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Species-And Temporal-Specific Coral Microbiome Fluctuations In AN ABSTRACT OF THE THESIS OF Erica Ewton for the degree of Master of Science in Microbiology presented on June 17, 2021. Title: Species- and Temporal-Specific Coral Microbiome Fluctuations in Response to a Natural Bleaching Event Abstract approved: ______________________________________________________ Andrew Thurber Corals provide a diversity of ecosystem services, are among the most biologically diverse ecosystems on Earth, and directly support ~500 million people globally; however, corals are increasingly experiencing significant threats and are undergoing severe bleaching events as the result of the warming climate. Using a two-year data set surrounding a massive bleaching event around the island of Mo’orea, French Polynesia, this study examines a vital determiner of coral health: its microbiome. We hypothesized that the microbiomes of the dominant corals Acropora hyacinthus, Pocillopora verrucosa, and Porites lobata would show stochastic responses to bleaching, yet degrees of resistance to bleaching would be coral species specific. Among all coral microbiomes, certain dominant families shifted in response to bleaching; however, coral species-specific responses were seen regarding fluctuations of Shannon diversity and richness, in addition to shifts in the relative abundance of the highly abundant family Endozoicomonas. Acropora hyacinthus bleached most readily. Pocillopora verrucosa had the lowest percent abundance of Endozoicomonas months before and during bleaching. In addition, it was the only coral species to have its microbiome increase in diversity and decrease in Endozoicomonas percent abundance before bleaching; however, its health trajectory followed that of Porites lobata relatively closely. Trends in the microbial community inhabiting Porites lobata including family level richness and diversity and Endozoicomonas levels followed those of Acropora hyacinthus closely. ©Copyright by Erica Ewton June 17, 2021 All Rights Reserved Species- and Temporal-Specific Coral Microbiome Fluctuations in Response to a Natural Bleaching Event by Erica Ewton A THESIS submitted to Oregon State University in partial fulfillment of the requirements for the degree of Master of Science Presented June 17, 2021 Commencement June 2022 Master of Science thesis of Erica Ewton presented on June 17, 2021. APPROVED: Major Professor, representing Microbiology Head of the of 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. Erica Ewton, Author ACKNOWLEDGEMENTS I would like to express sincere appreciation for a number of people who expanded my scientific and computational understanding, encouraged me to swim – not sink – amidst a sea of data, and immersed me in the down and dirty of ‘scientist’. Andrew, thank you for propelling me through such a foundational part of my career. You stuck with me through highs and lows and believed in my abilities before I even knew I had them. You taught me to assert rather than question my theories while still contemplating alternate views – this is a lesson I will carry ceaselessly. Thank you to my thesis committee for your flexibility and support through this unusual accelerated masters experience; your constructive feedback and seasoned points of view kept my project within reasonable bounds while expanding my view of possibilities. Thank you to my undergraduate and graduate professors who have broadened my understanding and self-confidence in microbiology. You taught me the material, but also how to conduct myself in scientific and professional settings through stellar examples that I strive to embody throughout my career. Thank you to the GeoMicrobiology group for all your support and enthusiasm for learning. You encouraged me to share my science in a welcoming atmosphere that boosted my presentation and discussion skills like no other environment. Thank you to the coding geniuses out there – those of you who stayed up late helping trouble shoot have taught me not only where the parentheses go but how far camaraderie does as well. Thank you to my close friends and fiancé for lifting my spirits during stressful times and reminding me that we are all simply human. Thank you to my undergraduate mentee Heather Hirsch for asking amazing questions and volunteering countless hours towards sample preparation. Thank you to the Thurber, Vega-Thurber, and Correa labs for collecting samples, processing some data, and sharing knowledge of protocols and the Mo’orea reef system. This research was supported in part by National Science Foundation, Biological Oceanography Grants: 1635913, 1933165, and 1635798. TABLE OF CONTENTS Page 1 Introduction ...……………………………………………………………………… 1 2 Materials and Methods …………..………………………………………………… 6 2.1 Site Description ………………………….....…………….……………… 6 2.2 Sample Recovery and Data Gathering……………...………….………… 7 2.3 DNA Extraction, Purification, Amplification, and Sequencing ………...10 2.4 Data Analysis ….………….…………………….……………………… 12 3 Results ……………………………………………………...……..……………… 12 3.1 Thermal Stress Event………………………....………………………… 12 3.2 16S Community Structure ……………….….………………………….. 14 4 Discussion ………………………….…………………………………………….. 29 5 Conclusion ………………………………….……………………………………. 36 Bibliography ……………………………………………………………………….. 38 Supplementary Materials …………………………………...……………………… 48 LIST OF FIGURES Figure Page 1. Picture of bleached corals …………………………………...…………………… 7 2. Spatial and temporal sampling distribution ……………………………………… 9 3. Temperature at all reefs ………………………………………………………… 13 4. Average coral health ……………………………………………..……………... 15 5. 3-dimensional non-metric multidimensional scaling plot …………...………..… 18 6. Average coral richness ………………………………………………………….. 20 7. Average Shannon diversity …………………………………….…………..…… 22 8. Stacked bar plot of most abundant families ………………………………..…… 24 9. Endozoicomonas average percent abundance …………….………………..…… 36 LIST OF TABLES Table Page 1. 3-way ANOVA statistics of coral health ………………………………..……… 16 2. Simple-simple main effects of coral health …………………………..………… 17 3. 3-way ANOVA statistics of coral richness ……………………..……………… 20 4. Simple-simple main effects of coral richness …………………………………... 21 5. Simple-simple main effects of Shannon diversity …………………..………..… 23 6. 3-way ANOVA statistics of Endozoicomonas percent abundance ………..…… 27 7. Simple-simple main effects of Endozoicomonas percent abundance ……..…… 28 8. PERMDISP dispersion statistics ………………….……………………………. 29 9. PERMDISP dispersion pairwise statistics ………………………...……………. 30 LIST OF SUPPLEMENTARY MATERIALS Material Page 1. Complete Data Analysis Pipeline …………………………...…………..……… 48 2. Complete Amplification Protocol …………………………...…………..……… 50 DEDICATION I would like to dedicate my thesis to my family: my mom, Stacey Schultz and my sister, Jessica Ewton. You both have always supported me in everything I did and dreamed of. Thank you. Introduction Though corals are estimated to cover only 0.1-0.5% of the ocean floor (Moberg & Folke, 1999), they provide a suite of services to life on Earth. Almost a third of the world’s marine fish species are found on coral reefs, which contribute 10% of fish consumed by humans (Lough & van Oppen, 2009). Their topography and primary production support ~25% of all described marine species (Knowlton, 2001). Coral reefs also supply people with other ecosystem services such as coastal protection, recreation, and cultural and historical context (Lough & van Oppen, 2009). Coral reefs act as carbon dioxide sinks over geological time scales (Hallock, 2001) and provide ~½ of the calcium delivered to the sea each year (Smith, 1978). A scleractinian coral is composed of three distinct sets of organisms that interact with each other to make up the holobiont: eukaryotic coral, dinoflagellate photosynthetic symbiont, and microbiome. In fact, there is evidence of cophylogeny and phylosymbiosis between the coral and its symbiont, indicating an intricate relationship between these members of the coral holobiont (Pollock et al., 2018). Further, the microbiome of a reef-forming coral determines the health of a reef (Bourne et al., 2016). Corals host a metabolically diverse yet taxonomically restricted set of vital microorganisms in their tissues, skeleton, and mucus that together define the coral phenotype. A key example of the importance of a coral’s microbiome occurs when the coral is exposed to stressful conditions including increased temperature (Lesser et al., 1990; Maher et al., 2020; McGinty et al., 2012), nitrogen (Burkepile et al., 2020; Vega-Thurber et al., 2014), phosphate (Rosset et al., 2017; Vega-Thurber et al., 2014), urea (Burkepile et al., 2020), sugars (Pogoreutz et al., 2017), irradiance 1 (Hawkins et al., 2015), and ultraviolet light (Lesser et al., 1990) or lack thereof (Hawkins et al., 2015). Temperature is the best studied of these stressors. It has been shown that during temperature stress the symbiotic dinoflagellates express decreased photosystem health, resulting in the formation of reactive oxygen species (ROS); this erodes the mutualistic symbiosis, resulting in loss of the symbiont (Nielsen et al., 2018). This process is termed bleaching due to a corresponding loss of color that leaves the coral bleach-white. If the stressor is ameliorated, the coral host can reacquire its symbiont and persist; however, if the coral is unable to, it will die (Ainsworth et al., 2016). In some cases, stressors
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