Theses and Dissertations at Montana State University (MSU)
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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.Item Geobiological interactions of archaeal populations in acidic and alkaline geothermal springs of Yellowstone National Park, WY, USA(Montana State University - Bozeman, College of Agriculture, 2015) Beam, Jacob Preston; Chairperson, Graduate Committee: William P. Inskeep; Zackary J. Jay, Mark A. Kozubal and William P. Inskeep were co-authors of the article, 'Niche specialization of novel thaumarchaeota to oxic and hypoxic acidic geothermal springs in Yellowstone National Park' in the journal 'The International Society for Microbial Ecology journal' which is contained within this thesis.; Hans C. Bernstein, Zackary J. Jay, Mark A. Kozubal, Ryan deM. Jennings, Susannah G. Tringe and William P. Inskeep were co-authors of the article, 'Assembly and succession of iron oxide microbial mat communities in acidic geothermal springs' submitted to the journal 'Geobiology' which is contained within this thesis.; Zackary J. Jay, Markus C. Schmid, Margaret F. Romine, Douglas B. Rusch, Ryan deM. Jennings, Mark A. Kozubal, Susannah G. Tringe, Michael Wagner and William P. Inskeep were co-authors of the article, 'In situ ecophysiology of an uncultured lineage of aigarchaeota from an oxic hot spring filamentous 'streamer' community' in the journal 'International Society for Microbial Ecology journal' which is contained within this thesis.Microbial communities in high-temperature acidic and alkaline geothermal springs contain abundant, novel Archaea whose role in biogeochemical cycling and community function in microbial mats is not described. This thesis utilized a complementary suite of analyses that included aqueous and solid phase geochemistry, community genomics, phylogenomics, targeted 16S rRNA gene sequencing, community transcriptomics, and microscopy to elucidate the role of novel archaeal populations in acidic sulfur and iron rich hot springs in Norris Geyser Basin, Yellowstone National Park (YNP), and alkaline microbial 'streamer' communities in Lower Geyser Basin, YNP. Novel members of the archaeal phylum, Thaumarchaeota were identified in oxic iron oxide mats and hypoxic elemental sulfur sediments in acidic geothermal springs. These two different groups of Thaumarchaeota likely utilize organic carbon as electron donors and exhibited metabolic capacities based on the presence and absence of oxygen (e.g., heme copper oxidases). The assembly and succession of iron oxide mats in acidic geothermal springs showed later colonization (> 40 d) of Thaumarchaeota. Early colonizers (< 7 d) of Fe(III)-oxide mats include Hydrogenobaculum spp. (Aquificales) and the iron-oxidizing Metallosphaera yellowstonensis (7 - 14 d), which accrete copious amounts of Fe(III)-oxides. Interaction of Hydrogenobaculum and M. yellowstonensis is important to mat formation and subsequent later colonization of heterotrophic archaea (> 40 d). The succession of these communities follows a repeatable pattern, which exhibits interplay among oxygen flux, hydrodynamics, and microbial growth. The biogeochemical and micromorphological signatures may be important for the interpretation of ancient Fe(III)-oxide geothermal deposits. Interactions between Archaea and Aquificales are also important in oxic, alkaline 'streamer' communities, which contain a novel Aigarchaeota population and Thermocrinis spp. This Aigarchaeota population (Candidatus "Calditenuis aerorheumensis") exhibits a filamentous morphology and was intricately associated with Thermocrinis spp. C. aerorheumensis is an aerobic chemoorganotroph. Oxygen is the predominant electron acceptor of C. aerorheumensis, and mRNA transcripts were elevated for heme copper oxidase complexes. Organic carbon electron donors may come from bacteria in close proximity and/or dissolved organic carbon. Archaeal interactions with Aquificales contribute to higher-order level properties (e.g., biomineralization, metabolite sharing) that are important in the formation of hot spring microbial mats and streamer communities.