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Harnessing Omic Approaches to Understand How Carbon HARNESSING OMIC APPROACHES TO UNDERSTAND HOW CARBON, NITROGEN, AND SULFUR CYCLING ARE PARTITIONED IN DEEP SEA AND SEDIMENT MICROBIAL COMMUNITIES by Brett Joseph Baker A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Geology) in the University of Michigan 2014 Doctoral Committee: Associate Professor Gregory James Dick, Chair Research Professor Jeffrey C. Alt Professor Joel D. Blum Assistant Professor Vincent J. Denef Professor Donald R. Zak © Brett Baker 2014 To my family: My parents, Bruce and Diana Baker, my son, Silas Baker, and my wife, Angela Baker. ii ACKNOWLEDGEMENTS This dissertation is a product of four years of fun I had learning about marine microbiology, which will likely continue the rest of my life. Firstly, I would like to thank my advisor, Gregory Dick, for providing a rich research atmosphere and laboratory. I consider Greg to be one of my greatest allies and friends. I am especially appreciative to him for teaching me so much about microbial oceanography. I have also been privileged to have an extremely helpful committee: Joel Blum, Jeffrey Alt, Vincent Denef and Donald Zak; whom I can honestly say I have learned a great deal from each of them. You never stop learning and they have proven that to be true. I would like to thank my co-authors and collaborators: Andreas Teske, Cody Sheik, Brandy Toner, Cassandre Lazar, Chris Tayler, James Cavalcoli, and Jill Banfield. Andreas has believed in my research from the beginning and has allowed me to invade his marine sediment research domain. Cody has become a friend and has provided endless insights about microbial physiology. Cassandre has been integral in initiating sediment project chapter V. Brandy has become one of my closest colleagues and will continue to be in the future. Thanks to Chris and James for all the lively discussions and contributions to chapter IV. Thanks to Jill for the support for the past 15 years and giving me the push I needed to go back and get my PhD. I have learned more from Jill than I can possibly say in a few sentences. I would like to thank all the members of the Greg Dick lab at Michigan, past and present for their assistance including; Ryan Lesniewski, Alex Voorhies, Meng Li, Daniel Reed, Paul Den Uyl, Cody Sheik, Sunit Jain, Karthik Antharman and Daniel Marcus. I could tell you how wonderful it has been to be in laboratory where everyone gets along so well and helps each other. I am grateful to funding agencies for supporting my dissertation research. The Guaymas Basin project was supported by Gordon and Betty Moore Foundation Grant GBMF2609, the National Science Foundation Grant OCE 1029242 and the University of Michigan Rackham Graduate School Predoctoral Fellowship Program. National Science Foundation Grant OCE1038006. Thanks to the Office Staff and Support Staff at the Department of Earth and Environmental Sciences. iii TABLE OF CONTENTS DEDICATION. ............................................................................................................................... ii ACKNOWLEDGEMENTS ........................................................................................................... iii LIST OF FIGURES ..................................................................................................................... viii LIST OF TABLES ......................................................................................................................... xi LIST OF APPENDICES ............................................................................................................... xii ABSTRACT ................................................................................................................................. xiii CHAPTER I .................................................................................................................................. 1 INTRODUCTION......................................................................................................................... 1 1.1 Nitrogen cycling in the Guaymas Basin deep sea and hydrothermal plumes ....................... 2 1.2 Microbial geochemical cycling in sediments ........................................................................ 3 1.3 Structure of the dissertation................................................................................................... 5 1.4 References ............................................................................................................................. 6 CHAPTER II ................................................................................................................................. 9 OMIC APPROACHES IN MICROBIAL ECOLOGY: CHARTING THE UNKNOWN .... 9 2.1 Summary ............................................................................................................................... 9 2.2 Introduction ......................................................................................................................... 10 2.3 Understanding Microbial Communities in the Wild ........................................................... 12 2.4 Data Assembly Is Critical when Analyzing Microbial Communities ................................. 13 2.5 Filling in the Tree of Life .................................................................................................... 17 2.5 Outlook ................................................................................................................................ 19 2.7 References ........................................................................................................................... 19 CHAPTER III ............................................................................................................................. 21 GENOME-ENABLED TRANSCRIPTOMICS REVEALS ARCHAEAL POPULATIONS THAT DRIVE NITRIFICATION IN A DEEP-SEA HYDROTHERMAL PLUME ........... 21 3.1 Abstract ............................................................................................................................... 21 3.2 Introduction ......................................................................................................................... 22 3.3 Materials and Methods ........................................................................................................ 24 iv Sample Collection and processing. ........................................................................................ 24 Genomic analyses. ................................................................................................................. 25 cDNA analyses ...................................................................................................................... 25 3.4 Results and disccusion ........................................................................................................ 26 Community genomics and transcriptomics reveals multiple populations of Marine Group I Archaea in the deep Gulf of California ................................................................................. 26 Comparison of the metagenome and metatranscriptome to N. maritimus. ........................... 27 Enhancement of AOA in plumes and dominance over AOB. ............................................... 29 Species-resolved transcriptomics of ammonia oxidation genes. ........................................... 31 Genomic insights into the carbon metabolism of GB MGI. .................................................. 33 Nitrogen and energy metabolism of GB MGI ....................................................................... 34 3.6 Conclusions ......................................................................................................................... 36 3.7 Appendix A ......................................................................................................................... 37 CHAPTER III Supplementary Information .............................................................................. 37 3.8 References ........................................................................................................................... 43 CHAPTER IV.............................................................................................................................. 48 COMMUNITY TRANSCRIPTOMIC ASSEMBLY REVEALS MICROBES THAT CONTRIBUTE TO DEEP-SEA CARBON AND NITROGEN CYCLING ......................... 48 4.1 Abstract ............................................................................................................................... 48 4.2 Introduction ......................................................................................................................... 49 4.3 Materials and Methods ........................................................................................................ 51 Sample collection and processing. ......................................................................................... 51 rRNA-based taxonomy abundance assessment. .................................................................... 51 cDNA sequencing and analyses. ........................................................................................... 51 Phylogenetic analyses. ........................................................................................................... 52 Identification of NOB and anammox transcripts. .................................................................. 53 Analyses of transcript sequence variants. .............................................................................
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