Theses and Dissertations at Montana State University (MSU)
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Item 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.Item An investigation of coliform contamination in private well water on the Crow Reservation(Montana State University - Bozeman, College of Agriculture, 2019) Three Irons, Emery UP; Chairperson, Graduate Committee: Scott Powell; Margaret Eggers (co-chair)The Crow reservation has a rural population that depends on home well water for domestic use. Many of the home wells do not have a suitable well cap, allowing a potential pathway of bacterial contamination of groundwater. Fecal coliform is associated with acute health problems, such as gastrointestinal illness, diarrhea, and cramps. Therefore, total coliform contamination of well water is an important health concern among Crow home well users. This research examines patterns in total coliform contamination among home well samples with respect to a suite of well and local aquifer characteristics thought to influence vulnerability to contamination, including well protection factors. Well and aquifer characteristics considered in this research include: the geologic production formation, local land cover, and distance to the nearest river. Well protection factors include: cap type, cap condition, depth of completion and time since completion (or age). One hundred water quality samples were collected from home wells along the Little Big Horn River in 2017, and available data on the character of those wells and aquifers were collected for comparison with the patterns in fecal coliform contamination among the samples. Presence/absence of coliform contamination was assessed using the Colilert IDEXX Quanti-Tray 2000 method. Spatial variations in the characteristics of wells and aquifers were characterized through a combination of well logs, the National Land Cover Dataset, and the National Hydrography Dataset. Logistic regression was used to identify potential relationships between probability of coliform contamination and characteristics of associated wells and aquifers. Logistic regression models suggested two notable and statistically significant (? = 0.05 level) relationships: (1) wells completed in alluvium and farther from the river had a higher probability of total coliform contamination, and (2) wells with old style caps had a higher probability of total coliform contamination. The government of the Crow tribe can decide how to use the results for mitigation efforts and awareness for homeowners with contaminated wells. Also, the Crow Water Quality Project should archive and consider these results for future research, planning, development, and management.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 Groundwater nitrate transport and residence time in a vulnerable aquifer under dryland cereal production(Montana State University - Bozeman, College of Agriculture, 2013) Miller, Christine Ross; Chairperson, Graduate Committee: Stephanie A. Ewing; Stephanie A. Ewing, W. Adam Sigler, E. N. J. Brookshire, Clain A. Jones, Douglas Jackson-Smith and Gary S. Weissmann were co-authors of the article, 'Groundwater nitrate transport and residence time in a vulnerable aquifer under dryland cereal production' submitted to the journal 'Journal of geophysical research - biogeosciences' which is contained within this thesis.Selection of agricultural management practices to reduce nitrate leaching from soils can only be successful if both nitrate loading rates from soils to shallow aquifers and groundwater residence times are quantified. Elevated nitrate concentrations in shallow unconfined aquifers are commonly observed in agricultural areas as a result of increased N inputs. In the Judith River Watershed (JRW) in central Montana, USA, notably high nitrate concentrations in groundwater and stream water have exceeded the U.S. EPA drinking water standard of 10 mg L -1 for at least two decades. This large (24,400 ha) watershed drains immediately into the Missouri River, a tributary of the Mississippi River. Over an eleven month period in 2012, we measured groundwater and surface water nitrate concentrations across a hydrologically isolated strath terrace. We use the resulting data to constrain nitrate accumulation dynamics in the shallow aquifer. Nitrate is relatively conservative in this location, as it is high in groundwater (17.57 +/- 4.29 mg L -1; all groundwater samples pooled together), and remains high in streams and springs that drain the landform (15.67 +/- 9.45 mg L -1; all surface water and spring samples pooled together). We use a numerical model to simulate the character of nitrate accumulation in the aquifer as a whole, in order to evaluate how the entire period of cultivation has contributed to current nitrate concentrations, and begin to predict response times for effects of land use change. We consider the effect of groundwater residence time and travel time on nitrate loading using particle tracking in a three dimensional model aquifer. We find no correlation with nitrate concentrations in groundwater and emerging surface waters, and suggest approaches for improving both the geometry of the model and the selection of sites in future work. Overall, our results imply that groundwater residence times are several decades at most, suggesting that similar timeframes will be needed to reduce overall nitrate concentrations in groundwater and emergent streams to below drinking water standards. Preliminary evaluation of several management scenarios suggests that both increased fertilizer use efficiency and rotational strategies may be needed to prevent the loss of soil N to groundwater.Item Hydrogeology of surficial, unconsolidated quaternary aquifers, Maynard Creek catchment, Bridger Range, Montana(Montana State University - Bozeman, College of Letters & Science, 1996) Whittingham, John F.Item Paleochannel aquifer potential at Montana State University : a test of hypotheses(Montana State University - Bozeman, College of Letters & Science, 1989) Donohue, David AllenItem Hydrogeology and geothermal potential of the Radersburg Valley, Broadwater County, Montana(Montana State University - Bozeman, College of Letters & Science, 1984) Wyatt, Glen MiltonItem A finite difference groundwater model for the East Decker, Montana mine(Montana State University - Bozeman, College of Engineering, 1980) Engelmann, Richard H.