Theses and Dissertations at Montana State University (MSU)
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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 Stability and expression of a plasmid-borne TCE degradative pathway in suspended and biofilm cultures(Montana State University - Bozeman, College of Engineering, 1995) Sharp, Robert Raymond, IIIItem Processes affecting solute transport through soils : preferential flow and microbial degradation(Montana State University - Bozeman, College of Agriculture, 1997) Langner, Heiko WalterItem Acid mine waste pollution abatement, Sand Coulee Creek, Montana(Montana State University - Bozeman, College of Engineering, 1970) McArthur, George MorrisItem Biodegradation of 2,4-dichlorophenoxyacetic acid (2,4-D) and pentachlorophenol (PCP) in soils(Montana State University - Bozeman, College of Agriculture, 1997) Doughten, Ronald AllenItem Salmonid response to superfund remediation in Silver Bow Creek, Montana(Montana State University - Bozeman, College of Letters & Science, 2013) Naughton, Joseph Patrick; Chairperson, Graduate Committee: Thomas E. McMahon; Robert E. Gresswell (co-chair)Uncontrolled disposal of hard rock mining wastes in the Butte hill mining district of Montana, led to the extirpation of fish from Silver Bow Creek throughout the 20th century. Superfund remediation has been ongoing since 1998 and metal concentrations are reduced. However, water quality remains poor due to inadequate treatment of municipal sewage. To assess the effectiveness of Superfund remediation in reestablishing salmonid populations, we evaluated seasonal salmonid abundance and movement in the Silver Bow Creek watershed over a 3-year period. Spatially-continuous abundance surveys were conducted in 34 main stem stream km and each sampled westslope cutthroat trout Oncorhynchus clarkii lewisi (n = 787) and brook trout Salvelinus fontinalis (n = 1,846) was PIT-tagged. Movements of PIT-tagged individuals were monitored at seven stationary antenna sites and during six seasonal portable antenna surveys. Monthly synoptic water quality samples were collected. In the main stem, water quality was poor below the wastewater effluent and was characterized by acutely toxic copper concentrations, elevated ammonia levels (e.g., NH 3-N = 2.8 mg/L), and hypoxia during summer nights (e.g., DO = 1.4 mg/L). Longitudinal abundance of salmonids closely resembled the longitudinal trend in DO. Regression analysis revealed strong associations between salmonid occurrence and abundance with DO (positive) and copper (negative) concentrations during the summer. However, westslope cutthroat trout relative abundance increased between summer and winter in remediated segments that had been hypoxic during the summer. Few brook trout recolonized the remediated main stem during the study period and the wastewater effluent may have deterred brook trout movement. Westslope cutthroat trout moved into remediated segments during the late summer and early fall as hypoxia subsided. The majority of westslope cutthroat trout sampled in the main stem were large-bodied adults (> or = 200 mm TL) contrasting with the predominantly small-bodied counterparts in the tributaries. Despite hypoxia and copper toxicity, recolonization of indigenous westslope cutthroat trout apparently was driven by the reexpression of a fluvial-adfluvial migratory behavior, a pattern that was not possible during the 100-150 years of main stem contamination.