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Diversity and Distribution of Diatom Endosymbionts in Amphistegina Spp. (Foraminifera) Based on Molecular and Morphological Techniques Kwasi H

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Diversity and Distribution of Diatom Endosymbionts in Amphistegina Spp. (Foraminifera) Based on Molecular and Morphological Techniques Kwasi H University of South Florida Scholar Commons Graduate Theses and Dissertations Graduate School 6-28-2016 Diversity and Distribution of Diatom Endosymbionts in Amphistegina spp. (Foraminifera) Based on Molecular and Morphological Techniques Kwasi H. Barnes University of South Florida, [email protected] Follow this and additional works at: http://scholarcommons.usf.edu/etd Part of the Aquaculture and Fisheries Commons, Genetics Commons, and the Systems Biology Commons Scholar Commons Citation Barnes, Kwasi H., "Diversity and Distribution of Diatom Endosymbionts in Amphistegina spp. (Foraminifera) Based on Molecular and Morphological Techniques" (2016). Graduate Theses and Dissertations. http://scholarcommons.usf.edu/etd/6177 This Thesis is brought to you for free and open access by the Graduate School at Scholar Commons. It has been accepted for inclusion in Graduate Theses and Dissertations by an authorized administrator of Scholar Commons. For more information, please contact [email protected]. Diversity and Distribution of Diatom Endosymbionts in Amphistegina spp. (Foraminifera) Based on Molecular and Morphological Techniques by Kwasi H. Barnes A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy with a concentration in Biological Oceanography College of Marine Science University of South Florida Major Professor: Pamela Hallock Muller, Ph.D. Mya Breitbart, Ph.D. James Garey, Ph.D. Dale Griffin, Ph.D. John Paul, Ph.D Date of Approval: June 3, 2016 Keywords: DNA Extraction, Sequencing, Denaturing Gradient Gel Electrophoresis, Symbiosis, Phylogenetics, Bioinformatics Copyright © 2016, Kwasi H. Barnes DEDICATION I dedicate my dissertation to the “girls” of my life whose love and support got me to this point: my wife Seraphine, daughters Nykiia and Melody, and my “Granny” singing and dancing with the angels. Thank you all for your love, support, and inspiration. To my daughters: The most important ingredients to success are hard work and perseverance. However, sometimes you need the love, kindness, or help of others to achieve your goals. Always work your hardest and never give up, but also be kind, respectful, and gracious to others along the way—because burnt bridges are difficult, and sometimes even impossible, to cross! My “Granny” taught me that, my wife exemplifies it, and we hope to pass that life lesson on to you. ACKNOWLEDGMENTS I am eternally grateful to my major professor Dr. Pamela Hallock Muller for the immeasurable effort, dedication, and time she has invested in my academic and professional growth. Dr. Hallock Muller was largely responsible or intricately involved in every process that allowed me to complete my dissertation. There has never been a question, problem, or request that she wasn’t able to help me with directly or guide me in the right direction. I can honestly say that I have never ended a conversation with her not feeling better or wiser than when I started. Dr. Hallock Muller is a great scientist, excellent mentor, and a truly kind and wonderful person. I am tremendously appreciative of my committee members’ advice, assistance, and the opportunity to complete my dissertation. I am truly grateful to Dr. Breitbart for stepping in and agreeing to serve on my committee, and for her truly insightful, thought provoking, and helpful edits, suggestions, and questions. I want to thank Dr. Dale Griffin immensely for his advice and availability to discuss all things regarding my molecular data and improving its presentation. I am very grateful to Dr. James Garey for his advice, suggestions, and the use of his labs. I want to thank Dr. John Paul for his advice, suggestions, and for his assistance securing funding for me to conduct my molecular work. I am also grateful to Dr. Gabriel Vargo for his advice and suggestions, particularly about culturing diatoms when I was having very low success rates. I want to acknowledge and thank Prof. John J. Lee, City University of New York, for providing the baseline research for which this entire dissertation extended from. I am also very thankful for the diatom cultures he provided for me to use as references and his suggestions regarding culture techniques. I am extremely thankful for the academic and research funding from the following sources: National Sea Grant, Environmental Marine Biotechnology Award No. NA86RG0052, Am.7.1 (Cheryl Woodley, PI); NOAA-NURC-UNCW subcontract 2004-19B (Pamela Hallock, PI); US National Science Foundation Biocomplexity Awards No. CHE-0221834 (T. Pichler, PI) and OCE-0221763 (J. Paul, PI); US Geological Survey/University of South Florida Cooperative Agreement 99HQAG0004; Field support by the Florida Institute of Oceanography. Additional financial support was provided by the University of South Florida, Office of Graduate Studies and the College of Marine Science. Thanks to Dr. Edward VanVleet, Dr. David Naar, Brittany Sheehy, Dr. Jacqueline Dixon, Dr. Teresa Greely (GK-12 Fellowship), Rod Hale, and many others at USF for their assistance with enrollment, fellowships, grants, and tuition assistance. I would like to thank the following people for graciously providing samples: Lore Ayoub (Cayman Islands), Elizabeth Carnahan (Florida Keys), Kate Ciembronowicz (Pulley Ridge), Elizabeth Fisher (Florida Keys, Bahamas, and Jamaica), Pamela Hallock Muller (Florida Keys and Hawaii), John Lee (Diatom Cultures), Matt Lybolt (Florida Middle Grounds), Bryan McCloskey (PNG), and Dana Williams (Navassa and Grenadines). I also thank Katie Rathmell, Jen Dupont, Jim Ivey, Roy Price and KML staff for their assistance with collecting samples from the Keys in Sept 2004, and May and June 2005. Collections in Biscayne National Park were permitted by BISC-2001-SCI-0022, BISC-2002-SCI-0012 and BISC-2003-SCI-0019 from the National Park Service and FKNMS—2001-008, 2003-002, and 2005-002 from the Florida Keys National Marine Sanctuary. I would like to thank the following people for advice, assistance, and general support: Tony Greco, Boris Wawrik, Stefi Depovic, Steve Massey, Bina Nayak (Valerie Harwood Lab) with DGGE and Todd LaJeunesse with DGGE, Michael Martinez, Natasha Mendez, and so many others along the way! Last, but certainly not least, I would like to thank my wife, Dr. Seraphine Pitt Barnes for her love, patience, and support beyond my merit! TABLE OF CONTENTS List of Tables ................................................................................................................................. iv List of Figures ..................................................................................................................................v Abstract ........................................................................................................................................ viii Preface..............................................................................................................................................1 Chapter 1: Introduction, Objectives, Significance of Study, and Literature Review ......................5 Objectives of this Study .......................................................................................................5 Brief Description and Importance of Foraminifera .............................................................6 Symbiosis in Foraminifera ...................................................................................................8 The Decline of Reefs and the Growing Need for Bioindicators of Reef Health ...............10 Chapter 2: Spatial and Temporal Distribution of Algal Taxa Cultured from Foraminifers of the Genus Amphistegina ......................................................................................................20 Abstract ..............................................................................................................................20 Introduction ........................................................................................................................21 Methods and Materials .......................................................................................................22 Results ................................................................................................................................26 Temporal Studies ...................................................................................................28 Geographic Distributions .......................................................................................29 Depth Trends ..........................................................................................................30 Other Taxa Isolated ................................................................................................30 Discussion ..........................................................................................................................31 Chapter 3: Spatial and Temporal Distributions of Algal Endosymbionts in Amphistegina gibbosa from the Florida Keys: DNA Extraction and Sequencing..........................................56 Abstract ..............................................................................................................................56 Introduction ........................................................................................................................57 Methods and Materials .......................................................................................................59 Sample collection and preparation for DNA extraction ........................................59
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