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Diversity of Understudied Archaeal and Bacterial Populations of Yellowstone National Park: from Genes to Genomes Daniel Colman

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Diversity of Understudied Archaeal and Bacterial Populations of Yellowstone National Park: from Genes to Genomes Daniel Colman University of New Mexico UNM Digital Repository Biology ETDs Electronic Theses and Dissertations 7-1-2015 Diversity of understudied archaeal and bacterial populations of Yellowstone National Park: from genes to genomes Daniel Colman Follow this and additional works at: https://digitalrepository.unm.edu/biol_etds Recommended Citation Colman, Daniel. "Diversity of understudied archaeal and bacterial populations of Yellowstone National Park: from genes to genomes." (2015). https://digitalrepository.unm.edu/biol_etds/18 This Dissertation is brought to you for free and open access by the Electronic Theses and Dissertations at UNM Digital Repository. It has been accepted for inclusion in Biology ETDs by an authorized administrator of UNM Digital Repository. For more information, please contact [email protected]. Daniel Robert Colman Candidate Biology Department This dissertation is approved, and it is acceptable in quality and form for publication: Approved by the Dissertation Committee: Cristina Takacs-Vesbach , Chairperson Robert Sinsabaugh Laura Crossey Diana Northup i Diversity of understudied archaeal and bacterial populations from Yellowstone National Park: from genes to genomes by Daniel Robert Colman B.S. Biology, University of New Mexico, 2009 DISSERTATION Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy Biology The University of New Mexico Albuquerque, New Mexico July 2015 ii DEDICATION I would like to dedicate this dissertation to my late grandfather, Kenneth Leo Colman, associate professor of Animal Science in the Wool laboratory at Montana State University, who even very near the end of his earthly tenure, thought it pertinent to quiz my knowledge of oxidized nitrogen compounds. He was a man of great curiosity about the natural world, and to whom I owe an acknowledgement for his legacy of intellectual (and actual) wanderlust. iii ACKNOWLEDGEMENTS I acknowledge the invaluable support, mentoring and advocacy from my dissertation advisor, Dr. Cristina Takacs-Vesbach as well as my dissertation committee members and mentors: Dr. Laura Crossey, Dr. Robert Sinsabaugh and Dr. Diana Northup. I appreciate the mentoring and support from numerous other faculty and staff in the Biology department at the University of New Mexico and Dr. William Inskeep at Montana State University. I also thank former members of the Takacs-Vesbach lab and my fellow graduate students for their support, mentorship, advice and scientific inspiration throughout my dissertation work including Dr. David Van Horn, Dr. Justine Hall, Dr. Matthew Kirk, Dr. Jordan Okie, Dr. Kendra Maas, Dr. Shannon Fitzpatrick, Levi Gray, Jason Dugger and many others. I would also like to acknowledge the personal support from Beverly Marrs and my family who were instrumental in encouraging my forward progress throughout the process of completing the research described herein. iv Diversity of understudied archaeal and bacterial populations of Yellowstone National Park: from genes to genomes by Daniel Robert Colman B.S. Biology, University of New Mexico 2009 Ph.D, Biology, University of New Mexico, 2015 ABSTRACT Yellowstone National Park (YNP) thermal springs have been a crucial resource for the discovery and characterization of microbial biodiversity. The use of cultivation- independent methods has documented many new phyla of uncultured Archaea and Bacteria within thermal springs. Here, I describe the phylogenetic diversity and distribution of Archaea within the YNP thermal spring ecosystem and the phylogenetic and physiologic characterization of novel, uncultured hyperthermophilic bacterial lineages from metagenomic data. In chapter two, I evaluated the efficacy of commonly used, 'universal' archaeal- specific 16S rRNA gene PCR primers in detecting archaeal phylogenetic diversity. In chapter three, using the PCR primers that would provide the best representation of archaeal communities, I used high-throughput 454 pyrosequencing to analyze the phylogenetic diversity and distribution of Archaea and Bacteria among 33 YNP springs. The results indicated that Archaea were ubiquitously distributed across YNP springs and exhibited significant taxonomic diversity across springs but were overall less v phylogenetically diverse in the YNP system than Bacteria. pH, followed by temperature primarily explained the distribution of both archaeal and bacterial taxonomic distribution. Co-occurence analysis suggested a substantial number of putative interactions across the YNP system between and within domains. The results from these two chapters provide the largest survey of Archaea in any thermal system to date and contribute to our understanding of their phylogenetic diversity and ecology in such systems. In Chapter 4, I report the phylogenetic and physiologic characterization of novel, deep-branching bacterial phylotypes from metagenomic data from two YNP springs. Genome assemblies representing four populations were recovered from Aquificaceae- dominated community metagenomes from two high-temperature, circumneutral YNP springs. Phylogenetic analyses indicated they belonged to two distinct, deep-branching bacterial lineages, one of which has no currently characterized genome references. The lineages appeared to be heteroorganotrophs based on metabolic reconstructions and also were both putatively capable of using energy conserved from organic carbon degradation to fuel aerobic respiration. Analysis of the ecological distribution of these populations confirmed that they are currently restricted to high-temperature circumneutral terrestrial springs, largely within YNP. The characterization of these populations provides important physiologic context for the deepest-branching bacterial lineages and valuable genomic references for uncultured, ubiquitously distributed hyperthermophilic Bacteria. vi Table of Contents Chapter 1: INTRODUCTION .................................................................................. 1 References ............................................................................................................. 5 Chapter 2: DETECTION AND ANALYSIS OF ELUSIVE MEMBERS OF A NOVEL AND DIVERSE ARCHAEAL COMMUNITY WITHIN A THERMAL SPRING STREAMER CONSORTIUM ................................................................................ 9 Abstract ................................................................................................................. 9 Introduction ........................................................................................................... 10 Materials and Methods .......................................................................................... 12 Results and Discussion ......................................................................................... 15 Acknowledgements ............................................................................................... 19 References ............................................................................................................. 20 Tables .................................................................................................................... 24 Figures................................................................................................................... 25 Supplementary Tables ........................................................................................... 28 Chapter 3: PHYLOGENETIC DIVERSITY AND DISTRIBUTION OF ARCHAEA AND BACTERIA AMONG YELLOWSTONE NATIONAL PARK HOT SPRINGS .................................................................................................................................. 32 Abstract ................................................................................................................. 32 Introduction ........................................................................................................... 33 Materials and Methods .......................................................................................... 35 Results ................................................................................................................... 40 vii Discussion ............................................................................................................. 46 Conclusions ........................................................................................................... 59 Acknowledgements ............................................................................................... 59 References ............................................................................................................. 60 Tables .................................................................................................................... 68 Figures................................................................................................................... 73 Supplementary Figures ......................................................................................... 84 Chapter 4: CHARACTERIZATION OF NOVEL, DEEP-BRANCHING HETEROTROPHIC BACTERIAL POPULATIONS RECOVERED FROM THERMAL SPRING METAGENOMES .................................................................................. 88 Abstract ................................................................................................................. 88 Introduction ........................................................................................................... 89 Materials and Methods .........................................................................................
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