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Item Linking geochemistry with microbial community structure and function in sulfidic geothermal systems of Yellowstone National Park(Montana State University - Bozeman, College of Agriculture, 2015) Jay, Zackary James; Chairperson, Graduate Committee: William P. Inskeep; Doug B. Rusch, Susannah G. Tringe, Connor Bailey, Ryan M. Jennings and William P. Inskeep were co-authors of the article, 'Predominant acidilobus-like populations from geothermal environments in Yellowstone National Park exhibit similar metabolic potential in different hypoxic microbial communities' in the journal 'Applied and environmental microbiology' which is contained within this thesis.; Jacob P. Beam, Alice Dohnalkova, Regina Lohmayer, Brynna Bodle, Brita Planer-Friedrich, Margaret Romine and William P. Inskeep were co-authors of the article, 'Pyrobaculum yellowstonensis strain WP30 respires on elemental sulfur and/or arsenate in circumneutral sulfidic geothermal sediments of Yellowstone National Park' submitted to the journal 'Applied and environmental microbiology' which is contained within this thesis.; Doug B. Rusch, Jacob P. Beam, Mark A. Kozubal, Ryan M. Jennings and William P. Inskeep were co-authors of the article, 'The distribution, diversity and function of predominant Thermoproteales phylotypes in Yellowstone National Park' submitted to the journal 'ISME J' which is contained within this thesis.Members of the archaeal phylum Crenarchaeota are often associated with microbial communities in high-temperature (> 70 °C) geothermal springs. Environmental genome sequencing (metagenomics) has revealed that populations of Sulfolobales, Desulfurococcales, and Thermoproteales are abundant in hypoxic elemental sulfur sediments of Yellowstone National Park (YNP) and possess enzyme complexes that are implicated in the cycling of carbon, sulfur, and arsenic. Therefore, the primary objectives of this work were to (i) identify the abundant Desulfurococcales and Thermoproteales sequences in these habitats, (ii) characterize the growth and curate the genome of the first Thermoproteales representative isolated from YNP (Pyrobaculum yellowstonensis strain WP30), and (iii) establish a linkage between geochemistry and microbial community structure and function by identifying key proteins that are important to these populations in situ. The primary Desulfurococcales populations were related to Acidilobus spp. and exhibited similar metabolic potential in near-neutral (pH 4 - 6) hypoxic elemental sulfur sediments and acidic (pH ~3) iron oxide mats. These populations are primarily anaerobic heterotrophs that ferment complex organic carbon and are auxotrophic with regards to numerous vitamins and cofactors. These organisms are often found together with members of the Thermoproteales, which are widely distributed in elemental sulfur sediments, acidic iron oxide mats, and streamer communities. P. yellowstonensis strain WP30 was obtained from a hypoxic elemental sulfur sediment habitat with high concentrations of arsenic. This organism was shown to reduce elemental sulfur and/or arsenate in the presence of yeast extract. The complete genome of str. WP30 contained numerous dimethylsulfoxide molybopterin (DMSO-MPT) proteins, which are inovolved in redox reactions of inorganic constituents (i.e. sulfur and arsenic), and genomic comparisons revealed that this organism is closely related to native Pyrobaculum populations. The distribution of Thermoproteales populations was correlated with pH, while the presence of respiratory complexes (terminal oxidases, DMSO-MPT, and dissimilatory sulfate reductases) was correlated with the presence of key electron donors and acceptors. Intron sequences identified in Thermoproteales 16S rRNA genes and were shown in silico to prevent the binding of 'universal' primers that are often used in environmental surveys. These metagenomic, microbiological, and geochemical studies have advanced the understanding of Crenarchaeota diversity and function in YNP.