Theses and Dissertations at Montana State University (MSU)
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Item Organocatalytic approaches to claisen rearrangements of acid sensitive substrates(Montana State University - Bozeman, College of Letters & Science, 2021) Casey, Aoife; Chairperson, Graduate Committee: Matthew CookCyclopentanes and cyclopentenes are present in many natural products and pharmaceuticals. Despite their presence in many natural products and pharmaceuticals there are few general methods to synthesize highly functionalized 5-membered carbocycles. Using substituted allyl vinyl ethers, highly functionalized 5-membered carbocycles can be accessed through a Claisen rearrangement followed by an intramolecular Sakurai reaction. Due to the acid sensitive nature of these allyl vinyl ethers, Lewis acid catalysis is not a viable reaction pathway but the use of H-bond donors as organocatalysts is an attractive method to develop a synthetic methodology to access 5-membered carbocycles. Through NMR and computational studies, the activation parameters of a these HBD catalyzed Claisen rearrangement has been studied and further knowledge into the mechanism of these reaction pathways has been gained.Item Bacterial and archaeal community diversity in relation to organic carbon consumption and sulfate gradients in the Powder River Basin(Montana State University - Bozeman, College of Letters & Science, 2019) Schweitzer, Hannah Doris; Chairperson, Graduate Committee: Matthew Fields and Sara Branco (co-chair); Elliott Barnhart, Al Cunningham and Matthew Fields were co-authors of the article, 'Comparison of attached and planktonic microbial assemblages across geochemically distinct coal seam habitats' submitted to the journal 'International journal of coal geology' which is contained within this dissertation.; Daniel Ritter, Jennifer McIntosh, Elliott Barnhart, Al B. Cunningham, David Vinson, William Orem and Matthew Fields were co-authors of the article, 'Changes in microbial communities and associated water and geochemistry across a sulfate gradient in coal beds: Powder River Basin, USA' submitted to the journal 'Geochimica et cosmochimica acta' which is contained within this dissertation.; Heidi J. Smith was an author and Elliott P. Barnhart, William Orem, Robin Gerlach and Matthew W. Fields were co-authors of the article, 'Linking organic matter degradation and microbial assemblage composition to subsurface methane production in the Powder River Basin' submitted to the journal 'Applied and environmental microbiology' which is contained within this dissertation.; Heidi J. Smith, Elliott P. Barnhart, Boris Wawrik, Amy Callaghan, Luke McKay, Robin Gerlach and Matthew W. Fields were co-authors of the article, 'Metagenomic analysis of recalcitrant rich coal seams from coal seams with varying sulfate concentrations' submitted to the journal 'Applied and environmental microbiology' which is contained within this dissertation.The rate limiting step in biogenic coal bed methane production has been attributed to the predominantly recalcitrant composition of coal, making it difficult for bacteria to anaerobically break down into methanogenic substrates. The significance of different carbon (C) cycling pathways involved in the turnover of recalcitrant, terrestrial C under various redox conditions is still a topic of debate, and in fact, unknown C cycling metabolic pathways are still being discovered in sub-oxic and anoxic environments. Redox transitions exist along gradients of increasingly recalcitrant C in many environments, and subsurface environments represent a large reservoir of C. The Powder River Basin in southeastern Montana is a model environment for studying in situ redox gradients for terrestrial subsurface C and were selected to investigate i) the temporal and spatial variation in the microbial assemblage from four different coal seams with varying depth profiles, ii) the physicochemical controls that impact the turnover of recalcitrant coal to methane, and iii) the functional potential for hydrocarbon degradation under different sulfate concentrations. Similar to the methane-sulfate critical zone in marine habitats, the presented work highlights the crucial role sulfate has on microbial assemblages, methane production, and C consumption in shallow coal seams. Given the accepted differences between groundwater and surface-associated communities of subsurface porous media, diffusive microbial samplers packed with native coal material were used to enhance the establishment of microbial communities that better re-capitulated in situ communities. The microbial community inhabiting low sulfate coal seams consisted of sequences indicative of syntrophic bacteria such as Syntrophomonas and Hydrogenophaga which have previously demonstrated degradation of polycyclic aromatic hydrocarbons (PAH) and coupled growth with hydrogenotrophic methanogens. The assemblages inhabiting high sulfate coal seams were comprised of methylotrophic methanogens and sulfate reducing bacteria. Methylotrophic methanogens are observed in methane producing coal seams that have intermediate levels of sulfate, suggesting an important transition role in early stage methanogenesis. Low sulfate microcosms experienced an increase in humic-like material and consumed more C compared to high sulfate conditions that demonstrated changes in more labile C, including amino acid-like molecules. Moreover, we used a highly curated anaerobic and aerobic hydrocarbon degradation (AnHyDeg and AromaDeg) and redox (nitrogen, sulfur, methane cycle) gene database and pipeline to analyze metagenomic samples that were obtained from three different coal beds that had increasing sulfate levels. While the functional potential for methanogenesis (mcrA) was detected in all metagenomes, the diversity and relative quantity of these genes was greater in the coal beds that contained methane. Of interest was a significantly greater percentage of aerobic hydrocarbon degradation genes (dioxygenases) from one of the methane-containing coal bed samples. These metabolic markers were identified in co-assembled metagenomes. These results provide an enhanced understanding of recalcitrant carbon turnover in the terrestrial subsurface under different redox conditions and the presumptive metabolic capacities involved in subsurface C turnover in relationship to biogenic CH4.Item Microbial community composition and the transformation of dissolved organic matter in supraglacial environments(Montana State University - Bozeman, College of Agriculture, 2016) Smith, Heidi Jean; Chairperson, Graduate Committee: Christine Foreman; Markus Dieser and Christine Foreman were co-authors of the article, 'Organic matter shapes community compositon in glacial environments' submitted to the journal 'International Society for Microbial Ecology (ISME)' which is contained within this dissertation.; Rachel Foster, Diane McKnight, John Lisle, Daniela Tienken, Marcel Kuypers and Christine Foreman were co-authors of the article, 'Microbial formation of labile glacial organic carbon' submitted to the journal 'Nature geosciences' which is contained within this dissertation.; Michelle Tigges, Juliana D'Andrilli, Albert Parker, Brian Bothner and Christine Foreman were co-authors of the article, 'Supraglacial dissolved organic matter: a labile but unsustainable carbon source' submitted to the journal 'Limnology and oceanography' which is contained within this dissertation.; Amber Schmidt, Rachel Foster, Sten Littmann, Marcel Kuypers and Christine Foreman were co-authors of the article, 'Biofilms on glacial surfaces: hotspots for biological activity' submitted to the journal 'Nature biofilms and microbiomes' which is contained within this dissertation.Relating microbial community composition to ecosystem function is a fundamental goal in ecological analyses, with physico-chemical parameters largely controlling this relationship. This investigation aimed to elucidate the impact of physicochemical factors on biodiversity in glacial habitats, with an emphasis on dissolved organic matter (DOM). DOM is a complex mixture of organic compounds and the primary substrate for microbial activity. Considering the variety of DOM sources in aquatic systems, little is still known about the biological release and bio-transformation of microbially-derived, autochthonous DOM. Continental Antarctica, typically lacking terrestrial carbon inputs, is largely governed by autochthonous DOM, making it an ideal site to investigate microbial biodiversity and the microbial formation of DOM. Different glacial ecosystems were selected, with a strong focus on the supraglacial Cotton Glacier stream, to investigate: i) the microbial diversity and underlying environmental factors governing biogeographical trends, ii) the contribution of exuded carbon to the DOM pool and subsequent heterotrophic uptake/transformation, and iii) how biofilm influences nutrient cycling in supraglacial environments. Findings from this study highlight distinct microbial assemblages in meltwater streams/sediments, ice, snow, and cryoconite across local and regional geographic scales. Specifically, nutrient availability and DOM quality influenced trends in microbial diversity. In situ DOM exudation was sufficiently high to support bacterial carbon demands, while the spatial organization of microorganisms in biofilms was advantageous in transferring nutrients between community members. Furthermore, compared to other more recalcitrant and chemically heterogeneous DOM sources, the highly labile supraglacial DOM was unable to sustain the same magnitude of microbial metabolism. The present study revealed dynamic carbon cycling in supraglacial environments, mediated by the tight coupling between in situ carbon fixation, DOM exudation, and rapid consumption. Statistical analyses failed to show the impact of any physical parameters on community composition. However, data from the Greenland Ice Sheet imply that interactions between community composition and meltwater dynamics are susceptible to environmental changes, shifting ecosystem function and microbial communities, with unforeseen consequences to downstream environments. A multi-scale approach contributed to a better understanding of microbial biogeography, carbon cycling, and cellular spatial organization in glacial surface environments.Item The application of mass spectrometry-based 'omics technologies to investigate environmental interactions of microbial systems(Montana State University - Bozeman, College of Letters & Science, 2015) Tigges, Michelle Marie; Chairperson, Graduate Committee: Brian Bothner; Michelle Tigges and Heidi Smith were main authors, and Juliana D'Andrill, Al Parker, Brian Bothner and Christine Foreman were co-authors of the article, 'Lability of environmental dissolved organic matter drives dynamic microbial processing' submitted to the journal 'Proceedings of the National Academy of Sciences' which is contained within this thesis.Microorganisms interact with their surroundings and each other. However, these interactions are complex and difficult to understand. This research presents the utilization of simplified environmental microbial systems from the extremes of life to gain insight into the roles of microbes in diverse processes including biogeochemical cycling and viral infection. The complex mixture of organic compounds within aquatic systems, known as dissolved organic matter (DOM), is an integral component of the global carbon cycle. It is a carbon source for microbial activity and impacts biogeochemical and ecological processes. However, little is known about the release and bioconversion of these compounds. This thesis presents a liquid chromatography coupled mass spectrometry (LCMS) based exometabolomics approach to chemically characterize the interaction between DOM and the representative microbial species that transform it. This work illustrates for the first time the ability to measure the relative abundance of molecular constituents of DOM during heterotrophic bacterial processing. Processing was shown to be dynamic over time, even with only single organism interactions. A LCMS based proxy was established to predict the lability of DOM carbon sources, and the labile nature of the source was shown to be a significant factor in DOM processing by single organisms. Further, the temporal interaction of two ecologically relevant beta-Proteobacteria with DOM from the Cotton Glacier, Antarctica highlight the importance of understanding the diversity of single organism DOM interactions to interpret community level bacterial interactions. LCMS-based 'omics techniques can also be utilized to characterize the changes in protein expression associated with viral infection of hyperthermophilic archaea. Viral-host interactions in Sulfolobus archaeal systems are poorly understood, and exhibit a diversity of regulation patterns. LCMS-based shotgun proteomics was utilized to characterize the temporal response of Sulfolobus islandicus to infection by Sulfolobus islandicus rod-shaped virus (SIRV2). The strengths and weaknesses of label-free protein quantitation techniques were assessed, enabling the detection of the regulation of SIRV2 proteins over time and identification of key host responses to infection. Together these studies show the impact of LCMS based 'omics technologies in bringing new insights into environmental microbial interactions.Item Structural studies of organic titanium compounds(Montana State University - Bozeman, College of Letters & Science, 1967) Watenpaugh, Keith DonaldItem Reactor optimization of volatilized p-xylene metabolism(Montana State University - Bozeman, College of Engineering, 1993) Vaughn, Barbara ChristineItem Electric and bond moments of some carbon, silicon and titanium organic compounds(Montana State University - Bozeman, College of Letters & Science, 1949) Katz, WalterItem Ecosystem dynamics and temporal variations in a microbially dominated, coastal antarctic lake(Montana State University - Bozeman, College of Agriculture, 2009) Dieser, Markus; Chairperson, Graduate Committee: John C. Priscu; Christine Foreman (co-chair)This study investigated the microbial ecology of Pony Lake, Antarctica. The main objectives of this research were to 1) characterize physicochemical parameters in Pony Lake during the transition from ice covered to ice free, 2) highlight seasonal and inter-seasonal alterations in lake parameters, 3) relate the physicochemical conditions in the ice and water column to microbial processes and community structure, 4) characterize the effects of phototransformation of dissolved organic matter (DOM) on its bioavailability to bacteria, and 5) demonstrate the role of carotenoid pigments in protecting cells against environmental stresses. Also included are results from three McMurdo Dry Valley lakes on the survivability of microbes encapsulated within the lake ice covers. The results of this study highlight the sensitivity of Antarctic environments and the close coupling of environmental conditions and biological processes. Inter-seasonal differences in weather conditions and snow accumulation strongly affected the physicochemistry of this lacustrine system. Biological processes were closely tied to the physicochemical lake conditions. As a consequence planktonic abundances, production rates, and community structure evolved distinctly in each year. Bacterial production was regulated by the quality of DOM. Whereas nutrient availability appeared to play a minor role in eutrophic Pony Lake water, it became more critical for microbial communities found within the ice column of Antarctic lakes. Especially in the ice cover of the McMurdo Dry Valley lakes, enhanced microbial diversity and survivability was associated with particles (nutrient enriched micro-zones) within an otherwise ultra-oligotrophic habitat. In Pony Lake ice, microbial activity and community structure differed with respect to different strata within the ice column, induced by freeze-concentration of solutes, bioavailability of DOM, and oxygen gradients. A comparison of carotenoid pigmented and non-pigmented heterotrophic bacteria indicated that pigmentation provides enhanced resistance to environmental stresses such as freeze-thaw cycles or solar radiation. Collectively, the Pony Lake data demonstrated that microorganisms that persist throughout the year were able to survive much more severe conditions while entrapped within the ice compared to those observed in the lake water during summer months. Further, this study contributes to a better understanding of the biogeochemical carbon cycle in a microbially dominated system.Item Diffuse reflectance spectroscopy for the characterization of calcareous glacial till soils from north central Montana(Montana State University - Bozeman, College of Agriculture, 2006) Steward, Genevieve Christine; Chairperson, Graduate Committee: David Brown.Diffuse reflective spectroscopy (DRS) is a method of soil carbon (C) quantification. In this study, the Vis-NIR (350 - 2500 nm) and MIR (2500-25000 nm) regions were evaluated to determine respective predictive accuracies of soil organic and inorganic carbon (SOC and SIC, respectively). The dataset included 315 soil samples of glacial till origin, obtained from six independent farm sites within the Golden Triangle region of Montana, with depths ranging from 0-100 cm. For Vis-NIR analysis, Local vs. Regional vs. Global calibration sets were compared by six-fold cross validation by site of C predictions developed by Partial Least Squares (PLS) regression and Boosted Regression Trees (BRT). First derivative spectral data was used along with four preparation methods: (i) field moist and (ii) dry cores, (iii) 2-mm sieved ("Sieved") and (iv) milled samples (<200-um, "Milled") were used to evaluate the potential application to in-situ analysis. The most accurate SOC predictions were from Milled samples using a Local calibration set. SOC predictions were a result of SOM electronic absorptions within the visible region.