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A Microbiomic Approach to the Characterization of the Impacts and Influences of Viral, Bacterial, and Harmful Algal Bloom Toxins on the Bottlenose Dolphin

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A Microbiomic Approach to the Characterization of the Impacts and Influences of Viral, Bacterial, and Harmful Algal Bloom Toxins on the Bottlenose Dolphin The University of Southern Mississippi The Aquila Digital Community Dissertations Fall 12-2016 A Microbiomic Approach to the Characterization of the Impacts and Influences of Viral, Bacterial, and Harmful Algal Bloom Toxins on the Bottlenose Dolphin Corey David Russo University of Southern Mississippi Follow this and additional works at: https://aquila.usm.edu/dissertations Part of the Animal Sciences Commons, Biology Commons, Diseases Commons, Ecology and Evolutionary Biology Commons, Genetics and Genomics Commons, Immunology and Infectious Disease Commons, Microbiology Commons, and the Pharmacology, Toxicology and Environmental Health Commons Recommended Citation Russo, Corey David, "A Microbiomic Approach to the Characterization of the Impacts and Influences of Viral, Bacterial, and Harmful Algal Bloom Toxins on the Bottlenose Dolphin" (2016). Dissertations. 898. https://aquila.usm.edu/dissertations/898 This Dissertation is brought to you for free and open access by The Aquila Digital Community. It has been accepted for inclusion in Dissertations by an authorized administrator of The Aquila Digital Community. For more information, please contact [email protected]. A MICROBIOMIC APPROACH TO THE CHARACTERIZATION OF THE IMPACTS AND INFLUENCES OF VIRAL, BACTERIAL, AND HARMFUL ALGAL BLOOM TOXINS ON THE BOTTLENOSE DOLPHIN by Corey David Russo A Dissertation Submitted to the Graduate School and the School of Ocean Science and Technology at The University of Southern Mississippi in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy Approved: ________________________________________________ Dr. Darrell J. Grimes, Committee Chair Professor, Ocean Science and Technology ________________________________________________ Dr. Jeffrey M. Lotz, Committee Member Professor, Ocean Science and Technology ________________________________________________ Dr. Robert J. Griffitt, Committee Member Assistant Professor, Ocean Science and Technology ________________________________________________ Dr. R.D. Ellender, Committee Member Professor Emeritus, Biological Sciences ________________________________________________ Dr. Karen S. Coats Dean of the Graduate School December 2016 COPYRIGHT BY Corey David Russo 2016 Published by the Graduate School ABSTRACT A MICROBIOMIC APPROACH TO THE CHARACTERIZATION OF THE IMPACTS AND INFLUENCES OF VIRAL, BACTERIAL, AND HARMFUL ALGAL BLOOM TOXINS ON THE BOTTLENOSE DOLPHIN by Corey David Russo December 2016 As apex predators that display high site fidelity Tursiops truncatus (bottlenose dolphin) are indicators of marine ecosystem health. Bottlenose dolphins, additionally, display pathogenesis and immune response similar to that of humans. Humans and coastal bottlenose dolphins, in particular, are constantly exposed to the same industrial, agricultural and domestic toxins and pathogens, contaminants and pollutants. Thus, studies on the bottlenose dolphin are also valuable in bridging the gap between ocean and human health. Bottlenose dolphins are susceptible to viral bacterial and toxin infection. Infection in the bottlenose dolphin manifests itself in the form of mass stranding events, unusual mortality events, chronic infection, clinically expressed disease, and unapparent/sustained infections. The focus of this dissertation project is the role and characterization of microorganisms’ impact on bottlenose dolphin stranding events. In accordance with the three main contributors of bottlenose dolphin stranding events this dissertation employed molecular techniques and next generation sequencing technology for viral, bacterial and harmful algal bloom toxin assessment on dolphins and model organisms. The viromics portion of this dissertation, for instance, took a random hexamer approach towards purified viral RNA and DNA, contributing 86 viruses from BND serum not previously reported in the BND. The bacteriomics portion of this project, ii additionally, took a 16sPCR approach towards purified bacterial nucleic acid associated with BND skin, demonstrating differences in bacterial diversity and abundance in coastal and offshore BND ecotypes. The effects of harmful algal bloom domoic acid exposure to zebrafish, finally, took a 16sPCR and qPCR approach to illustrate shifts in zebrafish gut microbiome and changes in transcriptional regulation, respectively. iii ACKNOWLEDGMENTS I am grateful and wish to acknowledge my mentor Dr. Robert Meyers and colleagues at the Gulf Coast Research Laboratory. RM and colleagues of the GCRL were continued sources of constructive criticism and creative thought. I acknowledge and thank the J. Craig Venter Institute for allowing me to work out of their genomic medicine laboratory for providing laboratory space and equipment to accomplish the viromics components of this dissertation. Specifically, Dr. Karen Nelson and Dr. Manolito Torralba of the JCVI, provided much guidance and support and have been and will continue to be primary collaborators for research studies moving forward. I also acknowledge with immense gratitude my committee members: Dr. Joe Griffitt, Dr. RD Ellender and Dr. Jeffrey Lotz. I want to thank JG in particular for providing workspace and equipment for the toxicology components of this dissertation. I also thank JG for his solicited and frequently unsolicited constructive criticism throughout this process I acknowledge and am incredibly grateful to my major Professor, Dr. D.J. Grimes, who believed in my visions and goals and allowed me to expand his bacteriocentric microbiology lab to research that included: viruses, diatoms and non culture based molecular approaches towards microbiology. DJG never stifled my creativity in regards to study designs or approaches and always shared and supported in my endeavors as a doctoral researcher iv DEDICATION I am eternally grateful for the unconditional love and endless support of my beautiful wife Krista Gaude Russo and family, near and far. The overcoming and success of the trials, tribulations and endurances associated with a vigorous PhD program was made possible because of KGR and family. This dissertation, in turn, is dedicated to them. v TABLE OF CONTENTS ABSTRACT ........................................................................................................................ ii ACKNOWLEDGMENTS ................................................................................................. iv DEDICATION .................................................................................................................... v LIST OF TABLES ............................................................................................................. xi LIST OF ILLUSTRATIONS ............................................................................................ xii LIST OF ABBREVIATIONS .......................................................................................... xiv CHAPTER I - INTRODUCTION ...................................................................................... 1 Bottlenose Dolphins and Bottlenose Dolphin Stranding Events .................................... 1 Viruses in the Marine Setting and Viral Contribution to BND Disease ..................... 4 Bacteria in the Marine Setting and Bacterial Contribution to BND Disease .............. 7 Toxins in the Marine Setting with Emphasis on Biotoxins (Harmful Algal Bloom Toxins) and Toxins Contributions to BND Disease ................................................. 10 Putting it All Together: Microbiomics (BND and Zebrafish) .................................. 14 Research Considerations ............................................................................................... 28 Sampling Sites .......................................................................................................... 28 The Bottlenose Dolphin as an Ideal Subject of Study .............................................. 29 CHAPTER II - A REVIEW OF VIRAL SPECIES REPORTED TO BE INFECTIOUS FOR TURSIOPS TRUNCATUS (BOTTLENOSE DOLPHIN) ...................................... 31 Abstract ......................................................................................................................... 31 vi Introduction ................................................................................................................... 31 Viruses Infectious to the Bottlenose Dolphin ............................................................... 35 Alpha and Gammaherpesvirus .................................................................................. 35 Calicivirus ................................................................................................................. 39 Bottlenose Dolhin Enterovirus (BDEV) ................................................................... 42 Papillomavirus – Tursiops Truncates Papillomavirus (TtPV) .................................. 44 Poxvirus .................................................................................................................... 45 Tursiops Truncates Parainfluenza Virus (TtPIV) ..................................................... 48 Dolphin Morbillivirus (DMV) .................................................................................. 49 Conclusions ................................................................................................................... 51 CHAPTER III - A VIROMIC STUDY ON SERUM COLLECTED FROM WILD TURSIOPS TRUNCATUS (BOTTLENOSE DOLPHIN) ............................................... 53 Abstract ........................................................................................................................
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