Theses and Dissertations at Montana State University (MSU)
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Item Microbially induced calcium carbonate precipitation: meso-scale optimization and micro-scale characterization(Montana State University - Bozeman, College of Engineering, 2020) Zambare, Neerja Milind; Chairperson, Graduate Committee: Robin Gerlach and Ellen G. Lauchnor (co-chair); Ellen Lauchnor and Robin Gerlach were co-authors of the article, 'Controlling the distribution of microbially precipitated calcium carbonate in radial flow environments' in the journal 'Environmental science and technology' which is contained within this dissertation.; Robin Gerlach and Ellen Lauchnor were co-authors of the article, 'Spatio-temporal dynamics of strontium partitioning with microbially induced calcium carbonate precipitation in porous media flow cells' submitted to the journal 'Environmental science & technology' which is contained within this dissertation.; Robin Gerlach and Ellen Lauchnor were co-authors of the article, 'Co-precipitation of strontium and barium' submitted to the journal 'Environmental science & technology' which is contained within this dissertation.; Nada Naser, Robin Gerlach and Connie Chang were co-authors of the article, 'Visualizing microbially induced mineral precipitation from single cells using drop-based microfluidics' submitted to the journal 'Nature methods' which is contained within this dissertation.Microorganisms have the potential to impact processes on a scale orders of magnitude larger than their size. For example, microbe-mineral interactions at the micro-scale can drive macro-scale processes such as rock formation and weathering. Many bioremediation technologies derive inspiration from microbial mineralization processes. Microbially induced calcium carbonate precipitation (MICP) can produce calcium carbonate (CaCO 3) precipitates which can be utilized as a biological cement to strengthen porous media by reducing fluid permeability in subsurface fractures or as an immobilization matrix to remove metal contaminants dissolved in groundwater. To make MICP a feasible and successful bioremediation technology in the world outside the lab, it is necessary to bridge the gap between the meso-scale research studies and macro-scale applications. This thesis focuses on such meso-scale studies but also contributes to bridging the gap in the other direction, i.e., meso-scale to micro-scale to gain a fundamental understanding of the cellular level processes behind MICP. The research presented here investigates two applications of MICP with a focus on controlling precipitate distribution and process efficiency in target environments. Subsurface precipitate distribution and metal partitioning during MICP were studied in novel reactive transport systems that mimic application-environment conditions. A radial flow reactor was used to study the spatial distribution of precipitates in conditions similar to subsurface injection well environments. The distribution and degree of metal partitioning during MICP was investigated in batch reactors and porous media flow cells to study kinetics and reactive transport effects on kinetics. In the radial flow environment, more precipitates formed away from the center injection zone. Results showed that longer reactant residence times and an equimolar ratio of calcium to urea were able to maximize precipitation efficiency. Metal partitioning could be maximized at low reactant flow rates and low metal concentrations. The novel flow cell set up used revealed a spatial decoupling between ureolysis and precipitation. A micro-scale investigation of the fundamental MICP process itself is presented wherein microbe-mineral interactions are observed at the cell level. A semi-correlative approach to investigating individual precipitates in microdroplets is presented, using a multitude of microscopy and microanalysis techniques. The presented studies capture MICP across a range of scales.Item A study of bio-mineralization for the application of reducing leakage potential of geologically stored CO 2(Montana State University - Bozeman, College of Engineering, 2019) Daily, Ryanne Leigh; Chairperson, Graduate Committee: Adrienne PhillipsA primary concern of carbon capture and storage (CCS) is leakage of the stored carbon dioxide (CO 2) from the subsurface back to the surface. To ensure long term storage of the CO 2, mitigation strategies are being developed to seal high permeability regions, such as fractures present in the caprock or the near wellbore environment. Ureolysis induced calcium carbonate precipitation (UICP) is a widely investigated technology utilizing the enzymatically driven process of ureolysis to alter the properties of porous media. The advantage of this technology over traditional fracture sealing methods, such as well cement, is the use of low-viscosity aqueous fluids enabling access to smaller fractures. However, CCS reservoirs provide a problematic environment for microbial activity due to the acidity of dissolved CO 2, high pressures, and elevated temperatures. A flow-through pressurized reactor experiment and batch high-pressure ureolysis rate experiments were conducted to investigate the application of UICP technology to mitigate CO 2 migration. First, UICP was induced in two composite rock cores in an environment simulating a CCS reservoir, using a high-pressure axial flow reactor, with an initial and final exposure of the rock cores to a carbonated brine. As a result of UICP, the apparent permeability of the rock cores were reduced by 5-orders of magnitude. The CO 2 challenge increased apparent permeability by 4-orders of magnitude, likely due to a preferential flow path created through the calcium carbonate (CaCO 3) seal, which was found with X-ray microcomputed tomography (micro-CT) imaging. The porosity of the composite rock cores was assessed throughout the experiment with two non-invasive technologies, micro-CT and nuclear magnetic resonance (NMR), both reported a significant decrease in porosity due to UICP and a slight increase after the CO 2 exposure. Second, ureolysis kinetics were assessed in the presence of a pressurized carbonated brine at pressures between 0 and 4 MPa. The kinetic studies were performed in a high-pressure batch reactor connected to high-pressure pH and conductivity probes. Samples could not be taken from the batch reactor without losing pressure; thus, conductivity was used as a surrogate measurement for urea concentration. It was found that, for the pressures tested, JBM urease was capable of hydrolyzing urea in the presence of a pressurized carbonated brine. It was also hypothesized that the rate observed at each experimental pressure may have been dependent on the buffered pH of the system. The combination of these studies suggests that, if the challenge of dissolution could be overcome, bio-mineralization may be used to enhance CCS by reducing the permeability of CO 2 leakage pathways.Item The stoichiometry of nutrient and energy transfer: from organelles to organisms(Montana State University - Bozeman, College of Engineering, 2016) Hunt, Kristopher Allen; Chairperson, Graduate Committee: Ross Carlson; James P. Folsom, Reed L. Taffs and Ross P. Carlson were co-authors of the article, 'Complete enumeration of elementary flux modes through scalable, demand-based subnetwork definition' in the journal 'Bioinformatics' which is contained within this thesis.; Ashley E. Beck was an author and Hans C. Bernstein and Ross P. Carlson were co-authors of the article, 'Interpreting and designing microbial communities for bioprocess applications, from components to interactions to emergent properties' in the journal 'Biotechnology for biofuel production and optimization' which is contained within this thesis.; Ryan deM. Jennings, William P. Inskeep and Ross P. Carlson were co-authors of the article, 'Stoichiometric modeling of assimilatory and dissimilatory biomass utilization in a microbial community' in the journal 'Environmental microbiology' which is contained within this thesis.; Ryan deM. Jennings, William P. Inskeep and Ross P. Carlson were co-authors of the article, 'Multiscale analysis of autotroph-heterotroph interactions in a high-temperature microbial community' submitted to the journal 'The International Society for Microbial Ecology journal' which is contained within this thesis.; Natasha D. Mallette, Brent M. Peyton and Ross P. Carlson were co-authors of the article, 'Theoretical and practical limitations of hydrocarbon production for a cellulolytic, endophytic filamentous fungus' submitted to the journal 'Metabolic engineering' which is contained within this thesis.All life requires the acquisition and transformation of nutrients and energy, driving processes from cellular nutrient flow to planetary biogeochemical cycling. However, the organisms and communities responsible for these processes are often uncultivable and too complex to observe directly and understand. Stoichiometric modeling, a systems biology approach, analyzes the reactions in an organism and incorporates data from multiple sources to extract biologically meaningful parameters, such as theoretical limits of conversion and yields of a metabolism. These limits and yields quantify relationships between organisms to establish governing principles, from resource requirements to community productivity as a function of population composition. The presented work expanded the stoichiometric modeling algorithm and identified fundamental principles that govern nutrient and energy transfer associated with heterotrophy, community composition, and intracellular compartmentalization. A scalable routine capable of analyzing complex metabolic networks by dividing them into tractable subnetworks was demonstrated for a eukaryotic diatom. The metabolic model contained approximately two billion routes through the network and established an international benchmark for elementary flux mode analysis. Additionally, a heterotrophic archaeon was examined for the resource requirements while consuming 29 different forms of biomass derived dissolved organic carbon. These resource requirements and limitations establish a basis to analyze heterotrophy with regard to the limiting nutrient in a variety of systems. The resulting resource requirements of heterotrophy were incorporated into a community where an iron oxidizing autotroph was hypothesized to be the primary source of carbon and energy. Analysis of the community model and in situ measurements of iron and oxygen utilization indicated additional electron donors were required to account for the observed acquisition of nutrients in some communities. Finally, limits and resource requirements for fungal production of hydrocarbons were identified as a function of carbon and energy partitioning using simulated genetic modifications, providing context regarding endophytic production of bioactive molecules for host resistance as well as endophyte capacity as a petroleum producing alternative.Item Rates of cellular attachment to an established biofilm(Montana State University - Bozeman, College of Engineering, 1991) Gunawan, J. CahyonoItem Systems analysis of engineered and natural microbial consortia(Montana State University - Bozeman, College of Engineering, 2013) Bernstein, Hans Christopher; Chairperson, Graduate Committee: Ross Carlson; Ross P. Carlson was a co-author of the article, 'Microbial consortia engineering for cellular factories: in vitro to in silico systems' in the journal 'Computational and structural biotechnology journal' which is contained within this thesis.; Ross P. Carlson was a co-author of the article, 'Design, construction and characterization methodologies for synthetic microbial consortia' in the book 'Methods in molecular biology, engineering multicellular system' which is contained within this thesis.; Steven D. Paulson and Ross P. Carlson were co-authors of the article, 'Synthetic Escherichia coli consortia engineered for syntrophy demonstrate enhanced biomass productivity' in the journal 'Journal of biotechnology' which is contained within this thesis.; Maureen Kessano, Karen Moll, Terence Smith, Robin Gerlach, Ross P. Carlson, Brent M. Peyton, Robert D. Gardner and Ronald C. Sims were co-authors of the article, 'Direct measurement and characterization of active photosynthesis zones inside biofuel producing and waste-water remediating algal biofilms' submitted to the journal 'Biotechnology and bioengineering' which is contained within this thesis.; Jacob P. Beam, Mark A. Kozubal, Ross P. Carlson and William P. Inskeep were co-authors of the article, 'In situ analysis of oxygen consumption and diffusive transport in high-temperature acidic iron-oxide microbial mats' in the journal 'Environmental Microbiology' which is contained within this thesis.; Alissa Bleem, Steven Davis and Ross P. Carlson were co-authors of the article, 'Chacterization of an artificial photoautotrophic-heterotrophic biofilm consortium composed of synechococcus PCC 7002 and Escherichia coli MG1655' which is contained within this thesis.Microorganisms are ubiquitous and typically exist within complex interacting communities or consortia. Microbial consortia are capable of cooperating in a coordinated fashion to extract mass and free energy from their environment. Chemical and biological engineers have long been keen to harness microbial processes for the development of technologies with applications ranging from energy capture to environmental remediation to human health. The pursuit of novel microbial biotechnologies has given rise to the relatively new discipline of microbial consortia engineering, which differs from and expands upon more traditional monoculture based practices. Many successful examples of applied and/or engineered microbial consortia mimic fundamental ecological strategies observed from nature, highlighting the importance for engineers to study natural biological phenomena. The overarching goal for this dissertation was to observe and quantitatively characterize interactions and physical phenomena occurring within select microbial consortial systems. The technical research presented here explores microbial consortia on three main fronts: (i) metabolically engineered heterotrophic systems, (ii) photoautotrophic-heterotrophic biofilm systems and (iii) naturally occurring thermo-acidophilic microbial mat systems. The metabolically engineered systems were designed to mimic a common ecological strategy involving syntrophic metabolite exchange via primary-productivity coupled with secondary consumption of potentially inhibitory byproducts (i.e., acetic acid). This system exhibited enhanced biomass productivity as compared to monoculture controls. The primary-productivity concept was also explored, in a more traditional sense, by characterizing production, consumption and exchanges of oxygen within photoautotrophic-heterotrophic biofilm systems. Tight spatial coupling of oxygenic-photosynthesis and aerobic-respiration was observed in both biofuel producing and waste-water remediating biofilm communities. The role of oxygen as an important terminal electron acceptor was also investigated in pristine Fe(III)-oxide microbial mats from geothermal springs located in Yellowstone National Park (USA). For these systems, oxygen availability defines ecological niche environments that spatially govern specific community member abundances and activities. Classical chemical engineering reaction and diffusion analysis was used to model concentration dependent oxygen consumption kinetics and establish that these mats are likely mass transfer limited. Both primary-productivity and microbially mediated oxygen reactions are interrelated, cross-cutting themes throughout this dissertation. The research described here is interdisciplinary chemical engineering that utilizes fundamental microbial ecology as a foundational platform.