Biogeochemistry of Environmental Gradients in Serpentinization-Influenced Groundwater at the Coast Range Ophiolite Microbial Observatory, California
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BIOGEOCHEMISTRY OF ENVIRONMENTAL GRADIENTS IN SERPENTINIZATION-INFLUENCED GROUNDWATER AT THE COAST RANGE OPHIOLITE MICROBIAL OBSERVATORY, CALIFORNIA By Mary C. Sabuda A THESIS Submitted to Michigan State University in partial fulfillment of the requirements for the degree of Geological Sciences--Master of Science 2017 ABSTRACT BIOGEOCHEMISTRY OF ENVIRONMENTAL GRADIENTS IN SERPENTINIZATION-INFLUENCED GROUNDWATER AT THE COAST RANGE OPHIOLITE MICROBIAL OBSERVATORY, CALIFORNIA By Mary C. Sabuda Serpentinization of ultramafic rock in ophiolite complexes along continental margins leads to the mobilization of volatiles and reduced carbon compounds that can be used as sources of energy by subsurface microbial communities. The extent to Which sulfur compounds can serve as electron acceptors in anoxic serpentinizing systems and their role in biogenic carbon cycling remains to be elucidated. Large scale processes at CROMO Were studied using geochemical analyses, bioenergetics calculations, microscopic cell counts, and 16S rRNA sequencing to identify the population of sulfate reducers and methane cyclers. Shotgun metagenomic and metatranscriptomic sequencing identified the production of key genes for sulfate reduction, sulfide oxidation, and thiosulfate disproportionation. Small scale processes at CROMO Were identified through a depth profile of CSW1.1. With Water pumped directly from the well, microcosms Were created to measure the groWth of microbial 13 communities in the presence of CH4. Thiosulfate or Fe(OH)3 were injected as electron acceptors, with the addition of O2 gas in designated “oxic” bottles. The highest cell 13 13 groWth and biogenic DIC production occurred in “anoxic” CH4 + thiosulfate amended bottles, With Trueperaceae dominating both the profile of CSW1.1 and the microcosms. The biogeochemistry of CROMO yields insight into the potential for sulfur and methane cycling Within this cryptic serpentinite environment found throughout the World. Copyright by MARY C. SABUDA 2017 ACKNOWLEDGEMENTS This Work Was made possible with the advice and support of many people. First, a huge, endless thank you to Dr. Matt Schrenk for his support, guidance, and unWavering confidence in me throughout the past tWo years. You have been an incredible mentor and I deeply value all the opportunities I have had While a member of your laboratory. Thank you for encouraging me to earn a Ph.D. I Would also like to thank Dani Morgan-Smith, Lindsay Putman, Heather Miller, and Lauren Seyler for being great lab mates and for making room 144 feel like home. You all have made my experience at MSU one that I Will strive to find again through my Ph.D. Work and beyond. I Would like to thank the entire CROMO team, including Dr. Tom McCollom, Dr. DaWn Cardace, Dr. Tori Hoehler, Mike Kubo, and Dr. Masako Tominaga, I Want to extend an extra thank you to Dr. Tori Hoehler and Mike Kubo for hosting and mentoring me throughout my time at NASA Ames Research Center throughout the summer of 2016. Working on a part of my thesis project at NASA Was incredible, and I thank Tori and Mike for this once in a lifetime opportunity. It Was an honor Working With you both. Additionally, thanks to the NASA Astrobiology Institute for funding this research at CROMO through the NAI CAN-7 Rock PoWered Life grant. Thank you to my committee members, Dr. Matt Schrenk, Dr. Kazem Kashefi, Dr. David Long, and Dr. Jay Zarnetske for their essential advice and input on this Work. Thanks to the Michigan State Department of Earth and Environmental Sciences for the guidance, felloWships, and scholarships that made my research possible. iv Thanks to Lindsay Putman, Megan Hudak, Jordan Salley, and Laney Hart for being the best friends and lab mates throughout our time at MSU. You kept me sane throughout these past feW years and I am extremely thankful. A big thank you is for my incredible family, including my mother Mrs. Karen Sabuda for inspiring me to earn a Master’s degree and reach higher. Thanks to my father, Mr. David Sabuda, for his constant encouragement, daily notes to “have a day”, and conversations about environmental politics. Thank you to my brother, Mr. Steven Sabuda, for alWays knoWing hoW to make me laugh, and for alWays being there for me. We have been through everything together, and I am so lucky to have you. Thanks to my family for alWays relaying me to and from the airport at any hour Whenever I had to travel for this research. I am thankful for those unfortunately short car rides, infrequent nights at home, and care packages of groceries before leaving for the next destination or heading back to MSU. Thank you to my amazing grandparents for their support and encouragement, and for alWays reminding me that there’s more to life than Work. Thank you to Mr. Sean Hughes, my rock, for his unWavering support and advice throughout the countless struggles of my Master’s degree. I love you all, and I thank you very much. v PREFACE This work was written for publication in Nature Geoscience and Geochemistry, Geophysics, Geosystems (G3), for chapters two and three, respectively. vi TABLE OF CONTENTS LIST OF TABLES ............................................................................................................ ix LIST OF FIGURES ........................................................................................................... x KEY TO ABBREVIATIONS ............................................................................................. xi CHAPTER 1 – Introduction .............................................................................................. 1 Serpentinization ..................................................................................................... 1 CROMO Field Site ................................................................................................. 3 Microbial Metabolic Potential ................................................................................. 4 REFERENCES ...................................................................................................... 7 CHAPTER 2 – Sulfur Biogeochemistry is an Important Link BetWeen Marine and Terrestrial Serpentinizing Systems ................................................................................. 10 Abstract................................................................................................................ 10 Introduction .......................................................................................................... 11 CROMO Chemistry Is Unique Among Ophiolites ................................................ 12 Sulfur Metabolisms Are Energetically Favorable ................................................. 17 Shotgun -Omics Analyses Confirm Microbes Cycle Sulfur Compounds ............. 21 Methods ............................................................................................................... 27 Aqueous Geochemistry ............................................................................ 27 Gibbs Free Energy Calculations ............................................................... 30 Microbial Cell Enumeration ....................................................................... 31 Extraction of DNA and RNA ...................................................................... 31 Bacterial 16S rRNA Amplicon Sequencing, and Data Analysis ................ 32 Metagenomic Sample Preparation, Sequencing, and Data Analysis ....... 34 APPENDIX........................................................................................................... 37 REFERENCES .................................................................................................... 52 CHAPTER 3 – Biologically-catalyzed Methane Oxidation in Serpentinite-Hosted GroundWater ................................................................................................................... 62 Abstract................................................................................................................ 62 Introduction .......................................................................................................... 64 Water-Rock Interactions ........................................................................... 64 Background ......................................................................................................... 67 Ultramafic Peridotite Alteration to Serpentinite ......................................... 67 Gases Produced, Carbon Cycling ............................................................ 68 Serpentinite-Influenced Biogeochemistry ................................................. 69 CROMO Site Description .......................................................................... 70 Serpentinization Influenced Microbiology ................................................. 74 Methods ............................................................................................................... 75 vii Profile Sampling ........................................................................................ 75 16S rRNA Gene Amplicon Sequencing and Data Analysis ...................... 76 Cell Abundance ........................................................................................ 78 Aqueous Geochemistry ............................................................................ 79 Gibbs Free Energy Calculations ............................................................... 82 Microcosm Experiments ............................................................................ 83 Results