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Item Bacterial community dynamics and variability in shallow aquifers(Montana State University - Bozeman, College of Letters & Science, 2019) Zelaya, Anna Jesus; Chairperson, Graduate Committee: Matthew Fields; Albert E. Parker, Kathryn L. Bailey, Ping Zhang, Joy Van Nostrand, Ning Daliang, Dwayne A. Elias, Jizhong Zhou, Terry C. Hazen, Adam P. Arkin and Matthew W. Fields were co-authors of the article, 'High spatiotemporal variability of bacterial diversity over short time scales with unique geohydrochemistry within a shallow, pristine aquifer' which is contained within this thesis.; Albert E. Parker, Kathryn L. Bailey, Ping Zhang, Joy Van Nostrand, Ning Daliang, Dwayne A. Elias, Jizhong Zhou, Terry C. Hazen, Adam P. Arkin and Matthew W. Fields were co-authors of the article, 'Population filtering in sediment biofilms from dynamic, source planktonic communities' which is contained within this thesis.; Sara Altenburg, Kathryn L. Bailey, Heidi J. Smith, Dwayne A. Elias and Matthew W. Fields were co-authors of the article, 'Community structure across particle size in-vitro and in-situ' which is contained within this thesis.; Heidi J. Smith, Frederick von Netzer and Matthew W. Fields were co-authors of the article, 'Contribution of total and viable DNA pools on diversity estimates of contaminated and non-contaminated subsurface sediments and groundwater' which is contained within this thesis.The shallow, terrestrial subsurface plays an important role in sustaining life above ground. Globally, subsurface environments are becoming increasingly threatened by anthropogenic sources of contamination and disturbance. The Oak Ridge Reservation (ORR) played an important role in the development of nuclear weapons during World War II. In the process, the underlying subsurface became contaminated with radioactive and hazardous wastes. Strategies to remediate polluted subsurface environments such as Oak Ridge have included natural attenuation by resident microbes such as bacteria. Such studies would be aided by a thorough understanding of the natural variability of microbial diversity over space and time in uncontaminated environments. We examined microbial community diversity and variability in both contaminated and non-contaminated sites of the ORR via ss-rRNA paired-end sequencing. An initial in-situ spatiotemporal survey of non-contaminated groundwater was conducted in order to understand how diversity changes over time in an undisturbed aquifer. Moreover, different models were used to estimate possible causal relationships between geochemical parameters and population distribution. Additionally, surrogate sediment samplers were filled with native sediment to assess the diversity of the attached bacterial fraction. Communities observed in the attached fraction were a subset of groundwater communities, although the dominant fractions of each were distinct. After initial assessment, in-vitro groundwater was used as both a nutrient source and microbial inoculum for bioreactors filled with glass beads of various sizes in order to understand particle size effects on community dynamics. Potential viability of resident microbes in both contaminated and non-contaminated groundwater and cored sediments was assessed using PMA-Seq and other complementary methods. Collectively, results show that 1) microbial communities in groundwater are highly dynamic over short timescales, 2) corresponding changes in geochemistry are mostly weakly related to changes in community structure (except perhaps after a disturbance or stress period), 3) community assembly may be affected by pore space volume, 4) PMA-viable populations differ between solid and aqueous fractions, 5) most subsurface cells are intact, and 6) traditional estimates of largely abundant populations may be influenced by the presence of DNA from non-viable members, resulting in less abundant populations being unmeasured or underestimated. The results of this study have implications for sampling and appropriate estimations of microbial populations in situ as well as the inherent variability in an uncontaminated shallow aquifer.Item 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 Binary population biofilms(Montana State University - Bozeman, College of Engineering, 1987) Sievel, Maarten AlexanderItem Biofilm detachment(Montana State University - Bozeman, College of Engineering, 1986) Bakke, RuneItem Kinetics of biofilm detachment(Montana State University - Bozeman, College of Engineering, 1992) Peyton, Brent MichaelItem 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.