Theses and Dissertations at Montana State University (MSU)
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Item Understanding physiological adaptations, metabolic potential and ecology in a novel photoautotrophic alga for biofuel production(Montana State University - Bozeman, College of Letters & Science, 2019) Corredor Arias, Luisa Fernanda; Chairperson, Graduate Committee: Matthew Fields; Elliot B. Barnhart, Al Parker, Robin Gerlach and Matthew W. Fields were co-authors of the article, 'Impact of temperature, nitrate concentration, PH and bicarbonate addition on biomass and lipid accumulation of a sporulating green alga' which is contained within this dissertation.; Thiru Ramaraj, Huyen Bui, Mensur Dlakic, Robin Gerlach and Matthew W. Fields were co-authors of the article, 'Genomic insights into a sporulating, non-motile, oligotrophic green microalga (PW95)' which is contained within this dissertation.; Huyen Bui, Thiru Ramaraj, Robin Gerlach and Matthew W. Fields were co-authors of the article, 'Transcriptomic profiling of Chlamydomonas-like PW95 cultivated in coal bed methane production water with the native microbial community' which is contained within this dissertation.; Anna J. Zelaya, Robin Gerlach and Matthew W. Fields were co-authors of the article, 'Associations between sympatric bacterial groups and a novel green alga cultivated in coal bed methane production water' which is contained within this dissertation.Commercial implementation of microalgal biomass as bio-oil/chemical feedstocks has been difficult to achieve, and challenges include water/nutrient sources, CO 2 delivery, and community dynamics of mixed cultures. We employed an integrated approach to the study of microalgal production systems to advance towards sustainable implementation of industrial microalgal biofuel production using a native alga (Chlamydomonas-like alga, PW95) isolated from Coal Bed Methane (CBM) production water. Our approach was based on the evaluation of PW95 physiological responses to combinations of growth constraints, the determination of its genomic and functional potential, phylogenetic relations and the implementation of an ecosystem view to algal biomass production. PW95 growth and lipid accumulation (biofuel potential) were ascertained in standardized media and CBM water through the evaluation of mixed effects of temperatures, nitrate levels, pH, and bicarbonate to elucidate interactions between multiple environmental variables and nutritional levels. The biofuel potential of PW95 ranges between 20-32% depending on culture conditions and our results suggest an important interaction between low nitrate levels, high temperature, and elevated pH for trade-offs between biomass and lipid production in the alga. Whole genome sequence was employed to predict biological and metabolic capacity in PW95, and the expression of these capabilities during growth in CBM water with the native microbial consortia was evaluated using RNA sequencing. genome determination and assembly resulted in a draft genome size of 92 Mbp with 14,000 genes predicted and 402 pathways mapped in the KEGG database. The gene complement of PW95 provided a glance into life in an oligotrophic environment (CBM water) and evidence of essential metabolic pathways for cell growth, survival and maintenance, also relevant for cultivation and value-added products generation. Microbial composition and shifts during growth were identified, as well as the algal phycosome. During growth in CBM water, PW95 appeared to be supported by a native microbial consortium and differential expression analysis showed basic metabolic functions and adaptive physiological responses. Our findings build on previous knowledge for improved algal culturing for biomass and industry-valued products while exploring the biology of an organism with relevant impact in energy and water resource management.Item Investigation of field relevant parameters for microbially enhanced coalbed methane scale up(Montana State University - Bozeman, College of Engineering, 2019) Platt, George Addison; Chairperson, Graduate Committee: Robin Gerlach; K. J. Davis, E. P. Barnhart, M. W. Fields and R. Gerlach were co-authors of the article, 'Optimization of 13C-algae amendment concentration for enhanced coal dependent methanogenesis' submitted to the journal 'International journal of coal geology' which is contained within this thesis.; K. J. Davis, H. D. Schweitzer, H. J. Smith, E. P. Barnhart, M. W. Fields, R. Gerlach were co-authors of the article, 'Algal amendment enhances biogenic methane production from coals of different thermal maturity' submitted to the journal 'International journal of coal geology' which is contained within this thesis.Energy production from coal is projected to decline significantly over the next 30 years, due to concerns over anthropogenic carbon emissions, climate change, and cost. As coal-based energy production decreases, the demand for natural gas is expected to increase. Coalbed methane (CBM), a biogenic natural gas resource found in subsurface coal beds, may aid in meeting the projected increase in demand. However, costs associated with traditional CBM extraction currently make utilizing this resource economically prohibitive due to slow coal-to-methane conversion rates and the necessity to treat co-produced water. Algae can be cultivated in co-produced formation water and the addition of very small amounts of this algal biomass can increase coal-to-methane conversion rates. The goal of this work was to determine the optimal algae amendment concentration for the enhancement of microbial coal-to-methane conversion to maximize return on investment. Concentrations of 13C-labeled algae amendment ranging from 0.01-0.50 g/L (equivalent to 0.0001-0.005 g per g of coal) were tested in coal-containing batch microcosms. Enhanced methane production was observed in all amended microcosms and maximum methane production occurred between 169-203 days earlier than in unamended microcosms. When as little as 0.01 g/L algae amendment was added, 13CH 4 and 12CH 4 tracking revealed that the improvement in coal-to-methane conversion kinetics was due to enhanced coal degradation. Increasing amendment concentrations to 0.05-0.50 g/L improved coal-to-methane conversion rates further, but improvements from amendment concentrations above 0.05 g/L were insignificant. The geologic scope of this CBM enhancement strategy was investigated by studying methane production from five coals ranging in thermal maturity. Biogenic methane was produced from all coals, with subbituminous coals generally producing more methane than thermally mature bituminous coals. The addition of algae amendment to thermally mature coal microcosms resulted in methane production that was comparable to production from unamended, thermally immature coals. This improvement was associated with an increased relative abundance of coal degrading microorganisms. Collectively, this work demonstrates that algae amendment concentrations can be reduced further (to 0.01-0.05 g/L) relative to the previously investigated concentrations (ranging from 0.1-0.5 g/L) and still improve coal-to-methane conversion rates for a range of coal sources.Item Bacterial and archaeal community diversity in relation to organic carbon consumption and sulfate gradients in the Powder River Basin(Montana State University - Bozeman, College of Letters & Science, 2019) Schweitzer, Hannah Doris; Chairperson, Graduate Committee: Matthew Fields and Sara Branco (co-chair); Elliott Barnhart, Al Cunningham and Matthew Fields were co-authors of the article, 'Comparison of attached and planktonic microbial assemblages across geochemically distinct coal seam habitats' submitted to the journal 'International journal of coal geology' which is contained within this dissertation.; Daniel Ritter, Jennifer McIntosh, Elliott Barnhart, Al B. Cunningham, David Vinson, William Orem and Matthew Fields were co-authors of the article, 'Changes in microbial communities and associated water and geochemistry across a sulfate gradient in coal beds: Powder River Basin, USA' submitted to the journal 'Geochimica et cosmochimica acta' which is contained within this dissertation.; Heidi J. Smith was an author and Elliott P. Barnhart, William Orem, Robin Gerlach and Matthew W. Fields were co-authors of the article, 'Linking organic matter degradation and microbial assemblage composition to subsurface methane production in the Powder River Basin' submitted to the journal 'Applied and environmental microbiology' which is contained within this dissertation.; Heidi J. Smith, Elliott P. Barnhart, Boris Wawrik, Amy Callaghan, Luke McKay, Robin Gerlach and Matthew W. Fields were co-authors of the article, 'Metagenomic analysis of recalcitrant rich coal seams from coal seams with varying sulfate concentrations' submitted to the journal 'Applied and environmental microbiology' which is contained within this dissertation.The rate limiting step in biogenic coal bed methane production has been attributed to the predominantly recalcitrant composition of coal, making it difficult for bacteria to anaerobically break down into methanogenic substrates. The significance of different carbon (C) cycling pathways involved in the turnover of recalcitrant, terrestrial C under various redox conditions is still a topic of debate, and in fact, unknown C cycling metabolic pathways are still being discovered in sub-oxic and anoxic environments. Redox transitions exist along gradients of increasingly recalcitrant C in many environments, and subsurface environments represent a large reservoir of C. The Powder River Basin in southeastern Montana is a model environment for studying in situ redox gradients for terrestrial subsurface C and were selected to investigate i) the temporal and spatial variation in the microbial assemblage from four different coal seams with varying depth profiles, ii) the physicochemical controls that impact the turnover of recalcitrant coal to methane, and iii) the functional potential for hydrocarbon degradation under different sulfate concentrations. Similar to the methane-sulfate critical zone in marine habitats, the presented work highlights the crucial role sulfate has on microbial assemblages, methane production, and C consumption in shallow coal seams. Given the accepted differences between groundwater and surface-associated communities of subsurface porous media, diffusive microbial samplers packed with native coal material were used to enhance the establishment of microbial communities that better re-capitulated in situ communities. The microbial community inhabiting low sulfate coal seams consisted of sequences indicative of syntrophic bacteria such as Syntrophomonas and Hydrogenophaga which have previously demonstrated degradation of polycyclic aromatic hydrocarbons (PAH) and coupled growth with hydrogenotrophic methanogens. The assemblages inhabiting high sulfate coal seams were comprised of methylotrophic methanogens and sulfate reducing bacteria. Methylotrophic methanogens are observed in methane producing coal seams that have intermediate levels of sulfate, suggesting an important transition role in early stage methanogenesis. Low sulfate microcosms experienced an increase in humic-like material and consumed more C compared to high sulfate conditions that demonstrated changes in more labile C, including amino acid-like molecules. Moreover, we used a highly curated anaerobic and aerobic hydrocarbon degradation (AnHyDeg and AromaDeg) and redox (nitrogen, sulfur, methane cycle) gene database and pipeline to analyze metagenomic samples that were obtained from three different coal beds that had increasing sulfate levels. While the functional potential for methanogenesis (mcrA) was detected in all metagenomes, the diversity and relative quantity of these genes was greater in the coal beds that contained methane. Of interest was a significantly greater percentage of aerobic hydrocarbon degradation genes (dioxygenases) from one of the methane-containing coal bed samples. These metabolic markers were identified in co-assembled metagenomes. These results provide an enhanced understanding of recalcitrant carbon turnover in the terrestrial subsurface under different redox conditions and the presumptive metabolic capacities involved in subsurface C turnover in relationship to biogenic CH4.Item Coalbed methane reclamation activities in the Powder River Basin, Wyoming: social and policy dimensions of environmental legacy management(Montana State University - Bozeman, College of Letters & Science, 2020) Walsh, Kathryn Bills; Chairperson, Graduate Committee: Julia Hobson Haggerty; Julia H. Haggerty was a co-author of the article, 'Governing unconventional legacies: lessons from the coalbed methane boom in Wyoming' in 'Governing Shale Gas: Development, Citizen Participation and Decision Making in the US, Canada, Australia and Europe' which is contained within this dissertation.; Julia H. Haggerty was a co-author of the article, 'Social license to operate during Wyoming's coalbed methane boom: implications of private participation' in the journal 'Energy policy' which is contained within this dissertation.; Julia H. Haggerty was a co-author of the article, 'The 'learn as you go' approach: a cautionary tale of environmental legacy management in Wyoming's coalbed methane fields' which is contained within this dissertation.The United States is producing more oil and natural gas than ever before. Sites of production are contributing to the known land-use phenomenon of energy sprawl, though little is known about how these sites will be reclaimed and how legacy effects will be governed and managed. Reclamation returns degraded energy landscapes to some productive capacity in order to avoid permanent environmental harm. Thus far, the technical aspects of reclamation have been the topic of most research while the human dimensions are under-studied. This research draws attention to the social and political dimensions of environmental legacy management. A period of coalbed methane development in the Powder River Basin, Wyoming (1999-2009) provides an instructive case study to investigate the legacy effects of energy resource development. After a decade of coalbed methane production, about 5,700 orphaned wells remained without viable industry operators to fund and manage well-plugging and reclamation. This dissertation uses a qualitative case study approach including document analysis, policy analysis, and forty semi-structured interviews with local surface owners, attorneys, state and federal regulators, local government officials, and industry personnel. Contextual research revealed that management of post-production oil and gas is a highly complex governance challenge made more complicated by the split estate property regime that characterizes the American West. Empirical research found that environmental legacy issues are exacerbated by 'private participation'. Applying a framework tied to the concept of social license to operate, investigation of surface owner-industry relations revealed that individuals played a critical role in decision-making processes. Surface owner's private participation resulted in decisions to forgo reclamation and integrate CBM-related infrastructure into ranching operations, therefore contributing to the scale and extent of environmental legacies. This dissertation also found that an adaptive, or 'learn as you go', policy approach in Wyoming enabled cost-shifting mechanisms to gain foothold, creating serious long-term environmental costs. Three specific cost-shifting mechanisms for CBM were identified: regulatory misalignment, overadaptation to the oil and gas industry, and industry bankruptcy. Together this dissertation highlights the importance of studying the social and political dimensions of post-production oil and gas activities for more effective environmental legacy management.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 Evaluation of a green alga isolate for growth and lipid accumulation in coal bed methane water from the Powder River Basin(Montana State University - Bozeman, College of Engineering, 2015) Hodgskiss, Logan Henry; Chairperson, Graduate Committee: Alfred B. Cunningham; Matthew W. Fields was a co-author of the article, 'Growth of a native algal species in coal bed methane water for biofuel and biomass accumulation' submitted to the journal 'Environmental Science and Technology' which is contained within this thesis.Coal bed methane (CBM) production ponds are being constructed more frequently in areas such as the Powder River Basin in Montana and Wyoming where methane production has been active in the past decade. These ponds are currently not being utilized and are holding billions of gallons of water. The extracted water in these ponds is presently being discharged to local stream drainages or infiltrating into the surrounding soil. The environmental impacts of this increase in water can have negative effects on the surrounding areas. The purpose of this thesis is to explore the possibility of using CBM production ponds in the Powder River Basin, in Montana and Wyoming, for the growth of microalgae and the production of biodiesel from their accumulated lipids. Microalgae have been known to grow in other bodies of undesirable water and research has been ongoing on how to effectively use microalgae as a resource by stimulating lipid accumulation through the use of various environmental stressors. Coal bed methane ponds already provide a source of non-potable water for microalgae cultivation. Exploring the possibility of making these ponds a growth medium for microalgae is the first step in determining whether they can be turned into a productive energy resource. A native green alga, CBMW, has been isolated from a CBM production pond in northeastern Wyoming. CBMW has been cultured and grown under laboratory conditions in sterile CBM water and Bold's Basal Medium (BBM). Chlorophyll levels, biomass growth, pH, lipid accumulation, and water chemistry were tracked while CBMW was grown in sterile CBM water to understand how the alga responds to varying environmental conditions. When grown under the right environmental conditions isolate CBMW increased biomass and accumulated lipids. These results suggest that attempting to grow CBMW on a larger scale in CBM production water could be an effective method to produce biodiesel while utilizing a potentially problematic water source.Item In situ and enhanced coal-bed methane production from the Powder River Basin(Montana State University - Bozeman, College of Letters & Science, 2014) Barnhart, Elliott Paul; Chairperson, Graduate Committee: Matthew Fields; Kara Bowen De León, Bradley D. Ramsay, Alfred B. Cunningham, and Matthew W. Fields were co-authors of the article, 'Investigation of coal-associated bacterial and archaeal populations from a diffusive microbial sampler (DMS)' in the journal 'International journal of coal geology' which is contained within this thesis.; Bradley D. Ramsay, Kara Bowen De León, Kristen A. Brileya, Denise M. Akob, Richard E. Macur, Alfred B. Cunningham, Matthew W. Fields were co-authors of the article, 'Stimulation of coal-dependent methanogenesis with native microbial consortia from the Powder River Basin' submitted to the journal 'Applied and environmental microbiology' which is contained within this thesis.; Kiki Johnson, Kristopher A. Hunt, Sean Cleveland, Marcella A. McClure, Matthew W. Fields were co-authors of the article, 'Genomic insight into the evolution of the acetate switch in archaea' submitted to the journal 'Nature' which is contained within this thesis.The majority of the coal in the Powder River Basin (PRB) is located in formations too deep to be economically mined but microorganisms within some of these deep coal seams generate coal-bed methane (CBM) which can be harvested and utilized as an energy source. However, little is known about the in situ microbial community, the environmental conditions conducive to CBM production, or the microbial community interactions that promote CBM production. Several sampling locations within the PRB were identified as methane-producing sites based on geochemical analysis of groundwater. A diffusive microbial sampler (DMS) was utilized for microbial sampling which was loaded with coal and only opened at the bottom of the wells where the coal seam was exposed. Pyrotag analysis of DMS coal identified the predominant in situ bacterial and archaeal populations, providing insight into microbes generating CBM within the PRB. Changes in the composition and structure of microbial communities that occur under stimulated conditions were investigated by applying molecular methods in combination with cultivation techniques (with and without nutrient supplementation) to identify conditions which maximize methane production in batch, bench-scale incubations. Results from these studies indicated the addition of yeast extract resulted in an increase in methane production as well as a shift to a microbial population capable of acetate production and/or acetate utilization. Isolation methods targeting coal utilizing Bacteria and methanogenic Archaea were applied in addition to DNA based methods to infer microbial community members present within coalbeds. The acetoclastic methanogen Methanosarcina was isolated which is the only identified methanogen with the high-efficiency acetate kinase (Ack) / phosphotransacetylase (Pta) methane production pathway. This pathway provides increased growth and methane production when acetate concentrations are high which can result from microbial stimulation with nutrients. Genomic analysis revealed Ack evolved through gene duplication and divergence of acetyl CoA synthetase within the methanogenic genome. This research provided novel insight into the evolution of the high-efficiency Ack/Pta pathway. Collectively, this dissertation presents a novel link between the Ack/Pta pathway, stimulated CBM production and genomic insight into the development of this pathway.Item Effects of saline-sodic water on EC, SAR, and water retention(Montana State University - Bozeman, College of Agriculture, 2003) Robinson, Kimberly MarieItem Effects of irrigation water quality and water table position on plant biomass production, crude protein, and base cation removal(Montana State University - Bozeman, College of Agriculture, 2003) Phelps, Shannon DaleItem Forage quality characteristics of barley irrigated with coalbed methane water(Montana State University - Bozeman, College of Agriculture, 2006) Todd, Alison Lee; Chairperson, Graduate Committee: S. Dennis Cash.Two experiments were conducted to determine the effects of coalbed methane (CBM) discharge water as an irrigation source in comparison with the use of well water. Three plot trials were conducted in two consecutive growing seasons with three replicates of 14 barley cultivars under each water treatment. Barley cultivars were grown under covered greenhouses to prevent uncontrolled precipitation. Each greenhouse received one of two water treatments: either well water (EC = 0.43 dS m-1, SAR = 0.25) or synthesized CBM discharge water (EC = 1.6 dS m-1, SAR = 35). Plots were irrigated with 5.1 cm of respective treatment water on the day of seeding and flood irrigated with treatment water on a weekly basis. Cultivars were sampled on three cutting dates within each trial, when the majority of the entries were in the boot, anthesis, and milk stages of maturity. Barley forage was analyzed for yield, height, and forage quality with relation to livestock requirements. Cultivars were dried, ground and analyzed for yield, dry matter (DM), acid detergent fiber (ADF), neutral detergent fiber (NDF), crude protein (CP), nitrate (NO3-N) concentrations, in vitro dry matter digestibility (IVDMD), and mineral concentrations. Coalbed methane discharge water significantly reduced (P<0.10) barley forage yield, height, and NO3-N concentrations. Forages irrigated with well water yielded higher (P<0.10) than those irrigated with CBM water (6499 vs 4937 kg ha-1) and were taller (49 vs 36 cm). Nitrate concentrations were lower (P<.010) in forages irrigated with CBM water than well water (0.66 vs 3.3 mg g-1). No differences (P>0.10) were seen between water treatments for the remaining parameters. Use of CBM discharge water as an irrigation source reduced yield, had a negative impact on height, and CP concentrations and reduced nitrate concentrations. Few differences were detected in mineral concentrations between water treatments. More research is necessary to determine the long term impacts of CBM discharge water on soil and plant quality.