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Characterization of the Lucinid Bivalve

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Characterization of the Lucinid Bivalve Louisiana State University LSU Digital Commons LSU Master's Theses Graduate School 2008 Characterization of the lucinid bivalve-bacteria symbiotic system: the significance of the geochemical habitat on bacterial symbiont diversity and phylogeny Angela Marissa Green-Garcia Louisiana State University and Agricultural and Mechanical College, [email protected] Follow this and additional works at: https://digitalcommons.lsu.edu/gradschool_theses Part of the Earth Sciences Commons Recommended Citation Green-Garcia, Angela Marissa, "Characterization of the lucinid bivalve-bacteria symbiotic system: the significance of the geochemical habitat on bacterial symbiont diversity and phylogeny" (2008). LSU Master's Theses. 1970. https://digitalcommons.lsu.edu/gradschool_theses/1970 This Thesis is brought to you for free and open access by the Graduate School at LSU Digital Commons. It has been accepted for inclusion in LSU Master's Theses by an authorized graduate school editor of LSU Digital Commons. For more information, please contact [email protected]. CHARACTERIZATION OF THE LUCINID BIVALVE-BACTERIA SYMBIOTIC SYSTEM: THE SIGNIFICANCE OF THE GEOCHEMICAL HABITAT ON BACTERIAL SYMBIONT DIVERSITY AND PHYLOGENY A Thesis Submitted to the Graduate Faculty of the Louisiana State University and Agricultural and Mechanical College In partial fulfillment of the Requirements for the degree of Master of Science in The Department of Geology and Geophysics by Angela Marissa Green-Garcia B.S., University of Houston, 2003 May 2008 DEDICATION This thesis is dedicated to my father, Rudi, who in life and death, has been a driving force behind my pursuit of an education, and to my family, who has continuously supported me and encouraged me to achieve all of my goals. Thank you and I love you all. ii ACKNOWLEDGEMENTS I would like to thank Dr. Annette Engel for all her patience and help along this (what has felt like) endless process of researching, writing, and presenting the thesis. She has served as a constant source of support and guidance and her assistance has been invaluable. I could not have asked for a better mentor; she is someone I truly respect and admire. I would also like to thank the other members of my committee, Dr. Laurie Anderson and Dr. Huiming Bao, for all of their assistance. Also, thanks to Audrey Aronowsky for her help and direction, Maureen Thiessen for her awesome dedication and work ethic, and to Wanda LeBlanc for her help with soil XRD analysis, her patience, and her smile. In addition, I would like to thank my family, for all of the love and support that they have given me throughout all these years working to get to this point. Jeannie, you are a fabulous mother and thanks for being my shoulder to lean on and a constant source of encouragement. Angel, Tashi, and Adan thanks for making me strong. Ms. Lady G and Ms. Donna, thanks for all the encouraging kisses and all the snuggling. I love you all. Phroggie, thanks for the love and always taking care of me. For all of the amazing people I have met and shared this graduate experience with …whew! I can’t believe it’s over. Issaku; it has been fun, you are like a brother. Thanks for all the encouragement. Anna, thanks for the pep; you are a great girl and have been a delightful perky friend, as well as an amazing, positive voice through this experience. And, to TEAM NORAD, thanks for all of the unforgettable experiences in the field, all the GP, and the endless laughter. And, to anyone else I have not named, thank you. Funding for the thesis was provided by the Geoscience Alliance to Enhance Minority Participation (GAEMP) (NSF-OEDG #0303138) in the Department of Geology and Geophysics, and Sigma Xi by a Grants-in-Aid Research award. Thank you. iii TABLE OF CONTENTS DEDICATION...................................................................................................................................ii ACKNOWLEDGMENTS .................................................................................................................iii LIST OF TABLES.............................................................................................................................vi LIST OF FIGURES ...........................................................................................................................vii ABSTRACT.......................................................................................................................................viii INTRODUCTION .............................................................................................................................1 Background............................................................................................................................2 Morphology and Antiquity ....................................................................................................3 Host-Endosymbiont Relationship ..........................................................................................4 Objectives and Hypothesis.....................................................................................................6 Importance of Research .........................................................................................................8 MATERIALS AND METHODS.......................................................................................................9 Sample Collection..................................................................................................................9 Sediment Mineralogy by X-Ray Diffraction (XRD) .............................................................10 Gill Acquisition and DNA Extraction....................................................................................12 Sediment and DNA Extraction ..............................................................................................13 Polymerase Chain Reaction (PCR) Amplification, Cloning, and Sequencing ......................13 Sequence Analysis .................................................................................................................14 RESULTS ..........................................................................................................................................16 Aqueous Geochemical Analysis ............................................................................................16 Core Mineral Analysis ...........................................................................................................16 Gill Endosymbiont Diversity .................................................................................................18 Sediment Bacterial Diversity from Cedar Key, Florida.........................................................26 Microbial Diversity with Core Depth ....................................................................................32 DISCUSSION....................................................................................................................................36 Habitat Geochemistry and Mineralogy..................................................................................36 Intra- and Inter-Species Diversity..........................................................................................38 Free-living Bacterial Diversity ..............................................................................................39 Endosymbiont Sequence Diversity and Possible Metabolic Implications.............................41 CONCLUSIONS................................................................................................................................43 REFERENCES ..................................................................................................................................45 APPENDIX A: CORE MINERAL ANALYSIS AND XRD...........................................................53 iv APPENDIX B: TAXANOMIC DISTRIBUTION OF BACTERIAL CLONES ..............................61 VITA..................................................................................................................................................65 v LIST OF TABLES 1. Field geochemical data from Cedar Key, Florida............................................................16 2. Cation concentrations and anion concentrations of ocean and pore water Cedar Key, Florida...........................................................................................................17 3. Percentage abundances of minerals in core sediments, Cedar Key, Florida ...................17 4. Average genetic distance within host species form 16S rRNA gene sequences .............22 5. Average genetic distance between endosymbiont 16S rRNA gene sequences from different host taxa ............................................................................................................22 6. Distribution of 16S rRNA gene bacterial sequences from sediment cores at Cedar Key, Florida .....................................................................................................................33 vi LIST OF FIGURES 1. Maps of sample collections sites......................................................................................11 2. Rarefaction curves for endosymbiont 16S rRNA gene sequences ..................................20 3. Phylogenetic reconstruction based on Jukes-Cantor neighbor-joining analysis of 16S rRNA gene sequences of endosymbiont sequences retrieved from lucinid gills from Cedar Key and 16S rRNA sequences from sediments, representing the free-living habitat...............................................................................................................................21
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