Theses and Dissertations at Montana State University (MSU)
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Item An omics-based interrogation of disparate microbial systems: multi-omics analysis of a bio-mining archaeon and the effects of arsenic on the E. coli Lipidome(Montana State University - Bozeman, College of Letters & Science, 2023) Fausset, Hunter Lee; Chairperson, Graduate Committee: Brian Bothner; This is a manuscript style paper that includes co-authored chapters.Systems biology represents the next frontier in the elucidation of biochemical mechanisms, disease states, and microorganisms. Rather than approaching individual parts of an organism, such as a specific protein, molecule, or mRNA, a systems biology or "omics" investigation seeks to characterize all proteins, molecules, or RNA simultaneously. This is crucial, because all macromolecules in a lifeform exist in dynamic equilibria with those around them; no one biological process occurs in a vacuum. Omics investigations have ballooned in usage over the last decades due to scientists realizing their power in characterizing complex biological phenomena. This has also been spurred on by advances in technologies enabling the robust elucidation of thousands of molecules at once, particularly benefitting from the modernization of mass spectrometry. This technique can be used to study any number of biological problems including those presented here; a multi-omics investigation into a mineral- eating methanogen and a lipidomic characterization of arsenic exposure in a key member of the gut microbiome, E.coli. Methanosarcina barkeri, a widespread methanogen found in marine sediments, is able to reductively dissolve minerals such as pyrite (FeS2) to satisfy their iron and sulfur requirements. Presented here are two investigations containing transcriptomic, proteomic, metabolomic, and lipidomic analyses, performed in parallel on the same biomass. Together, these experiments suggest that the organism undergoes a significant phenotypic shift in response to changes in just two elements, Fe and S. Overall inferences are echoed in the small molecule analyses; the metabolomes and lipidome of the organism change similarly in to the proteome. Key sulfur equilibria are implied in the process, as are specific lipids, choline, and dethiobiotin. A similar approach was applied to E.coli treated with arsenic, as a proxy for understanding the detoxifcation that takes place in the gut microbiome after ingestion. Marked lipidomic changes were observed in E.coli resulting from treatment, which were dependent both on species of arsenic as well as presence of the Ars operon. As a foundational study, this work answered some and generated many more hypotheses on the biochemical fate of As in microorganisms in the gut microbiome.Item Reductive dissolution of pyrite by methanogens and its physiological and ecological consequences(Montana State University - Bozeman, College of Agriculture, 2022) Payne, Devon; Chairperson, Graduate Committee: Eric Boyd; This is a manuscript style paper that includes co-authored chapters.All life requires iron and sulfur, in particular, for use in metallocofactors of enzymes that catalyze chemistry that is essential for metabolism. In anaerobic environments, iron and sulfur are typically found in their reduced forms (ferrous iron and sulfide, respectively) that will react and form insoluble iron-sulfide minerals, such as pyrite. A consequence of this is that either iron or sulfur are typically limiting in solution, raising the question as to how anaerobes acquire these essential elements under such conditions. Here, it is demonstrated that anaerobic methanogens can reduce pyrite to release iron and sulfur that are assimilated by the cells to meet biosynthetic demands. Through a combination of growth experiments, -omics analyses, and microscopy, a model for the reductive dissolution of pyrite was established. In this model, direct contact between cells and pyrite is required for mineral reduction. When in direct contact, pyrite is reduced and sulfide is released, leaving a pyrrhotite secondary mineral on the surface. Iron solubilized from pyrrhotite reacts with sulfide in the growth medium to yield aqueous iron sulfur clusters that are assimilated by cells. Cells grown on pyrite exhibit phenotypic differences in comparison to traditionally grown cells provided with ferrous iron and sulfide. At a morphological level, pyrite-grown cells were 33% smaller than traditionally grown cells and hyperaccumulated iron as an intracellular mineral. When grown under nitrogen-fixing conditions, cells grown on pyrite had higher cell densities, growth yields, and growth rates in comparison to traditionally grown cells. Molybdate transporters were down expressed in pyrite-grown, nitrogen-fixing cells relative to traditionally-grown cells, consistent with sulfide limiting molybdate availability in the latter condition. Moreover, pyrite-grown cells could fix nitrogen at ~100-fold lower molybdenum concentration than traditionally grown cells, indicating differences in molybdenum requirements based on the iron and sulfur source provided. Together, these data highlight that in contemporary anoxic environments, iron-sulfide minerals are an important and even preferred source of iron and sulfur for methanogens. These findings provide insight into how ancient methanogens could have acquired iron and sulfur on an anoxic early Earth when one or both of these elements were likely only available as metal sulfides.Item Geochemical characteristics of a waste rock repository at a western gold mine(Montana State University - Bozeman, College of Agriculture, 1997) Outlaw, Jason DwayneItem Concentrated iron pyrite mine waste as an amendment for alkaline soils(Montana State University - Bozeman, College of Agriculture, 1994) Smith, Troy C.Item Clean tailing reclamation : revegetation of mill tailings following removal of pyrite and heavy metals(Montana State University - Bozeman, College of Agriculture, 1997) Krueger, Jane Marie