Theses and Dissertations at Montana State University (MSU)
Permanent URI for this collectionhttps://scholarworks.montana.edu/handle/1/733
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Item Identification of cellulolytic hot spring organisms through bioorthogonal labeling(Montana State University - Bozeman, College of Letters & Science, 2021) Reichart, Nicholas John; Chairperson, Graduate Committee: Roland Hatzenpichler; This is a manuscript style paper that includes co-authored chapters.Microbial physiology is the study of the metabolism and function of microorganisms. The recent expansion of genomic diversity has outpaced the description of physiology. To better understand microbial metabolisms and environmental processes, more detailed research is needed for both novel and undescribed microbes. While many new methods are being developed to describe in situ microbial activity, this dissertation implements bioorthogonal non-canonical amino acid tagging as a proxy to track metabolic activity of microbes under close to environment conditions. Using differential analyses on hot spring microbial communities, we were able to show that certain microbial taxa had preferential activity towards specific incubation amendments. Previous activity-based studies had shown that hot springs were a unique environment for discovering cellulolytic microbes that could be used in industrial processing of plant biomass. Herein, we used computational analysis to screen publicly available metagenomic datasets to identify the enzymatic potential of hot springs worldwide. The wide diversity of taxa and biomass degrading enzymes were investigated and hot springs were further highlighted as a system that could be used to find improvement for the industry of plant biomass degradation and processing. To build upon the cellulolytic potential found in hot spring metagenomic datasets, bioorthogonal non-canonical amino acid tagging coupled with fluorescence-activated cell sorting was applied to the biotechnological relevant field of plant biomass degradation to identify microbes involved in the cellulolytic process. Examination of the active microbes revealed difference in the community when supplemented with cellulose. Taken together, the work in this dissertation served to expand and apply the recent development of activity-based studies used to describe environmental microbial populations, with a focus on plant biomass degradation.Item Analysis of complex samples by mass spectrometry leads to insights into system dynamics(Montana State University - Bozeman, College of Letters & Science, 2021) Peach, Jesse Thomas; Chairperson, Graduate Committee: Brian Bothner; James Larson, Sutton Kanta, Eric Boltinghouse, Rebecca Mueller, Ganesh Balasubramanian, Mohammed Refai, Brent Peyton and Brian Bothner were co-authors of the article, 'Optimization of thermal small molecule and protein mass spectrometry analysis' submitted to the journal 'Analytical biochemistry' which is contained within this dissertation.; Rebecca Mueller, Dana Skorupa, Margaux Mesle, Sutton Kanta, Eric Boltinghouse, Bailey Sharon, Valerie Copie, Brian Bothner and Brent Peyton were co-authors of the article, 'Longitudinal meta-analysis of the Five Sisters Hot Springs in Yellowstone National Park reveals a dynamic thermoalkaline environment' submitted to the journal 'Environmental microbiology' which is contained within this dissertation.; Stephanie M. Wilson, Logan D. Gunderson, Lizzi Frothingham, Tan Tran, Seth T. Walk, Carl J. Yeoman, Brian Bothner and Mary P. Miles were co-authors of the article, 'Temporal metabolic response yields a dynamic biosignature of inflammation' submitted to the journal 'iScience' which is contained within this dissertation.Systems biology offers a holistic approach to biological science. In its most complete form, systems biology requires comprehensive data encompassing all of the parts or molecules across a set of hierarchical networks. To obtain and analyze the comprehensive and large datasets required for systems biology analysis, biologists have taken advantage of new technology and computational tools. Over the last few decades, advances in computational modeling and analysis technology has dramatically increased the efficacy of systems biology and the understanding of the natural world. However, systems biology is still an emerging discipline. The overwhelming scale of potential biological data that has yet to be described, coupled with interpretation and application obstacles, leaves much work to be accomplished. One aspect of systems biology that needs development is the interpretation and analysis of temporal biological data. Temporal data reveals more about biological phenomena than static data as biology is inherently dynamic. This dissertation explores the benefits of temporal profiling of complex samples to make time-resolved conclusions about complicated biological questions. Three research projects are the backbone of this document, with a chapter being devoted to each. Chapter 2 describes the development of a comprehensive method for extraction and mass spectrometry analysis of several different fractions from hot spring sediment. Chapter 3 delves into a multi-omics analysis tracking changes over the course of three years in a thermoalkaline spring system in Yellowstone National Park. It defines how specific extracellular small molecules correlate with microbial fitness. Specifically, how unique nitrogen and sulfur containing molecules in the sediment drive archaeal abundance and diversity. The final chapter introduces the concept of a 'dynamic biosignature', a set of metabolites that have similar responses to known biomarkers, in this case pro-inflammatory cytokines. A cohort of metabolites was identified that provided mechanistic insight into the inflammatory response. Overall, this dissertation provides examples of systems biology analysis and provides evidence that static, single time-point datasets fail to capture that which is the essence of biology - change.Item Free lipids of hot spring microbial mats of possible evolutionary significance(Montana State University - Bozeman, College of Letters & Science, 1988) Shiea, Jentaie