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Genomic Analysis of Uncultured Microbes in Marine Sediments

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Genomic Analysis of Uncultured Microbes in Marine Sediments University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Doctoral Dissertations Graduate School 12-2017 Singled Out: Genomic analysis of uncultured microbes in marine sediments Jordan Toby Bird University of Tennessee, [email protected] Follow this and additional works at: https://trace.tennessee.edu/utk_graddiss Recommended Citation Bird, Jordan Toby, "Singled Out: Genomic analysis of uncultured microbes in marine sediments. " PhD diss., University of Tennessee, 2017. https://trace.tennessee.edu/utk_graddiss/4829 This Dissertation is brought to you for free and open access by the Graduate School at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Doctoral Dissertations by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. To the Graduate Council: I am submitting herewith a dissertation written by Jordan Toby Bird entitled "Singled Out: Genomic analysis of uncultured microbes in marine sediments." I have examined the final electronic copy of this dissertation for form and content and recommend that it be accepted in partial fulfillment of the equirr ements for the degree of Doctor of Philosophy, with a major in Microbiology. Karen G. Lloyd, Major Professor We have read this dissertation and recommend its acceptance: Mircea Podar, Andrew D. Steen, Erik R. Zinser Accepted for the Council: Dixie L. Thompson Vice Provost and Dean of the Graduate School (Original signatures are on file with official studentecor r ds.) Singled Out: Genomic analysis of uncultured microbes in marine sediments A Dissertation Presented for the Doctor of Philosophy Degree The University of Tennessee, Knoxville Jordan Toby Bird December 2017 Copyright © 2017 by Jordan Bird All rights reserved. ii Dedication To my loving parents, Trent and Lori, and amazing and compassionate brother, Justin. iii Acknowledgements Firstly, this work would not have been possible without the support and guidance of my advisor, Karen G. Lloyd. She took a chance on a strong willed, challenging student to be her first graduate student. She went above and beyond her charge as an advisor, and her dogged pursuit of knowledge and endless generosity of spirit has been a welcomed constant in my life of the last five years. Moreover, she will forever on be a shining example of personhood in my life as her unwavering ability to see and address the humanity in every person she meets remains a model I will endeavor to emulate. Secondly, I would like to thank my friends and colleagues that have kept me grounded. A special thanks to those who have sat and listened to me during times of despair and to those who have celebrated with me in times of success. My fellow labmates—Joy, Richard, Katie, and Kate—have inspired me and endured me at my most outwardly cynical. Thanks to my SCALE-IT cohort and our leader Dr. Harry Richards. His pursuit to see us all succeed did result in some of the key learning experiences that I will carry with me through the next stage of my career. When I first visited the University of Tennessee, I noted the eagerness of the faculty to engage students, collaborate, and provide resources and ideas as a key part of my decision to enroll in the program. This observation has remained true throughout my years in Knoxville. To my Geobio peeps, you are always a source of inspiration for me, and the memories in science and community we shared are some of my fondest. Thanks to Dr. Brett Baker, Dr. Alexander Probst, and Dr. Brandi Reese for being wonderful and accommodating collaborators outside of UTK. To my family, whose support throughout my time here, but especially during the writing of this dissertation was crucial and extraordinary. I will forever be in debt to you. iv Abstract The vast majority of abundant taxa in marine sediment environments have not yielded to culture, leaving questions about their relationship to other taxa and their functional potential unanswered. However, in the absence of active cultures, careful application of various omics methods can be used to help us make useful inferences about their evolutionary history and how they have continued to survive in environments of extreme energy deprivation. For this dissertation, I have applied comparative genomics methods to members of two uncultured groups, the recently proposed Altiarchaeales order and a cosmopolitan taxon associated with the Actinobacteria phylum. Additionally, I combined transcript recruitment and metabolomic profiles to investigate metabolisms inferred from the single-cell amplified genomes extracted from members of a taxa that thrive in Baltic Sea sediment microbial communities. In Chapter II, I establish a phylogenetic relationship across distantly related members of the order Altiarchaeales and discuss environment-specific adaptations. In Chapter III, transcript recruitment and metabolite profiles support a community-wide focus on microbial persistence with active members of the uncultured Atribacteria phylum playing an important ecological role. In Chapter IV, my analysis leads to the proposal of the new class within the Actinobacteria. Osirisbacteria is a class of Actinobacteria that is specialized for life in anoxic environments. Overall, this work offers new insights into deeply-branching microbial taxa, improved understanding of recently considered branches of the evolutionary tree, and new perspective on metabolisms important for survival in low-energy marine sediment environments. v Table of Contents Chapter I: Introduction .................................................................................................................1 List of References .....................................................................................................................12 Chapter II: Culture independent genomic comparisons reveal environmental adaptations for Altiarchaeales .........................................................................................................................20 Abstract .....................................................................................................................................22 Introduction ..............................................................................................................................23 Materials and Methods ............................................................................................................26 Results .......................................................................................................................................32 Discussion ..................................................................................................................................44 Conclusion .................................................................................................................................50 Funding .....................................................................................................................................50 Acknowledgements ...................................................................................................................51 List of References .....................................................................................................................52 Chapter III: Atribacteria support community-wide microbial persistence through 44,000 years of Baltic Sea sedimentation ...............................................................................................59 Abstract .....................................................................................................................................61 Main Text ..................................................................................................................................62 Materials and Methods ............................................................................................................77 Acknowledgements ...................................................................................................................81 List of References .....................................................................................................................82 Chapter IV: Comparative genomic analysis reveals earliest branching Actinobacteria class, Candidatus Osiribacteria ............................................................................................................86 Abstract .....................................................................................................................................88 Introduction ..............................................................................................................................88 Results and Discussion .............................................................................................................89 Materials and Methods ..........................................................................................................104 Acknowledgements .................................................................................................................106 List of References ...................................................................................................................107 Chapter V: Conclusion ..............................................................................................................115 vi List of References ...................................................................................................................119
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