Theses and Dissertations at Montana State University (MSU)
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Item 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 ForemanPolar 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.Item 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. MenalledSoil 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.Item Diversity, productivity, and physiology of microorganisms in the stream-moat-lake transition of Lake Bonney, Antarctica(Montana State University - Bozeman, College of Agriculture, 2007) Moore, Joel Grant; Chairperson, Graduate Committee: John C. Priscu.Air temperatures exceeding 0°C in Taylor Valley, Antarctica 17-25 degree days each summer and constant solar irradiance melt glacial and lake ice to from liquid water moats at the edges of permanently ice-covered lakes. Moats are fed by glacial streams and interact with comparatively large volumes of ice-covered lake water. This study investigated stream influence on moat chemistry and microbial biomass, productivity and diversity in the moat of East Lake Bonney (ELB) and compared the moat to the ice-covered portion of ELB. Stream inflow was a source of dissolved ions, inorganic carbon (DIC) inorganic nitrogen (DIN), and soluble reactive phosphorus (SRP) to the moat. SRP was rapidly removed in the moat near the stream inflow. Melted ELB ice and biological uptake reduced concentrations of DIN and DIC, resulting in a negative relationship to the inflow. Stream nutrients were correlated with high chlorophyll a and bacterial biomass near the inflow, were positively correlated with bacterial diversity, and negatively correlated with phytoplankton diversity. Correlations between nutrient availability and microbial biomass suggest resource limitation with respect to DIN and SRP, and infer dependence of heterotrophic bacterioplankton on primary productivity.Item Microbial interactions with arsenite, hydrogen and sulfide in an acid-sulfate-chloride geothermal spring(Montana State University - Bozeman, College of Agriculture, 2008) D'Imperio, Seth; Chairperson, Graduate Committee: Timothy R. McDermott.The work presented in this thesis investigated the importance of hydrogen, sulfide and arsenite in microbial community structure and function within a model Acid-Sulfate- Chloride (ASC) spring in Yellowstone National Park. Previous studies in this spring found that microbial arsenite [As(III)] oxidation is absent in regions of the spring outflow channel where H 2S exceeds ~5 microM. Ex situ assays with microbial mat samples demonstrated immediate As(III) oxidation activity when H 2S was absent or in low concentrations, suggesting the presence of functional As(III) oxidase enzymes in regions of the spring where arsenite oxidation had not been previously observed. Cultivation efforts resulted in the isolation of an As(III)-oxidizing chemolithotroph phylogenetically related to the alpha-proteobacterium Acidicaldus. H 2S concentration appeared to be the most important constraint on spatial distribution of this organism. This was verified with pure culture modeling and kinetic experiments. Additionally, a study is presented that addresses the relative importance of dissolved hydrogen and sulfide for primary production in the same spring. Throughout the outflow channel where these gases could be detected, biological H 2S consumption rates exceeded those of H2 by at least three orders of magnitude. Molecular analysis showed that Hydrogenobaculum-like organisms dominate the microbial community in this region of the spring. Culturing efforts resulted in 30 Hydrogenobaculum isolates belonging to three distinct 16S rRNA gene phylotypes. The isolates varied with respect to electron donor (H 2S, H 2) and oxygen tolerance and requirement. These metabolic physiologies are consistent with in situ geochemical conditions. An isolate representative of the dominant 16S phylotype was used as a model organism for controlled studies to determine whether an organism capable of utilizing either of these substrates demonstrated preference for H 2S or H 2, or whether either electron donor exerted regulatory effects on the other. The organism studied utilized both H 2S and H 2 simultaneously and at rates roughly comparable to those measured in the ex situ field assays. Major conclusions drawn from this study are that phylogeny cannot be relied upon to predict physiology, and that, in ASC springs, H 2S clearly dominates H 2 as an energy source, both in terms of availability and apparent consumption rates.Item Ecological genomics of filamentous anoxygenic phototrophic bacteria inhabiting geothermal springs in Yellowstone National Park(Montana State University - Bozeman, College of Agriculture, 2012) Klatt, Christian Gerald; Chairperson, Graduate Committee: David M. Ward.; Donald A. Bryant and David M. Ward were co-authors of the article, 'Comparative genomics provides evidence for the 3-hydroxypropionate autotrophic pathway in filamentous anoxygenic phototrophic bacteria and in hot spring microbial mats' in the journal 'Environmental microbiology' which is contained within this thesis.; Jason M. Wood, Douglas B. Rusch, Mary M. Bateson, Natsuko Hamamura, John F. Heidelberg, Arthur R. Grossman, Devaki Bhaya, Frederick M. Cohan, Michael Kuhl, Donald A. Bryant and David M. Ward were co-authors of the article, 'Community ecology of hot spring cyanobacterial mats: predominant populations and their functional potential' in the journal 'The ISME journal' which is contained within this thesis.; William P. Inskeep, Zackary Jay, Douglas B. Rusch, Susannah G. Tringe, Mary N. Parenteau, David M. Ward, Sarah M. Boomer, Donald A. Bryant and Scott R. Miller were co-authors of the article, 'Community structure and function of high-temperature phototrophic microbial mats inhabiting diverse geothermal environments' in the journal 'Geobiology' which is contained within this thesis.; Zhenfeng Liu, Marcus Ludwig, Donald A. Bryant and David M. Ward were co-authors of the article, 'Temporal patterning of in situ gene expression in uncultivated phototrophic chloroflexi inhabiting an alkaline siliceous geothermal spring' in the journal 'The ISME journal' which is contained within this thesis.The filamentous anoxygenic phototrophic bacteria (FAPs) are dominant members of many phototrophic microbial mat communities in geothermal springs. In non-sulfidic springs, FAPs are known to primarily utilize photoheterotrophic metabolism, where they incorporate organic carbon sources such as glycolate or acetate, which are byproducts of cyanobacterial metabolism. Cultures of Chloroexus aurantiacus have also been shown to be capable of photoautotrophic metabolism via the 3-hydroxypropionate pathway in culture. FAPs in non-sulfidic springs have been shown to take up bicarbonate, and this behavior is stimulated by light, H 2, and H 2S. However, previously investigated mat communities contain FAPs that are more closely related to Roseiexus spp. which have not demonstrated autotrophic growth in culture. This work aimed to i ) determine whether Roseiexus spp. isolates and uncultured FAPs contain genes necessary for autotrophy, ii ) compare the community structures of FAPs in different environments, and iii ) observe patterns in gene transcription over an entire diel period, which may indicate how these organisms physiologically acclimate to changing environmental conditions. Comparisons among multiple genomes revealed that Roseiexus spp. contain genes necessary for the 3-hydroxypropionate pathway. A metagenomic investigation of the dominant constituents of the communities in Octopus Spring and Mushroom Spring resulted in the discovery of novel phototrophic organisms. Functional attributes were assigned to eight dominant ecological guilds, including three previously unknown phototrophic bacteria belonging to Kingdoms Acidobacteria, Chlorobi, and Chloroexi. Metagenomic sequencing of six communities from diverse geochemical environments revealed the presence of FAPs and other phototrophic bacteria, however there was evidence that some FAPs were unique to particular springs. Examination of transcripts produced by FAPs inhabiting Mushroom Spring indicated that genes related to phototrophy are most highly expressed at night, which presumably allows for phototrophic metabolism in the morning. Additionally, FAPs are predicted to utilize carbon and energy storage compounds such as polyglucose, wax esters, and polyhydroxyalkanoates. Based upon the transcription profiles of relevant genes, a model of their carbon and energy metabolism is proposed. Taken together, these genomic, metagenomic, and metatranscriptomic studies have advanced the understanding of FAP diversity and both the community and physiological ecology in geothermal springs.Item Microbial ecology of an Antarctic subglacial environment(Montana State University - Bozeman, College of Agriculture, 2005) Mikucki, Jill Ann; Chairperson, Graduate Committee: John C. Priscu.The research presented in this dissertation focused on the microbial ecology of the subglacial discharge from the Taylor Glacier in the McMurdo Dry Valleys, Antarctica. The major objectives of my research were to 1) define the biogeochemistry of the subglacial outflow 2) describe the microbial diversity of the subglacial outflow and 3) examine the impact of subglacial outflow on the geochemistry and biology of the west lobe of Lake Bonney, a lake that abuts the glacier. The subglacial outflow from the Taylor Glacier is known as Blood Falls owing to a visible accumulation of iron-oxides at the point where it flows from the snout of the glacier. The subglacial reservoir is thought to originate from the Pliocene Epoch (~5 Mya) when the dry valleys were fjordlands. The episodic release of subglacial water at Blood Falls provides a sample of what is believed to be ancient seawater trapped in the upper Taylor Valley and eventually covered by the Taylor Glacier as it advanced. Biogeochemical measurements, culture-based techniques, and molecular analysis (based on 16S rDNA sequences), were used to characterize microbes and chemistry associated with the subglacial outflow.Item Geothermal soil ecology in Yellowstone National Park(Montana State University - Bozeman, College of Agriculture, 2012) Meadow, James Francis; Chairperson, Graduate Committee: Catherine A. Zabinski.; Catherine A. Zabinski was a co-author of the article, 'Linking symbiont community structures in a model Arbuscular mycorrhizal system' in the journal 'New phytologist' which is contained within this thesis.; Catherine A. Zabinski was a co-author of the article, 'Prokaryotic communities differ along a geothermal soil photic gradient' in the journal 'Microbial ecology' which is contained within this thesis.Microbial communities in soil are among the most diverse and species-rich of any habitat, but we know surprisingly little about the factors that structure them. Geothermal soils present unique and relatively unexplored model systems in which to address ecological questions using soil microbial communities, since harsh conditions in these soils exert strong filters on most organisms. This work represents two very different approaches to studying soil ecology in geothermal soils in Yellowstone National Park: 1) Arbuscular mycorrhizal fungal (AMF) communities living in the roots of Mimulus gutattus in contrasting plant community types were compared to assess a link in community structure between plants and their AMF symbionts; and 2) soil microbial communities were surveyed across multiple spatial scales in an unstudied diatomaceous biological soil crust in alkaline siliceous geothermal soils, using bar-coded 454 pyrosequencing of 18S and 16S rDNA. Mycorrhizal communities living in plant roots from contrasting community types showed a striking difference in taxon richness and diversity that appears to transcend soil-chemical differences, though robust conclusions are difficult since plant and fungal communities are structured by some of the same confounding soil conditions. Cluster and discriminant analyses were employed to compare drivers of AMF community structure. Eukaryotic and prokaryotic communities in a diatomaceous biological soil crust differ significantly from that of an adjacent sinter soil, and along a photic depth gradient. Along with a description of this unique system, extensive multivariate community analyses were used to address outstanding questions of soil microbial community spatial heterogeneity and the methodologies best suited to the unique assumptions of these datasets. Depending on the intended scope of inference, much detail can be gained by investigation of microbial communities at the aggregate or soil particle scale, rather than through composite sampling. Additionally, beta-diversity patterns are apparent with relatively few sequences per sample.