin Mae McConnell September 6, 2019 Creative commons license Reef Microbiomes of Mo’orea, French Polynesia, a Socio-Ecological Island System by Kaitlin Mae McConnell A THESIS submitted to Oregon State University in partial fulfillment of the requirements for the degree of Master of Science Presented September 6, 2019 Commencement June 2020 Master of Science thesis of Kaitlin Mae McConnell presented on September 6, 2019 APPROVED: Major Professor, representing Microbiology Head of the Department of Microbiology Dean of the Graduate School I understand that my thesis will become part of the permanent collection of Oregon State University libraries. My signature below authorizes release of my thesis to any reader upon request. Kaitlin Mae McConnell, Author ACKNOWLEDGEMENTS It is exciting that this work is the result of collaborative efforts that began years before I arrived at Oregon State University and will continue well beyond the snapshot in time this thesis presents. Thank you to my thesis advisor, Dr. Andrew Thurber, for guiding me through the process of conducting and completing research, and for helping me out of the weeds as necessary. Thank you also for challenging me to stretch myself to achieve greater quality work, and to finish on time. Thank you to Dr. Rebecca Vega Thurber for your tireless work for coral reefs, for spearheading the Mo’orea Virus Project and for sharing some of your knowledge and skills with me in class, the field and in the lab. Thanks also to the many talented researchers, students and student volunteers that work on the Mo’orea Virus Project: Thurber, Vega Thurber, Correa and Burkepile Labs. I would like to give a special thank you to my labmates Sarah Seabrook and Katie Darr, and especially undergraduate volunteers Dylan Swift and Akshar Patel, for their hard work in preparing hundreds of samples for sequencing. Thank you to Dr. Michael Banks for being my advisor for the NRT program and providing guidance on my research. I so enjoyed our meetings and chats. Thank you so much for inviting me to join your vibrant lab community during Thursday meetings, for sharing interesting opportunities with me and also recommending me for them. It meant a lot that you would keep me in mind. I also am deeply grateful to the Banks Lab, especially David Jacobson, for your kindness and generosity when showing me how to amplify our samples more quickly using multi-channel pipettes and several thermocyclers. Thank you so much for welcoming me in your lab space at Hatfield, and for your hospitality-- I felt like a very well taken care of, honored guest. And, I am sure the efficiency I gained from working out of your lab played a major role in being able to finish this work on time. Also, the use of the online R interface on your super computer made the data analysis and visualization process so much quicker and less taxing on my poor, often melting laptop. Thank you Banks Lab, I so enjoyed spending time with you and I thank you all so much for your support. Thank you to the principle investigators of the NSF Research Traineeship program in Risk and Uncertainty Quantification in Marine Science for creating such a transformative and applicable graduate minor. And thank you, of course, to our Mo’orea Socio-Ecological Island System team: Brank Black, Risako Sakai, Adriana Messyasz and Aaron Weinstock. Go beavs, as they say! I would like to express my sincere gratitude to the wonderful and supportive community at the illustrious Oregon State University, who had not only had faith in a me when they decided to accept me into the historic Microbiology Department, but also saw me through to the end of my MS.Dr. Kim Halsey, thank you for providing our cohort with a safe, fun and constructive place to give our first, and probably worst, presentation of our future theses during your Scientific Skills course. Dr. Steve Giovannoni, thank you for getting me excited about microbes and reminding me that the some of the oldest questions, such as “How did life begin?” or “Where do we come from?” are not dead. Dr. Ricardo L’Atelier of CEOAS, I am grateful for our many conversations, and thank you for always having an open door. Thank you to my closest friends here, the Graduate Students! Thank you to the members of my committee whom I have not yet mentioned: Dr. Byron Crump, thank you for scripting help and for your honest advice. Dr. Scott Heppell, thank you for being a part of this process and for your insights. I would also like to express my gratitude to the rest of the many fine professors and faculty in Microbiology, CEOAS and Fisheries and Wildlife for such an enriching experience. Thank you to people of the Center for Genomic Research and Biocomputing. I am grateful to Chris Sullivan for his miraculous ability to assist and accommodate so many new biocomputing learners, including me. Thank you also to Ed Davis, who sent me a simple few lines of code which turned out to be a total game changer in my struggle with data analysis. Thank you to Mark Dasenko for troubleshooting and sequencing all of our samples. Also, I would like to thank Dr. Sam Bowser and Steve Clabuesch for bringing me to Antarctica with them and the B-043 team to collect forams in 2016, my first experience with microbiology. It wasn’t until then that I really felt empathy for the tiny beings I was disturbing while sifting through the cold, dark mud on the seafloor. Cheers to you for inspiring me to pursue a graduate education in Microbiology, and for the best collection of sci-fi and diving-related media west of the McMurdo Sound. Last but not least, thank you to my family, extended family and friends who were with me these last two years. What a ride! I love you. This work was supported by National Science Foundation Division of Graduate Education award 1545188 and National Science Foundation - Biological Oceanography Awards 1635913 and 1933165. This research was also supported by and used data from the Mo’orea LTER National Science Foundation – Oceanography – Award 1637396. DEDICATION Dedicated to my grandfather, John McConnell, who in 1969 designed the “authentic” Earth Flag, inspired by the view of the Earth from space. Dedicated also to the Micronesian islanders who, earlier this year, showed me the flag of the “Pacific Alternative,” a new Earth Flag depicting the Earth adorned with symbolic regalia on a background of stars and galaxies. CONTRIBUTION OF AUTHORS Chapter 1 Andrew R Thurber advised this thesis. He also conceived of the Mo’orea Virus Project from which the samples analyzed in this thesis were derived, participated in data collection, assisted in the data analysis and interpretation, and reviewed manuscripts.
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