Theses and Dissertations at Montana State University (MSU)

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A critical assessment of technologies for the study of organic matter in glaciers and ice sheets
(Montana State University - Bozeman, College of Agriculture, 2019) Willis, Madelyne Claire; Chairperson, Graduate Committee: Christine Foreman
Polar and temperate glaciers harbor active microbial communities and a substantial storage of organic carbon. These frozen ecosystems are especially sensitive to the effects of climate change and are expected to release roughly 15 teragrams of carbon by 2050. This creates a sense of urgency for further experimentation to increase our understanding of glacier ecosystem function and the impact glacier habitats have on local and global biogeochemical cycles. Due to the complex nature of organic matter, there is no single method which is suitable for every study. Technological advancements have improved methods for determining the quantity and quality of organic matter and emerging new technologies are providing faster and less-costly ways to overcome the challenges of working in these harsh environments. Consequently, a synthesis of peer-reviewed literature was conducted to summarize the current state of microbial ecology of glaciers and ice sheets, and to explore the techniques and new tools which are being developed to aid in the study of these rapidly disappearing ecosystems. The culmination of this work is an introduction and guide for analysts interested in examining the source, transformation history, and fate of organic matter in glacial systems. It was found that there is not one single technique superior to another, rather the appropriate technique is dependent on the questions being addressed and the resources available.
Evolutionary consequences of gene flow in the absence or inhibition of dispersal in microbial communities
(Montana State University - Bozeman, College of Agriculture, 2023) Munro-Ehrlich, Robert Mason; Chairperson, Graduate Committee: Jovanka Voyich-Kane; This is a manuscript style paper that includes co-authored chapters.
Much of our understanding of the evolutionary dynamics of microbial populations is derived from population level studies which focus on the immediately present populations and ignore the contributions of nearby communities. Microbial ecology studies typically do not distinguish between gene flow, i.e., the movement of genetic material between populations, and dispersal, i.e., the movement of those populations themselves. These two processes are indeed linked, but not identical. We have known for centuries that genetic material can be transferred between physically distant and taxonomically disparate microbial populations; molecular biology tools like cloning are dependent on this capability. In other words, gene flow can occur even without dispersal. However, our ecological and evolutionary studies of microbial populations typically fail to acknowledge the evolutionary impact and genetic contributions of outside populations. Unique evolutionary scenarios arise when dispersal between two or more populations is prevented or limited, but gene flow can still occur between them. We hypothesized that this scenario would impact microbial populations by facilitating speciation, selection, and local adaptation. We aimed to test this hypothesis by studying endemic Meiothermus populations inhabiting serpentinite rocks in the subsurface of the Samail ophiolite in Oman. Samail Ophiolite microbial communities, of which Meiothermus populations are a component, are dispersed across the subsurface and separated by meters of solid rock and by chemical and pH gradients spanning orders of magnitude. Despite barriers to dispersal that are significant enough to shape community structure, we found that gene flow still occurred between nearly all observed populations of Meiothermus. This gene flow is contributing to disruptive selection amongst cohabiting populations, and may also be contributing to local adaptation, both at the genetic and genomic level. We also identified potential mechanisms for this gene flow, including abundant viral elements. The sequence similarity of mobile genetic elements in these Meiothermus populations implies that this gene flow occurred after colonization by a common Meiothermus ancestor and that diversification is likely ongoing. To our knowledge, this is the first demonstration of gene flow across barriers to dispersal in an environmental microbial system. In conclusion, these results suggest that the capacity for microbial populations to undergo gene flow even in the absence or inhibition of dispersal is a natural process, has substantial consequences for the evolution of the effected population, and may also have consequences for the microbial and surrounding environment.
Genomic, microbial, and linear relationships between residual feed intake, dry matter intake, average daily gain, and post weaning weights in range sheep
(Montana State University - Bozeman, College of Agriculture, 2023) Schaub, Daniel James; Chairperson, Graduate Committee: Christian J. Posbergh
Over forty years, United States sheep producers have selectively bred range sheep for larger post-weaning weights using estimated breeding values. However, this has led to increased feed intake, prompting this study's objective to quantify the relationship between lamb growth estimated breeding values, feed intake, and feed efficiency. The study involved 40 Targhee and 40 Rambouillet ewe lambs weaned at four months and put on a GrowsafeTM feeding system for a 56-day experimental period, with ewes weighed weekly and at the start and end of the trial. Residual feed intake was calculated using body weights, average daily gain, and daily feed intake measurements. The ewe lambs' post-weaning weight estimated breeding value was associated to their phenotypic traits. These procedures were repeated when the same ewes were yearlings and at maintenance. The study found that while post-weaning weight estimated breeding values predicted dry matter intake (P<0.05), they lacked association with residual feed intake (P>0.05) in both experimental periods. However, the ewe's post-weaning weight estimated breeding value predicted mid-trial body weight in both periods (P<0.05). Thus, while selecting higher post- weaning weight animals may increase feed usage due to larger body size, it does not affect feed efficiency. Comparing the residual feed intake between the two experimental periods, growth residual feed intake measurements did not predict residual feed intake in maintenance. Therefore, caution should be used when utilizing residual feed intake from the growth period as an indicator of feed efficiency in maintenance. The study also examined rumen microbial profiles in sheep between the two experimental periods. Methanogenic archaea were relatively increased within the growth experimental period, where a pelleted diet was used, and cellulolytic bacteria were increased in the maintenance experimental period, where hay was provided. Since methanogens are associated with decreased feed efficiency, diet may play a role in changing a sheep's microbiome towards more feed efficient bacteria. Finally, a genome-wide association study found the Dmrt2 gene associated with DMI and RFI in maintenance. The Dmrt2 gene may regulate muscle and bone development in the early embryo, affecting feed efficiency in sheep later in life.
Biofilm distribution in a porous medium environment emulating shallow subsurface conditions
(Montana State University - Bozeman, College of Engineering, 2021) Massey, KaeLee Frances; Chairperson, Graduate Committee: Matthew Fields; Heidi J. Smith, Al B. Cunningham, Hannah Dreesbach, Luke J. McKay, Yupeng Fan, Ying Fu, Joy D. Van Nostrand, Jizhong Zhou, Katie F. Walker, Terry C. Hazen and Matthew W. Fields were co-authors of the article, 'Biofilm distribution in a porous medium reactor emulating shallow subsurface conditions' which is contained within this thesis.
Microorganisms in the terrestrial subsurface play important roles in nutrient cycling and degradation of anthropogenic contaminants, functions essential to the maintenance of healthy aquifers. Microorganisms have the potential to change the geochemical properties of the shallow terrestrial subsurface, and previous studies have uncovered significant roles microorganisms can play in groundwater processes, such as biogeochemical cycling. Much of the attention given to the shallow terrestrial subsurface has been focused on the effects of contamination and how microorganisms function in these systems, with far less emphasis on understanding how hydraulic properties influence subsurface microbial ecology. To fully understand how environmental factors impact microbial community dynamics, interactions, succession, colonization, and dispersal in the shallow subsurface environment it is essential to understand the link between microbiology and hydrology. In this thesis, an up-flow packed bed reactor (PBR) was designed to emulate select field conditions (i.e., flow rate and particle size) observed at the Oak Ridge National Laboratory-Field Research Center (ORNL-FRC) to observe how environmental factors influences metabolic activity, community establishment, and cell distribution in a micropore environment. Furthermore, we developed methods to visualize the localization of active and non-active cells within the porous medium. The goals of this thesis were to 1) understand how environmental variables impact distribution and metabolic activity of microbial cells in the soil pore microenvironment at the FRC using native sediment bug trap material, 2) evaluate the hydraulic properties of the presented up-flow packed bed reactor (PBR), 3) observe how inert, non-charged particles distribute in a porous media environment, and 4) observe the biofilm distribution a microorganism isolated from the ORNL-FRC using different inoculation strategies. Overall, the data demonstrates that the presented reactor system accurately emulates field conditions and environmental factors (pH, particle size, average pore velocity) and the distribution of cells in ex situ conditions. The results of this thesis have implications for elucidating the impacts of environmental factors on metabolic activity and cell distribution in a field relevant reactor system.
Response of soil bacterial communities to cropping systems, temporal changes, and environmental conditions in the northern Great Plains
(Montana State University - Bozeman, College of Agriculture, 2021) Ouverson, Laura Tindall; Chairperson, Graduate Committee: Fabian D. Menalled
Soil bacterial communities are essential components of the soil ecosystem that support crop production. However, agriculture in semiarid drylands and their associated soil bacterial communities face increasingly warmer and drier conditions due to climate change. Two complementary studies were conducted to assess the response of soil bacterial communities to cropping systems, temporal changes, and soil temperature and moisture conditions in semiarid, dryland agricultural systems of the Northern Great Plains. The first study focused on soil bacterial community response to crop phase in contrasting cropping systems (chemical inputs and no-till, USDA-certified organic tilled, and USDA-certified organic sheep grazed) over a growing season. Organic grazed management supported more diverse bacterial communities than chemical no-till, though diversity in all systems decreased over the growing season. Organic grazed bacterial communities were distinct from those in the organic tilled and chemical no-till systems. An interaction between cropping system and crop phase affected community dissimilarity, indicating that overarching management systems and environmental conditions are influential on soil bacterial communities. The second study evaluated soil bacterial communities in a winter wheat - cover crop or fallow rotation. Observations were conducted in the summer fallow and two cover crop mixtures differing by species composition and phenologies, terminated by three different methods (chemical, grazing, or haying), and subjected to either induced warmer/drier or ambient soil conditions. Only the presence and composition of cover crops affected bacterial community dissimilarity, where mid-season soil bacterial communities were distinct from early season and fallow communities. Bacterial communities responded to an interaction between the presence and composition of cover crops and environmental conditions, but not termination. No treatment effects were observed in bacterial communities in 2019, which could be attributed to above average rainfall. The results of these studies suggest cover crop mixtures including species tolerant to warmer and drier conditions can foster diverse soil bacterial communities compared to fallow soils. Overall, these studies contribute to a better understanding of how soil bacterial communities respond to soil health building practices in the Northern Great Plains. Cropping systems can foster unique soil bacterial communities, but these effects may be moderated by environmental and temporal conditions.
Rock powered life in the Samail ophiolite: an analog for early Earth
(Montana State University - Bozeman, College of Agriculture, 2021) Fones, Elizabeth Marie; Chairperson, Graduate Committee: Eric Boyd; Daniel R. Colman, Emily A. Kraus, Daniel B. Nothaft, Saroj Poudel, Kaitlin R. Rempfert, John R. Spear, Alexis S. Templeton and Eric S. Boyd were co-authors of the article, 'Physiological adaptations to serpentinization in the Samail ophiolite, Oman' in the journal 'The International Society for Microbial Ecology journal' which is contained within this dissertation.; Daniel R. Colman, Emily A. Kraus, Ramunas Stepanauskas, Alexis S. Templeton, John R. Spear and Eric S. Boyd were co-authors of the article, 'Diversification of methanogens into hyperalkaline serpentinizing environments through adaptations to minimize oxidant limitation' in the journal 'The International Society for Microbial Ecology journal' which is contained within this dissertation.; David W. Mogk, Alexis S. Templeton and Eric S. Boyd were co-authors of the article, 'Endolithic microbial carbon cycling activities in subsurface mafic and ultramafic igneous rock' which is contained within this dissertation.
Serpentinization is a geochemical process wherein the oxidation of Fe(II)-bearing minerals in ultramafic rock couples with the reduction of water to generate H 2, which in turn can reduce inorganic carbon to biologically useful substrates such as carbon monoxide and formate. Serpentinization has been proposed to fuel a subsurface biosphere and may have promoted life's emergence on early Earth. However, highly reacted waters exhibit high pH and low concentrations of potential electron acceptors for microbial metabolism, including CO 2. To characterize how serpentinization shapes the distribution and diversity of microbial life, direct cell counts, microcosm-based activity assays, and genomic inferences were performed on environmental rock and water samples from the Samail Ophiolite, Oman. Microbial communities were shaped by water type with cell densities and activities generally declining with increasing pH. However, cells inhabiting highly reacted waters exhibited adaptations enabling them to minimize stresses imposed by serpentinization, including preferentially assimilating carbon substrates for biomolecule synthesis rather than dissimilating them for energy generation, maintaining small genomes, and synthesizing proteins comprised of more reduced amino acids to minimize energetic costs and maximize protein stability in highly reducing waters. Two distinct lineages of a genus of methanogens, Methanobacterium, were recovered from subsurface waters. One lineage was most abundant in high pH waters exhibiting millimolar concentrations of H2, yet lacked two key oxidative [NiFe]-hydrogenases whose functions were presumably replaced by formate dehydrogenases that oxidize formate to yield reductant and CO 2. This allows cells to overcome CO 2/oxidant limitation in high pH waters via a pathway that is unique among characterized Methanobacteria. Finally, gabbro cores from the Stillwater Mine (Montana, U.S.A) were used to develop methods for detecting the activities of cells inhabiting mafic to ultramafic igneous rocks while controlling for potential contaminants. Optimized protocols were applied to rock cores from the Samail Ophiolite, where rates of biological formate and acetate metabolism were higher in rocks interfacing less reacted waters as compared with more extensively reacted waters, and in some cases may greatly exceed activities previously measured in fracture waters. This dissertation provides new insights into the distribution, activities, and adaptations exhibited by life in a modern serpentinizing environment.
Influence of lithogenic energy on subglacial microbial community composition
(Montana State University - Bozeman, College of Agriculture, 2021) Dunham, Eric Corwin; Chairperson, Graduate Committee: Eric Boyd; John E. Dore, Mark L. Skidmore, Eric E. Roden and Eric S. Boyd were co-authors of the article, 'Lithogenic hydrogen supports microbial primary production in subglacial and proglacial environments' in the journal 'Proceedings of the National Academy of Sciences of the United States of America' which is contained within this dissertation.; K. Rebecca Mitchell, Mark L. Skidmore and Eric S. Boyd were co-authors of the article, 'Influence of ferric iron on community composition in a basaltic glacial catchment' which is contained within this dissertation.
Chemosynthesis, the generation of biomass using chemical energy, supported life on early Earth and continues to sustain contemporary light-independent ecosystems. The mechanisms of nutrient release from the geosphere are critical to understanding the present and historical distribution and diversity of life. Glaciers release such nutrients through comminution of bedrock, continuously resurfacing reactive minerals that can be colonized and exploited by chemosynthetic microorganisms. Bedrock mineralogy influences the nutrients available in these environments, but little is known about which nutrients are most important or how they affect microbial community composition, particularly in catchments overlying igneous bedrock like basalt. Iron and silicate minerals, common in basalt, readily generate both reductants such as H 2 and oxidants such as Fe(III) through interactions with water. Abundant H 2 in meltwaters of the basalt-based Icelandic glacier Kotlujokull (KJ) were found to support sediment microbial communities better adapted to use H 2 in chemosynthetic metabolism than those found beneath the carbonate-based Robertson Glacier (RG), Canada. KJ communities exhibited shorter lag-times and faster rates of net H 2 oxidation and dark carbon dioxide (CO 2) fixation than those from RG. A KJ sediment enrichment culture provided with H 2, CO 2, and Fe(III) produced a chemolithoautotrophic population related to Rhodoferax ferrireducens, which was also detected using molecular techniques in sediments from Kaldalonsjokull (Kal), another basalt-based Icelandic glacier. The abundance and composition of microbial communities that colonized defined minerals incubated for 12 months in Kal meltwater streams were examined by extracting DNA and sequencing PCR-amplifiable 16S rRNA genes. DNA quantities and the composition of 16S rRNA genes recovered from Kal sediments were most similar to those recovered from incubated Fe(III)-bearing minerals hematite and magnetite, with putative Fe(III) reducers dominating all three communities. These findings point to the importance of bedrock mineral composition in influencing the supplies of nutrients like H 2 and Fe(III) that, in turn, influence the diversity, abundance, and activity of microbial communities in subglacial environments. They further indicate the potential for subglacial habitats to serve as refugia for microbial communities in the absence of sunlight, such as during Snowball Earth episodes, or on icy planets without photosynthetic life.
Hydrogen production from mechanically-activated basalt under experimental conditions simulating subglacial environments
(Montana State University - Bozeman, College of Letters & Science, 2019) Mitchell, Kari Rebecca; Chairperson, Graduate Committee: Mark L. Skidmore
Shearing of rocks containing silicate followed by reaction with water has previously been shown to produce hydrogen under experimental conditions relevant to subglacial environments. The abiotic production of hydrogen, carbon dioxide, methane, and other hydrocarbon gases has also been demonstrated in laboratory comminution experiments on rocks from glaciated catchments. Thus, the generation of these biologically useful gases (e.g. hydrogen and methane) beneath glaciers could serve as a source of reductant capable of sustaining microbial ecosystems beneath the ice. Despite the ubiquitous nature of basalt on both Earth and other planetary bodies, production of hydrogen and other gases from basalt through mechanical shearing and reaction with water has not been demonstrated. Basalts were collected from glaciated catchments in Iceland to test whether hydrogen and other gases were produced under laboratory conditions simulating glacial comminution. Rock samples were milled under an inert atmosphere, after which water was added and hydrogen and methane production measured over time. An average of 6.6 nmol hydrogen and 2.6 nmol methane per gram rock were produced after 168 hours from basalt samples tested; additionally, hydrogen peroxide and radicals were produced during grinding. The abiogenic production of hydrogen and methane under these simulated subglacial basaltic environments demonstrated in this study also has implications for supporting subglacial microbial communities during periods of extended glaciation, such as glacial-interglacial cycles in the Pleistocene and during the pervasive low-latitude glaciation of the Cryogenian. This mechanism of hydrogen production also has implications for the potential for life on icy worlds like Mars.
The influence of an iron deficient diet on the murine gut microbiome
(Montana State University - Bozeman, College of Letters & Science, 2019) Coe, Genevieve Lea; Chairperson, Graduate Committee: Jennifer DuBois
Iron is an essential nutrient for mammals 1. It is involved in multiple redox reactions that are essential for the survival of most organisms 2. There are two main types of iron that are absorbed from the diet: inorganic iron and heme 3. Dietary iron ingested by mammals is mostly absorbed in the small intestine; however, it is unclear whether the gut microbiome is involved in iron homeostasis or whether iron in the diet influences the microbiome. The goal of this project is to characterize the change in microbial composition in response to iron deficiency and iron repletion in conventional mice and define a baseline model for future studies involving the more complex human gut microbiome.
Temporal dynamics of Escherichia coli and the microbiome
(Montana State University - Bozeman, College of Letters & Science, 2020) Martinson, Jonathan Nathan Vernon; Chairperson, Graduate Committee: Seth Walk; Seth T. Walk was a co-author of the article, 'Escherichia coli residency in the gut of healthy human adults' submitted to the journal 'EcoSal plus' which is contained within this dissertation.; Nicholas V. Pinkham, Garrett W. Peters, Hanybul Cho, Jeremy Heng, Mychiel Rauch, Susan C. Broadaway and Seth T. Walk were co-authors of the article, 'Rethinking gut microbiome residency and the enterobacteriaceae in healthy human adults' in the journal 'The ISME journal' which is contained within this dissertation.; Nicholas V. Pinkham and Seth T. Walk were co-authors of the article, 'Phenotypic predictors of Escherichia coli residency in the gut of healthy human adults' submitted to the journal 'Applied and environmental microbiology' which is contained within this dissertation.
Over the past two decades, our understanding of the gut microbiome has increased dramatically. However, most studies involving healthy adults have relied almost exclusively on cross-sectional design, negating the changes occurring within an individual's microbiome through time. With this, we performed a small longitudinal study over a period of ~2 years with a cohort of 8 healthy adults. By sequencing the DNA encoding the 16S ribosomal RNA gene, we assessed the community level change in this cohort through time. Similar to previous findings, we found that using these methods there was remarkable stability through time with nearly 50% of the microbiome remaining the same throughout the study period in the participants. However, analysis of 16S ribosomal RNA sequences limits taxonomic resolution. By cultivating members of the Enterobacteriaceae, we found that turnover at the clone-level (below the species level) was common. Within the Enterobacteriaceae, Escherichia coli was the most numerically dominant species and most often observed as a long-term member of the gut (i.e. resident). Longitudinal analysis of Escherichia coli revealed that some phylogenetic groups within the species are more often long-term residents than other phylogroups. We next assessed the means by which the resident E. coli were capable of establishing and maintaining themselves in the gut. We found that residents were much more likely to produce antagonism (inhibition of other clones) than the E. coli that did not reside in the gut long-term.

Theses and Dissertations at Montana State University (MSU)

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