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Bacterial Communities Within the Microbiome of Three Shark Species in South Florida Waters

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Bacterial Communities Within the Microbiome of Three Shark Species in South Florida Waters Please do not remove this page Bacterial Communities Within the Microbiome of Three Shark Species in South Florida Waters Black, Chelsea Leigh https://scholarship.miami.edu/discovery/delivery/01UOML_INST:ResearchRepository/12356347670002976?l#13356347660002976 Black, C. L. (2020). Bacterial Communities Within the Microbiome of Three Shark Species in South Florida Waters [University of Miami]. https://scholarship.miami.edu/discovery/fulldisplay/alma991031454075202976/01UOML_INST:ResearchR epository Open Downloaded On 2021/09/28 07:30:20 -0400 Please do not remove this page UNIVERSITY OF MIAMI BACTERIAL COMMUNITIES WITHIN THE MICROBIOME OF THREE SHARK SPECIES IN SOUTH FLORIDA WATERS By Chelsea Leigh Black A THESIS Submitted to the Faculty of the University of Miami in partial fulfillment of the requirements for the degree of Master of Science Coral Gables, Florida May 2020 ã2020 Chelsea Leigh Black All Rights Reserved UNIVERSITY OF MIAMI A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science BACTERIAL COMMUNITIES WITHIN THE MICROBIOME OF THREE SHARK SPECIES IN SOUTH FLORIDA WATERS Chelsea Leigh Black Approved: Neil Hammerschlag, Ph.D. Maria Estevanez, M.A, M.B.A. Research Associate Professor Senior Lecturer Marine Ecosystems and Society Marine Ecosystems and Society Liza Merly, Ph.D. Guillermo Prado, Ph.D. Senior Lecturer Dean of the Graduate School Marine Biology and Ecology BLACK, CHELSEA LEIGH (M.S., Marine Ecosystems and Society) (May 2020) Bacterial Communities Within the Microbiome of Three Shark Species in South Florida Waters Abstract of a thesis at the University of Miami. Thesis supervised by Professor Neil Hammerschlag No. of pages in text: (81) Assessing shark health can provide information on species and environmental condition. One emerging measure of health status is the microbiome. The assemblage of bacterial communities within the microbiome of a host can provide insight into the environmental conditions and outside stressors a species is encountering. Anthropogenic pressures such as fishing and bycatch are well-known threats to global shark populations, however, habitat degradation and other environmental changes may actually contribute to their susceptibility to disease. Bacteria are known to have explicit roles in vertebrate tissues, so examining the bacterial communities across the microbiome may prove to be a useful tool for assessing the role of commensal bacteria in shark health and determining health status. This study characterized the bacterial communities within water samples and across several tissue sites of blacktip (Carcharhinus limbatus), bull (Carcharhinus leucas) and tiger (Galeocerdo cuvier) sharks off the coast of Miami, Florida through microbiological and molecular sequencing methods. Blacktip sharks displayed the highest bacterial diversity in terms of their microbiome. Planococcaceae bacteria possessing antibiotic compounds were unique to the skin of tiger sharks in this study, further highlighting the likelihood for species-specific bacteria. Further, known pathogens such as Vibrio and Staphylococcus were identified in the wounds of sharks in this study. While water samples did possess unique bacteria not identified on the sharks, it also included pathogenic bacteria that was identified in the wounds of blacktip and bull sharks. The results indicate that while some bacteria may be normal residents of the microbiome, the loss of protective dermal denticles due to a wound may provide opportunistic bacteria a chance to colonize in areas where they would not normally be found. It will be important for future work to continue investigating the bacterial communities found within the microbiome of sharks to determine which bacteria are normal colonizers and which species may be pathogenic invaders. Determining the presence of microbes and their functionality will provide insight into the role of the microbiome to host health, as well as the environmental conditions that these sharks are encountering. Acknowledgements I would like to thank my advisor, Dr. Neil Hammerschlag, for opening his door to me and trusting me as a valued member of the Shark Research and Conservation Program. The opportunities you have given me not only solidified my passion for marine biology, but instilled confidence to pursue this career. To my co-advisor, Dr. Liza Merly, thank you for your encouragement and guidance over the years as I learned microbiology. You made me believe in myself when I needed it most and I will always appreciate your patience and support. To Maria Estevanez, I appreciate your immeasurable kindness and encouragement through my entire academic career. Your smile was an illuminating force guiding me to the finish line. This thesis is a result of the lessons and encouragement provided to me by my committee and I will always value my time learning from them. I must thank my fellow SRC members, past and present, for the countless laughs and memories along the way. To Stephen Cain, thank you for being my career-coach, mentor, barista, but most importantly my good friend. You have imparted wisdom on me that I can never repay. To Shannon Moorhead, I am forever appreciative of everything you have taught me and for being my confidant. To Laura McDonnell, thank you for being a shoulder to lean on, the best travel buddy, and an inspiration. To Mitchell Rider for fueling me with donuts and assisting with my final analysis. To Patricia Albano for lifting my spirit with laughter. I must also thank Andy Fragola for trusting me to build on her research project and her mentorship in the lab. To Allison Banas for being an amazing undergraduate assistant and Julia Saltzman for making quite possibly every agar plate in this study. To Elana Rusnak for her guidance and company in the laB. It is through all of these people, and more, that my research was possible. iii I would also like to thank the friends I have made here at the University of Miami for their support through the ups and downs. To Megan Huse, Erin Cain, and Kathryn Grazioso- your friendships kept me sane during this journey. Thank you for providing me with encouragement along the way and celebrating each milestone with me. Last, but certainly not least, I would like to thank my family. Without my parents, a childhood dream would have remained just that. Thank you for instilling a passion for science within me and fostering my love for the ocean from a young age. It is because of your encouragement, love, and support that my hard work has come to fruition. There are no words to describe what you have given me, and I only hope to continue making you proud. This is dedicated to you. iv Table of Contents List of Figures.....................................................................................................................vi List of Tables.....................................................................................................................vii Chapters Introduction..............................................................................................................1 1. Marine Microbes................................................................................................4 2. Microbes as Indicators for Shark Health.........................................................13 3. Methods............................................................................................................26 4. Results..............................................................................................................34 5. Discussion........................................................................................................50 Conclusion.............................................................................................................60 Literature Cited..................................................................................................................62 Appendix A – Marine Agar Preparation............................................................................76 Appendix B – Slide Microscopy........................................................................................77 Appendix C – DNA Sequencing........................................................................................78 Appendix D – Statistics for Shannon’s Index Calculations...............................................80 v List of Figures Figure 1. Fishing method for safe capture of sharks.........................................................26 Figure 2. Process of microbial sampling...........................................................................27 Figure 3. Location of all sampled sharks within the study...............................................28 Figure 4. Process of culturing each cell scrape.................................................................30 Figure 5. Distribution of Gram-negative and Gram-positive across tissue sites..............35 Figure 6. Distribution of Gram-staining across all shark species and water samples.......36 Figure 7. Distribution of bacteria morphology types across all shark species..................38 Figure 8. Distribution of bacteria morphology shapes across all shark species...............39 Figure 9. Summary of taxonomic groups identified through DNA sequencing...............40 Figure 10. Total composition of bacteria phyla for sequenced samples...........................41 Figure 11. Distribution of phyla across species and tissue site.........................................42 Figure 12. Venn diagram
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