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The Trophic Ecology of Coral Reef Sponges in Caribbean Mesophotic Ecosystems

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The Trophic Ecology of Coral Reef Sponges in Caribbean Mesophotic Ecosystems University of New Hampshire University of New Hampshire Scholars' Repository Doctoral Dissertations Student Scholarship Fall 2020 The Trophic Ecology of Coral Reef Sponges in Caribbean Mesophotic Ecosystems Keir John Macartney University of New Hampshire, Durham Follow this and additional works at: https://scholars.unh.edu/dissertation Recommended Citation Macartney, Keir John, "The Trophic Ecology of Coral Reef Sponges in Caribbean Mesophotic Ecosystems" (2020). Doctoral Dissertations. 2531. https://scholars.unh.edu/dissertation/2531 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]. The Trophic Ecology of Coral Reef Sponges in Caribbean Mesophotic Ecosystems BY Keir J. Macartney Bachelor of Marine Biology (Honours), University of St Andrews, 2016 DISSERTATION Submitted to the University of New Hampshire in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy In Molecular and Evolutionary Systems Biology September 2020 i This dissertation was examined and approved in partial fulfillment of the requirements for the degree of Ph.D. in Molecular and Evolutionary Systems Biology by: Dissertation Director, Michael P. Lesser, Ph.D., Research Professor Emeritus, Molecular, Cellular and Biomedical Sciences, University of New Hampshire Marc Slattery, Ph.D., Professor, Pharmacognosy and Environmental Toxicology in BioMolecular Sciences, University of Mississippi Winsor Watson III, Ph.D., Professor Emeritus, Biological Sciences, University of New Hampshire David Plachetzki, Ph.D., Associate Professor, Molecular, Cellular and Biomedical Sciences, University of New Hampshire Stephen H. Jones, Ph.D., Associate Research Professor, Natural Resources and the Environment University of New Hampshire On August 21, 2020 Approval signatures are on file with the University of New Hampshire Graduate School. ii Dedication I would like to dedicate this work to my family. Your unrelenting support and encouragement towards my passion for marine biology put me firmly on the path to this moment. I could not have completed this work without you. iii Acknowledgements First, I want to thank my advisor, Dr. Michael Lesser, for his unwavering guidance and patience during my four years at UNH. I was as green as they come when I arrived at UNH to begin my graduate studies, but your support helped guide me through the many challenges that came up. None of this would have been possible without your Jedi-like wisdom. I would also like to thank my co-advisor, Dr. Marc Slattery, for his guidance on fieldwork and writing. The challenging questions you asked me about my work helped me think more critically about many topics. I would also like to thank the other members of my dissertation committee; Dr. Windsor Watson, Dr. David Plachetzki, Dr. Stephen Jones and Dr. Marianne Litvaitus. I appreciate the wisdom and advice you provided during meetings and for your comments on my work. I would like to thank the many other faculty members, postdoctoral researchers and UNH students who helped me with analyses and field work. To Dr. Deborah Gochfeld and Dr. Andia Chavez, thank you for your continued assistance during the many trips to the field and for your assistance in the wet laboratory. To Dr. Kathleen Morrow, thank you very much for your comments on many of my early presentations for conferences and showing me the ropes in laboratory. Thank you to Dr. M. Sabrina Pankey, for your extreme patience with the vast number of questions I had about molecular and statistical analyses, your continued support in all thing’s laboratory related and for the many helpful comments you have given me on manuscripts or presentations. Thank you to Liz Kintzing for keeping an eye on me during the many technical dives required for this dissertation and for fixing the many problems that cropped up in my CCR unit while we were in the field. Thank you to Amelia Clayshute for her tireless work on the proximate biochemical compositions of sponges. Thank you to Derek Rothenheber, Nate Ennis, Cooper Park, Devon O’Rourke for giving me advice on bioinformatic analyses. I would like to thank Meghan Hartwick for her help in navigating the fine points of formatting this dissertation and her advice on statistical methods. Thank you to Alaina Weinheimer for her continued patience with my endless questions about bioinformatics and the many scripts she helped me write. You kept me sane during the writing of this dissertation. Thanks to Matt Strobel, Jacob Koile and Jon Streter for cracking a couple of cold ones open with me when I needed a morale boost. I also want to thank the scientists at Mote Marine Laboratory and the University of St Andrews. In particular, thank you to Dr. Erinn Muller and Prof. Christopher Todd for inspiring me to pursue a graduate degree in this field. Lastly, I would also like to thank my family. To my Dad, thank you for all you have done to support me throughout the last few years. To my brother and sister, thanks for taking the time to encourage me when I was struggling. Without the love and support from my family this would not have been possible. All sample collections complied with the laws of the Cayman Islands and the United States of America. Support was provided by NSF Biological Oceanography (OCE– 1632348/1632333), NOAA NIUST (14U752) and the University of New Hampshire Marine Biology Small Grants fund. iv Table of Contents Dedication ..................................................................................................................................... iii Acknowledgements ...................................................................................................................... iv Table of Contents .......................................................................................................................... v List of Tables .............................................................................................................................. viii List of Figures ............................................................................................................................... ix Abstract ......................................................................................................................................... xi Chapter 1 ....................................................................................................................................... 1 Abstract ...................................................................................................................................... 2 Introduction ............................................................................................................................... 3 Materials and methods.............................................................................................................. 6 Bulk stable isotope analysis ..................................................................................................... 7 Compound specific isotope analysis of amino acids ............................................................... 7 Statistical analyses .................................................................................................................. 8 Results ...................................................................................................................................... 10 Sponge environment and survey results ................................................................................ 10 Bulk stable isotope analyses: ................................................................................................. 12 Compound specific isotope analyses of amino acids............................................................. 16 Discussion ................................................................................................................................. 21 Conclusions .............................................................................................................................. 29 Acknowledgements .................................................................................................................. 30 Literature Cited ....................................................................................................................... 31 Appendix 1 ................................................................................................................................... 40 Supplemental Information on Compound Specific Isotopic Analysis of Amino Acids (CSIA-AA)................................................................................................................................ 41 Justification for Assumptions Made in the SIAR4 Models ................................................. 42 Source Data for Bulk SIA and CSIA SIAR4 Models ........................................................... 46 Appendix References............................................................................................................... 48 Chapter 2 ..................................................................................................................................... 51 Abstract ...................................................................................................................................
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