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Item Evolution and function of flavin-based electron bifurcation(Montana State University - Bozeman, College of Letters & Science, 2018) Poudel, Saroj; Chairperson, Graduate Committee: Eric Boyd; John W. Peters (co-chair); Eric C. Dunham, Melody R. Lindsay, Maximiliano J. Amenabar, Elizabeth M. Fones, Daniel R. Colman and Eric S. Boyd were co-authors of the article, 'Origin and evolution of flavin-based electron bifurcating enzymes' in the journal 'Frontiers in microbiology' which is contained within this thesis.; Amaya M. Garcia Costas was an author and Anne-Frances Miller, Gerrit J. Schut, Rhesa N. Ledbetter, Kathryn R. Fixen, Lance C. Seefeldt, Michael W. W. Adams, Caroline S. Harwood, Eric S. Boyd and John W. Peters were co-authors of the article, 'Defining electron bifurcation in the electron transferring flavoprotein family' in the journal 'Journal of bacteriology' which is contained within this thesis.; Daniel R. Colman was an author and Kathryn R. Fixen, Rhesa N. Ledbetter, Yanning Zheng, Natasha Pence, Lance C. Seefeldt, John W. Peters, Caroline S. Harwood and Eric S. Boyd, were co-authors of the article, 'Electron transfer to nitrogenase in different genomic and metabolic backgrouns' in the journal 'Journal of bacteriology' which is contained within this thesis.Anaerobic microorganisms live in energy limited environments with low nutrient fluxes. Thus, selection has likely acted on these cells to innovate mechanisms that improve the efficiency of anaerobic energy metabolism. In 2008, the process of flavin-based electron bifurcation (FBEB) was discovered and has since been shown to be a critical process that allows anaerobic cells to overcome thermodynamic barriers and to improve metabolic efficiency. FBEB enzymes catalyze the coupling of exergonic and endergonic oxidation--reduction reactions with the same electron donor to circumvent thermodynamic barriers and minimize free energy loss. To date, a total of 12 FBEB enzymes have been discovered that share common features that include the presence of protein-bound flavin, the proposed site of bifurcation, and the electron carrier ferredoxin. Due to its recent discovery, a comprehensive description of the natural history of bifurcating enzymes is lacking. In this thesis, we report the taxonomic and ecological distribution, functional diversity, and evolutionary history of bifurcating enzyme homologs in available complete genomes and environmental metagenomes. Moreover, we investigated the functional and ecological constraints that led to the emergence of FBEB enzymes. Bioinformatics analyses revealed that FBEB enzyme homologs were primarily detected in the genomes of anaerobes, including those of sulfate-reducers, acetogens, fermenters, and methanogens. Phylogenetic analyses of these enzyme homologs suggest that they were not a property of the Last Universal Common Ancestor of Archaea and Bacteria indicating that they are a more recent evolutionary innovation. Consistent with the role of these enzymes in the energy metabolism of anaerobes, FBEB homologs were enriched in metagenomes from subsurface environments relative to those from surface environments. In fact, the earliest evolving homologs of most bifurcating enzymes were detected in subsurface environments, including fluids from subsurface rock fractures and hydrothermal systems. Together, these data highlight the central role that FBEB played and continued to play in the energy metabolism of anaerobic microbial cells inhabiting subsurface environments.Item Fermentation and anaerobic decomposition in a hot spring microbial mat(Montana State University - Bozeman, College of Agriculture, 1984) Anderson, Karen Leigh