Theses and Dissertations at Montana State University (MSU)
Permanent URI for this collectionhttps://scholarworks.montana.edu/handle/1/733
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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 Organic amendments for enhancing microbial coalbed methane production(Montana State University - Bozeman, College of Engineering, 2017) Davis, Katherine Jean; Chairperson, Graduate Committee: Robin Gerlach; Robin Gerlach was a co-author of the article, 'Transition of biogenic coal-to-methane conversion from the laboratory to the field: a review of important parameters and studies' submitted to the journal 'International Journal of coal geology' which is contained within this thesis.; Shipeng Lu, Elliott P. Barnhart, Albert E. Parker, Matthew W. Fields and Robin Gerlach were co-authors of the article, 'Type and amount of organic amendments affect enhanced biogenic methane production from coal and microbial community structure' submitted to the journal 'Fuel' which is contained within this thesis.; Elliott P. Barnhart, Matthew W. Fields and Robin Gerlach were co-authors of the article, 'Fate of carbon during enhanced microbial methane production from coal with repeated organic amendment' submitted to the journal 'Energy & Fuels' which is contained within this thesis.; Matthew W. Fields and Robin Gerlach were co-authors of the article, '13C-labeled amendments for enhanced biogenic methane production in coal systems indicate increased coal-to-methane conversion' submitted to the journal 'Nature' which is contained within this thesis.; George A. Platt, Randy Hiebert, Robert Hyatt, Matthew W. Fields and Robin Gerlach were co-authors of the article, 'Development and pilot testing of column reactors for the study of anaerobic subsurface process' submitted to the journal 'International Journal of Coal Geology' which is contained within this thesis.Coalbed methane (CBM) is natural gas found in subsurface coal beds and supplies approximately 4-6% of the annual U.S. natural gas requirements. Many unmineable coal beds contain CBM produced by native microbial communities. Enhancing the microbial processes for coal-to-methane conversion can increase the rates of CBM production and the amount of extractable natural gas in these coal beds. Strategies for enhancing microbially-produced CBM must be logistically attainable and economically practical. The goal of this dissertation work was to determine a feasible methane enhancement strategy using organic amendments to increase microbial coal-to-methane conversion. Four organic amendments were tested in coal-containing batch microcosms. Increased coal-to-methane conversion was demonstrated with small amounts of amendment addition, and all four tested amendments increased methane production similarly. Subsequent amendment addition produced smaller amounts of additional methane which appeared to be primarily due to amendment-to-methane conversion. 13 C-labeled algal and yeast amendments were used in coal systems for tracking carbon for methane production. It was shown that <22% of the amendment carbon was converted to methane. By tracking amendment carbon, it became clear that carbon sources besides coal and amendment are utilized for methane production; these carbon sources potentially include organic and inorganic carbon in the formation water and inoculum. Amendment strategies tested in batch systems were scaled up and applied to column reactors. Methane production from coal increased with small amounts of 13 C-labeled algal amendment addition. However, unlike in batch experiments, methane production rates in the column flow reactors did not slow or cease after 60-90 days, and methane was still being produced after 176 days when the study was terminated.Item Microbial diversity and zinc toxicity to Pseudomonas sp. from Coeur d'Alene River sediment(Montana State University - Bozeman, College of Engineering, 2007) Barua, Sutapa; Chairperson, Graduate Committee: Brent M. PeytonCoeur d'Alene River (CDAR) in northern Idaho is one of the metal contaminated rivers in US. The sediments of the river are enriched with As, Cd, Cu, Pb, and Zn which are toxic metals to humans and animals. It is hypothesized that microorganisms living in this river sediment can remove the metals and thus detoxify their environment. The objective of this work is to investigate the microbial communities existing in CDAR sediment using 16S ribosomal RNA (rRNA) gene sequencing and 16S rRNA gene microarray (PhyloChip) analysis. According to our phylogenetic analysis, the CDAR clones fell into 13 distinct phylogenetic classes including 2 environmental samples, 1 uncultured bacterium, and an unclassified Chloroflexi. The major representative genera found were Thiobacillus (7 of 91), Azoarcus (7/91), Acidobacterium (6/91), Burkholderia (5/91), Flavobacterium (5/91) and Janthinobacterium (5/91). PhyloChip data showed the presence of 1551 operational taxonomic units (OTUs). 97% of the clone library sequences matched at various taxonomic levels with the microarray results.