Chairperson, Graduate Committee: Eric BoydUrschel, Matthew RobertMichael D. Kubo, Tori M. Hoehler, John W. Peters and Eric S. Boyd were co-authors of the article, 'Carbon source preference in chemosynthetic hot spring communities' in the journal 'Applied and Environmental Microbiology' which is contained within this thesis.Matthew R. Urschel, Trinity L. Hamilton, Eric E. Roden and Eric S. Boyd were co-authors of the article, 'Substrate preference and uptake kinetics in a facultatively autotrophic and hyperthermophilic crenarchaeote' submitted to the journal 'Applied and environmental microbiology' which is contained within this thesis.2016-01-032016-01-032015https://scholarworks.montana.edu/handle/1/9084Microbial communities inhabiting high temperature (>73°C) environments are supported by chemical energy, providing a unique opportunity to investigate the processes that supported life prior to the advent of photosynthesis. Previous work has focused on the importance of autotrophy in supporting such communities, and recent reports of organic substrate utilization in several high temperature springs in Yellowstone National Park (YNP), Wyoming, USA suggest that chemosynthetic populations are facultatively autotrophic. Nevertheless, little is known about the factors influencing relative rates of autotrophy and heterotrophy in these systems, and few studies have addressed the potential role of facultative autotrophs in supporting these ecosystems. This work addressed these compelling questions using in situ microcosm assays to directly quantify organic and inorganic substrate transformation rates in 13 geochemically diverse YNP chemosynthetic communities. The results provide the first conclusive evidence that dominant autotrophs in these ecosystems are facultative, and can alter their metabolism over short time spans to preferentially exploit more thermodynamically favorable organic substrates at rates comparable to or exceeding those of inorganic substrate utilization. Multivariate statistical analysis of co-registered substrate transformation rates, geochemical measurements, and phylogenetic data collected from these communities suggests an important relationship between environmental variation, community composition, and the relative importance of autotrophic and heterotrophic metabolisms supporting these communities. Elevated formate utilization rates in crenarchaea-dominated chemosynthetic communities inhabiting acidic, sulfur-rich geothermal springs motivated the isolation of the first hyperthermophilic crenarchaeon (Thermoproteus sp CP80) capable of coupling formate oxidation to elemental sulfur reduction. Physiological characterization demonstrated that CP80 is a facultative autotroph that alters its metabolism to preferentially utilize formate over CO 2. Similar formate utilization characteristics by CP80 and its native population strongly suggests that this and other sulfur reducing crenarchaea may be responsible for high rates of formate utilization in high temperature, sulfur rich YNP systems. Overall, these results indicate an important, previously-underestimated role for organic substrates in supporting chemosynthetic communities inhabiting geochemically diverse YNP hot springs. Future work should focus on identifying additional organic carbon sources, measurement of carbon flux through chemosynthetic communities, and further characterization of the biochemical mechanisms underlying organic and inorganic substrate metabolismin Thermoproteus sp. CP80.enThermophilic microorganismsChemoautotrophic bacteriaHeterotrophic bacteriaDissertationCopyright 2015 by Matthew Robert Urschel