Scholarship & Research
Permanent URI for this communityhttps://scholarworks.montana.edu/handle/1/1
Browse
9 results
Search Results
Item Introducing the ArsR regulated arsenic stimulon(Montana State University - Bozeman, College of Agriculture, 2017) Saley, Tara Carolyne; Chairperson, Graduate Committee: Timothy McDermottThe United States EPA ranks arsenic as the number one environmental toxin. Since microorganisms are significant drivers of arsenic toxicity and mobility in nature, it is important to understand how microbes detect and react to arsenic. The microbial arsenic resistance operon (ars) is critical for sensing arsenic in the environment and controlling the cellular response to this toxin. The ars operon is minimally comprised of arsRBC, which codes for an ArsR transcriptional repressor, arsenite effluxer, and an arsenate reductase, respectively, with the operon negatively regulated by the transcriptional repressor, ArsR. Our model organism Agrobacterium tumefaciens 5A carries two ars operons, with each containing two arsR genes. We conducted an RNASeq study to examine the regulatory roles of the encoded four ArsR regulatory proteins as a function of +/- arsenite. We report that the regulatory influence of the ArsR proteins extends well beyond the ars operon, with both activation and repression effects. In addition to the expected arsenic resistance response, many cellular functions were impacted, including: phosphate acquisition/metabolism, sugar transport, chemotaxis, copper tolerance, and iron homeostasis. Each of the ArsR proteins uniquely influenced different sets of genes and an arsR regulatory hierarchy was observed, wherein ArsR1 is auto regulatory and negatively regulates arsR4, ArsR4 activates arsR2, and ArsR2 negatively regulates arsR3. ArsR3 is the least active with respect to number of genes regulated. To summarize, this study provides a more complete understanding of how microbial gene expression and biogeochemical cycling may be influenced by arsenic in the environment.Item Linking geochemistry with microbial community structure and function in sulfidic geothermal systems of Yellowstone National Park(Montana State University - Bozeman, College of Agriculture, 2015) Jay, Zackary James; Chairperson, Graduate Committee: William P. Inskeep; Doug B. Rusch, Susannah G. Tringe, Connor Bailey, Ryan M. Jennings and William P. Inskeep were co-authors of the article, 'Predominant acidilobus-like populations from geothermal environments in Yellowstone National Park exhibit similar metabolic potential in different hypoxic microbial communities' in the journal 'Applied and environmental microbiology' which is contained within this thesis.; Jacob P. Beam, Alice Dohnalkova, Regina Lohmayer, Brynna Bodle, Brita Planer-Friedrich, Margaret Romine and William P. Inskeep were co-authors of the article, 'Pyrobaculum yellowstonensis strain WP30 respires on elemental sulfur and/or arsenate in circumneutral sulfidic geothermal sediments of Yellowstone National Park' submitted to the journal 'Applied and environmental microbiology' which is contained within this thesis.; Doug B. Rusch, Jacob P. Beam, Mark A. Kozubal, Ryan M. Jennings and William P. Inskeep were co-authors of the article, 'The distribution, diversity and function of predominant Thermoproteales phylotypes in Yellowstone National Park' submitted to the journal 'ISME J' which is contained within this thesis.Members of the archaeal phylum Crenarchaeota are often associated with microbial communities in high-temperature (> 70 °C) geothermal springs. Environmental genome sequencing (metagenomics) has revealed that populations of Sulfolobales, Desulfurococcales, and Thermoproteales are abundant in hypoxic elemental sulfur sediments of Yellowstone National Park (YNP) and possess enzyme complexes that are implicated in the cycling of carbon, sulfur, and arsenic. Therefore, the primary objectives of this work were to (i) identify the abundant Desulfurococcales and Thermoproteales sequences in these habitats, (ii) characterize the growth and curate the genome of the first Thermoproteales representative isolated from YNP (Pyrobaculum yellowstonensis strain WP30), and (iii) establish a linkage between geochemistry and microbial community structure and function by identifying key proteins that are important to these populations in situ. The primary Desulfurococcales populations were related to Acidilobus spp. and exhibited similar metabolic potential in near-neutral (pH 4 - 6) hypoxic elemental sulfur sediments and acidic (pH ~3) iron oxide mats. These populations are primarily anaerobic heterotrophs that ferment complex organic carbon and are auxotrophic with regards to numerous vitamins and cofactors. These organisms are often found together with members of the Thermoproteales, which are widely distributed in elemental sulfur sediments, acidic iron oxide mats, and streamer communities. P. yellowstonensis strain WP30 was obtained from a hypoxic elemental sulfur sediment habitat with high concentrations of arsenic. This organism was shown to reduce elemental sulfur and/or arsenate in the presence of yeast extract. The complete genome of str. WP30 contained numerous dimethylsulfoxide molybopterin (DMSO-MPT) proteins, which are inovolved in redox reactions of inorganic constituents (i.e. sulfur and arsenic), and genomic comparisons revealed that this organism is closely related to native Pyrobaculum populations. The distribution of Thermoproteales populations was correlated with pH, while the presence of respiratory complexes (terminal oxidases, DMSO-MPT, and dissimilatory sulfate reductases) was correlated with the presence of key electron donors and acceptors. Intron sequences identified in Thermoproteales 16S rRNA genes and were shown in silico to prevent the binding of 'universal' primers that are often used in environmental surveys. These metagenomic, microbiological, and geochemical studies have advanced the understanding of Crenarchaeota diversity and function in YNP.Item Arsenite oxidation by a Hydrogenobaculum sp. isolated from Yellowstone National Park(Montana State University - Bozeman, College of Agriculture, 2002) Donahoe-Christiansen, JessicaItem Linking microbial populations and geochemical processes in soils, mine tailings, and geothermal environments(Montana State University - Bozeman, College of Agriculture, 2004) Macur, Richard Eugene; Chairperson, Graduate Committee: William P. Inskeep.The primary goal of this work was to identify and characterize the microbial populations responsible for transformations of As and 2,4-D in soils and waters. Chemical, spectroscopic, and microscopic techniques were used to characterize the aqueous and solid phase geochemistry of soils, mine tailings, and a geothermal spring. The role of specific microbial populations in these systems was examined using cultivation-independent molecular methods [total DNA extraction, 16S rDNA amplification, denaturing gradient gel electrophoresis (DGGE), and sequence analysis] coupled with either characterization of microorganisms isolated from the same systems, or inference of physiological characteristics from (i) closely related (16S rDNA sequence) cultured microorganisms and (ii) the geochemical environments in which they were detected. The microbial reduction of As(V) to As(III) and the subsequent effects on As mobilization in contaminated mine tailings was examined under transport conditions. Enhanced elution of As from mine tailings apparently resulted from the enrichment of aerobic As(V)-reducing Caulobacter leidyi, Sphingomonas yanoikuyae, and Rhizobium loti -like populations after liming. Arsenite was rapidly oxidized to As(V) via microbial activity in unsaturated Madison River Valley soil columns. Eight aerobic heterotrophic bacteria with varying As redox phenotypes were isolated from these columns. Three isolates, identified as Agrobacterium tumefaciens, Pseudomonas fluorescens, and Variovorax paradoxus -like organisms, were As(III) oxidizers and all were apparently important members of the soil microbial community responsible for net As(III) oxidation. Successional changes in microbial communities colonizing an As-rich acid-sulfate-chloride geothermal spring stream channel in Norris Geyser Basin of Yellowstone National Park were examined. Enhanced As(III) oxidation correlated in time and space with the appearance of three Hydrogenobaculum -like populations. The formation of an As(V)-rich hydrous-ferric-oxide mat correlated with the detection of Thiomonas, Acidimicrobium, and Metallosphaera —like populations whose nearest cultivated relatives (based on 16S rDNA sequence) were Fe-oxidizers. Fingerprints of microbial communities (DGGE) established under increasing concentrations of 2,4-D (0 - 500 mg kg'1) in batch soil microcosms showed that at least 100 mg kg'1 2,4-D was required to obtain apparent shifts in community structure. The microbial community selected at high 2,4-D concentrations was predominantly composed of Burkholderia -like populations, which harbored homologs of tfdA genes.Item Photochemical oxidation of arsenic(III) in ferrioxalate solutions and elk exposure to arsenic in Yellowstone's geothermal environments(Montana State University - Bozeman, College of Agriculture, 2002) Kocar, Benjamin DavidItem Uptake and phytotoxicity of arsenic III and V in four grass species(Montana State University - Bozeman, College of Agriculture, 1995) Tice, Stephanie WagnerItem Arsenic in soils of the Madison and upper Missouri River valleys(Montana State University - Bozeman, College of Agriculture, 1995) Keith, Kristin ElisabethItem Microbial and geochemical processes controlling the oxidation and reduction of arsenic in soils(Montana State University - Bozeman, College of Agriculture, 2007) Masur, Deanne Christine; Chairperson, Graduate Committee: William P. Inskeep.Arsenic (As) is a common contaminant in soil-water systems, where it exists predominately as arsenate (AsV) or arsenite (AsIII), the latter of which is considered to be the more mobile and toxic form. The amount of arsenite or arsenate in natural water systems is influenced by geochemical conditions and the presence of As transforming microorganisms. Consequently, the goals of this study were to evaluate the effects of: (i) arsenic concentration on microbial populations responsible for As oxidation-reduction in a previously uncontaminated soil, and (ii) phosphate:arsenic ratio on the oxidation or reduction of arsenic. Laboratory column experiments were conducted to evaluate the influence of soil arsenic concentration on microbial community composition and to identify microorganisms and mechanisms responsible for As transformations occurring under aerobic conditions. Indigenous microorganisms within a previously uncontaminated agricultural soil were exposed to arsenite or arsenate at three concentrations (2, 20 and 200 mg As L-1) for approximately 30 days.Item Emergence and growth of seven grass species across a gradient of metals and arsenic in lime-amended contaminated soils(Montana State University - Bozeman, College of Agriculture, 2009) Martin, Tara Noel; Chairperson, Graduate Committee: Dennis Neuman; Cliff Montagne (co-chair)Montana's Upper Clark Fork River Basin contains hundreds of square kilometers of land impacted by mine wastes and/or smelter emissions from decades of copper mining and related activities. Contaminated soils in the Basin are often acidic and highly enriched with the trace elements cadmium, copper, arsenic, lead, zinc, and others. Natural plant colonization is often impaired, as evidenced by barren areas that are so phytotoxic that normal germination and establishment cannot occur. One reclamation strategy being used is in-place treatment with soil amendments including lime and other products. This provides a more hospitable substrate for plants by raising pH and lowering the mobile and bioavailable fraction of metals. Since contaminants are not removed with in-place treatment, short-term and long-term effectiveness of the soil amendments and the vegetative cover continue to be debated. Several experimental plots within the Basin have been treated in-place, but have developed plant communities of limited diversity where some seeded species failed to establish or persist. A greenhouse pot study was used to determine site-specific toxicity thresholds across a dilution of total metals and arsenic that significantly reduced plant growth. Two sets of contaminated and reference soils collected from the Basin were mixed to obtain metal and arsenic concentration gradients from 244 to 5885 and 250 to 7521 mg/kg, respectively. Five native and two non-native grasses were grown in separate trials. Percent emergence, shoot height, total biomass and root mass ratio were analyzed. Sensitivity of the seven grasses varied according to the response measured and dilution series. Most species showed significant reductions in total biomass and shoot height when the sum of total metals and arsenic was 559 to 1900 mg/kg. Redtop (Agrostis gigantea Roth) was the most tolerant species, not displaying significant decreases in total biomass until the sum of total metals and arsenic reached 5783 mg/kg. Because the study used contaminated environmental samples and nonagricultural species, the results may better estimate site-specific ecological risk and toxicity thresholds for in-place treated soils in the UCFRB over studies performed in sand with inappropriate surrogate species.