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Geomicrobiology of Hydrogen in Yellowstone

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Geomicrobiology of Hydrogen in Yellowstone GEOMICROBIOLOGY OF HYDROGEN IN YELLOWSTONE HOT SPRINGS by Melody Rose Lindsay A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Microbiology MONTANA STATE UNIVERSITY Bozeman, Montana April 2019 ©COPYRIGHT by Melody Rose Lindsay 2019 All Rights Reserved ii ACKNOWLEDGEMENTS Firstly, I would like to thank my advisor, Dr. Eric Boyd for everything; his time, effort, advising, guidance, and patience. I thank him for guiding me through my graduate work and for teaching me to be the best scientist I can be. I would also like to thank my other committee members, past and present; including Dr. John Peters, Dr. Dan Colman, Dr. Mark Skidmore, and Dr. Mark Young. I also extend my sincere gratitude to all the collaborators I've had the privilege to work with: Dr. John Spear, Dr. Everett Shock, and Dr. Tori Hoehler for great research in Yellowstone, and the Ladies of the Lake GSLI crew Dr. Bonnie Baxter and Jaimi Butler. I also thank my labmates/friends, past and current for always being awesome: Max, Matt, Jayme, Saroj, Dan, Erik A., Eric D., Libby, and Devon. I would also like to thank the MBI staff, especially Ileana and Lisa, for all the help over the years. All the thanks to my mom, Dr. Holly Lindsay and my brother, Christopher for all the support and love during my life. Many thanks to my friends both far and near who supported me, sent cat/dog pictures, and video chatted, especially Karis, Kirsten, Kyle, James, and Liz. I would also like to thank my best friend and honorary field assistant David S. Pumpkins who always comes running with happy meows after every long day. Finally, I am also very thankful to the NASA Earth and Space Science Fellowship for supporting my graduate research, and to other sources of funding, including the TBI Turner Student Award, the Beverly Ferguson Graduate Student Award from the MBI Department, and the Doyle W. Stephens Award from Friends of Great Salt Lake. iii TABLE OF CONTENTS 1. GENERAL INTRODUCTION ........................................................................................1 Hydrogen in Microbial Metabolism .................................................................................3 Diversification of Hydrogenases ......................................................................................6 Hydrogen Metabolism in Hydrothermal Environments ..................................................9 Overarching Goals .........................................................................................................12 References ......................................................................................................................15 2. GEOLOGICAL SOURCE AND BIOLOGICAL FATE OF HYDROGEN IN YELLOWSTONE HOT SPRINGS ..........................................................................22 Contribution of Authors and Co-Authors ......................................................................22 Manuscript Information Page ........................................................................................24 Abstract ..........................................................................................................................25 Introduction ....................................................................................................................26 Materials and Methods ...................................................................................................28 Determination of hydrogenase protein encoding gene homolog abundance in chemosynthetic community metagenomes ........................................................28 Physical and chemical measurements ....................................................................30 DNA extraction ......................................................................................................31 PCR, quantitative PCR, and sequencing ................................................................31 Dilution to extinction cultivation assays ................................................................32 Metagenomic sequencing and analysis ..................................................................33 Identification and classification of [NiFe]- and [FeFe]-hydrogenase homologs in the SJ3 metagenome ..........................................................................35 RNA extraction, cDNA synthesis, and quantification of gene expression ............36 Results and Discussion ..................................................................................................38 Geological sources of H2 in Yellowstone hot springs ...........................................38 Biological fate of hydrogen in Yellowstone hot springs .......................................40 Conclusions ....................................................................................................................50 Acknowledgments ..........................................................................................................51 Figures............................................................................................................................52 Supplemental Tables ......................................................................................................58 Supplemental Figures .....................................................................................................62 Additional Supplemental Datasets .................................................................................68 References ......................................................................................................................69 3. SUBSURFACE PROCESSES INFLUENCE OXIDANT AVAILABILITY AND CHEMOAUTOTROPHIC HYDROGEN METABOLISM IN YELLOWSTONE HOT SPRINGS ..........................................................................76 Contribution of Authors and Co-Authors ......................................................................76 Manuscript Information Page ........................................................................................78 iv TABLE OF CONTENTS CONTINUED Abstract ..........................................................................................................................79 Introduction ....................................................................................................................80 Materials and Methods ...................................................................................................83 Description of sample sites and sample collection ................................................83 Physical and chemical measurements ....................................................................84 X-Ray diffraction (XRD) .......................................................................................87 RNA extraction and cDNA synthesis ....................................................................88 PCR, qPCR, and sequencing ..................................................................................88 Dissolved inorganic carbon assimilation assays ....................................................92 Hydrogen transformation assays ............................................................................93 Dilution to extinction cultivation assays ................................................................94 Results ............................................................................................................................97 Geochemistry .........................................................................................................97 Mineralogy ...........................................................................................................100 DIC and dissolved CO2 assimilation ....................................................................100 H2 transformation .................................................................................................101 Abundance of SSU rRNA gene transcripts ..........................................................102 Sediment community taxonomic diversity and composition ...............................103 Archaea ......................................................................................................103 Bacteria ......................................................................................................104 Eukarya ......................................................................................................105 Dilution to extinction cultivation assays ..............................................................106 Discussion ....................................................................................................................107 Conclusions ..................................................................................................................118 Acknowledgments ........................................................................................................119 Table ............................................................................................................................120 Figures..........................................................................................................................121 Supplemental Tables ....................................................................................................130 Supplemental Figures ...................................................................................................139 References ....................................................................................................................142
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