Scholarly Work - Center for Biofilm Engineering
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Item Subsurface hydrocarbon degradation strategies in low- and high-sulfate coal seam communities identified with activity-based metagenomics(Springer Science and Business Media LLC, 2022-02) Schweitzer, Hannah D.; Smith, Heidi J.; Barnhart, Elliott P.; McKay, Luke J.; Gerlach, Robin; Cunningham, Alfred B.; Malmstrom, Rex R.; Goudeau, Danielle; Fields, Matthew W.Environmentally relevant metagenomes and BONCAT-FACS derived translationally active metagenomes from Powder River Basin coal seams were investigated to elucidate potential genes and functional groups involved in hydrocarbon degradation to methane in coal seams with high- and low-sulfate levels. An advanced subsurface environmental sampler allowed the establishment of coal-associated microbial communities under in situ conditions for metagenomic analyses from environmental and translationally active populations. Metagenomic sequencing demonstrated that biosurfactants, aerobic dioxygenases, and anaerobic phenol degradation pathways were present in active populations across the sampled coal seams. In particular, results suggested the importance of anaerobic degradation pathways under high-sulfate conditions with an emphasis on fumarate addition. Under low-sulfate conditions, a mixture of both aerobic and anaerobic pathways was observed but with a predominance of aerobic dioxygenases. The putative low-molecular-weight biosurfactant, lichysein, appeared to play a more important role compared to rhamnolipids. The methods used in this study—subsurface environmental samplers in combination with metagenomic sequencing of both total and translationally active metagenomes—offer a deeper and environmentally relevant perspective on community genetic potential from coal seams poised at different redox conditions broadening the understanding of degradation strategies for subsurface carbon.Item Application of molecular techniques to elucidate the influence of cellulosic waste on the bacterial community structure at a simulated low level waste site(2010-03) Field, E. K.; D'Imperio, Seth; Miller, A. R.; VanEngelen, Michael R.; Gerlach, Robin; Lee, Brady D.; Apel, William A.; Peyton, Brent M.Low-level radioactive waste sites, including those at various U.S. Department of Energy (DOE) sites, frequently contain cellulosic waste in the form of paper towels, cardboard boxes, or wood contaminated with heavy metals and radionuclides such as chromium and uranium. To understand how the soil microbial community is influenced by the presence of cellulosic waste products, multiple soil samples were obtained from a non-radioactive model low-level waste test pit at the Idaho National Laboratory. Samples were analyzed using 16S rRNA gene clone libraries and 16S rRNA gene microarray (PhyloChip) analyses. Both methods revealed changes in the bacterial community structure with depth. In all samples, the PhyloChip detected significantly more Operational Taxonomic Units (OTUs), and therefore relative diversity, than the clone libraries. Diversity indices suggest that diversity is lowest in the Fill (F) and Fill Waste (FW) layers and greater in the Wood Waste (WW) and Waste Clay (WC) layers. Principal coordinates analysis and lineage specific analysis determined that Bacteroidetes and Actinobacteria phyla account for most of the significant differences observed between the layers. The decreased diversity in the FW layer and increased members of families containing known cellulose degrading microorganisms suggests the FW layer is an enrichment environment for these organisms. These results suggest that the presence of the cellulosic material significantly influences the bacterial community structure in a stratified soil system.Item Modeling biofilm growth in the presence of carbon dioxide and water flow in the subsurface(2010-07) Ebigbo, Anozie; Helmig, Rainer; Cunningham, Alfred B.; Class, Holger; Gerlach, RobinThe concentration of greenhouse gases—particularly carbon dioxide (CO2)—in the atmosphere has been on the rise in the past decades. One of the methods which have been proposed to help reduce anthropogenic CO2 emissions is the capture of CO2 from large, stationary point sources and storage in deep geological formations. The caprock is an impermeable geological layer which prevents the leakage of stored CO2, and its integrity is of utmost importance for storage security. Due to the high pressure build-up during injection, the caprock in the vicinity of the well is particularly at risk of fracturing. Biofilms could be used as biobarriers which help prevent the leakage of CO2 through the caprock in injection well vicinity by blocking leakage pathways. The biofilm could also protect well cement from corrosion by CO2-rich brine.The goal of this paper is to develop and test a numerical model which is capable of simulating the development of a biofilm in a CO2 storage reservoir. This involves the description of the growth of the biofilm, flow and transport in the geological formation, and the interaction between the biofilm and the flow processes. Important processes which are accounted for in the model include the effect of biofilm growth on the permeability of the formation, the hazardous effect of supercritical CO2 on suspended and attached bacteria, attachment and detachment of biomass, and two-phase fluid flow processes. The model is tested by comparing simulation results to experimental data.Item Reducing the risk of well bore leakage using engineered biomineralization barriers(2011-04) Cunningham, Alfred B.; Gerlach, Robin; Spangler, Lee H.; Mitchell, Andrew C.; Park, Saehan; Phillips, Adrienne J.If CO2 is injected in deep geological formations it is important that the receiving formation hassufficient porosity and permeability for storage and transmission and be overlain by a suitable low-permeability cap rock formation. When the resulting CO2 plume encounters a well bore, leakage may occur through various pathways in the “disturbed zone†surrounding the well casing. Gasda et al.[9], propose a method for determining effective well bore permeability from a field pressure test. If permeability results from such tests prove unacceptably large, strategies for in situ mitigation of potential leakage pathways become important. To be effective, leakage mitigation methods must block leakage pathways on timescales longer than the plume will be mobile, be able to be delivered without causing well screen plugging, and be resistant to supercritical CO2 (ScCO2) challenges. Traditional mitigation uses cement, a viscous fluid that requires a large enough aperture for delivery and that also must bond to the surrounding surfaces in order to be effective. Technologies that can be delivered via low viscosity fluids and that can effectively plug small aperture pathways, or even the porous rock surrounding the well could have significant advantages for some leakage scenarios.We propose a microbially mediated method for plugging preferential leakage pathways and/or porous media, thereby lowering the risk of unwanted upward migration of CO2, similar to thatdiscussed by Mitchell et al.[12].We examine the concept of using engineered microbial biofilms which are capable of precipitating crystalline calcium carbonate using the process of ureolysis. The resulting combination of biofilm plus mineral deposits, if targeted near points of CO2 injection, may result in the long-term sealing of preferential leakage pathways. Successful development of these biologically-based concepts could result in a CO2 leakage mitigation technology which can be applied either before CO2 injection or as a remedial measure. Results from laboratory column studies are presented which illustrate how biomineralization deposits can be developed along packed sand columns at length scales of 2.54 cm and 61 cm. Strategies for controlling mineral deposition of uniform thickness along the axis of flow are also discussed.Item Reduction of environmental and energy footprint of microalgal biodiesel production through material and energy integration(2012-03) Chowdhury, R.; Viamajala, Sridhar; Gerlach, RobinThe life cycle impacts were assessed for an integrated microalgal biodiesel production system that facilitates energy- and nutrient- recovery through anaerobic digestion, and utilizes glycerol generated within the facility for additional heterotrophic biodiesel production. Results show that when external fossil energy inputs are lowered through process integration, the energy demand, global warming potential (GWP), and process water demand decrease significantly and become less sensitive to algal lipid content. When substitution allocation is used to assign additional credit for avoidance of fossil energy use (through utilization of recycled nutrients and biogas), GWP and water demand can, in fact, increase with increase in lipid content. Relative to stand-alone algal biofuel facilities, energy demand can be lowered by 3–14 GJ per ton of biodiesel through process integration. GWP of biodiesel from the integrated system can be lowered by up to 71% compared to petroleum fuel. Evaporative water loss was the primary water demand driver.Item Dissolved inorganic carbon enhanced growth, nutrient uptake, and lipid accumulation in wastewater grown microalgal biofilms(2015-03) Kesaano, M.; Gardner, Robert D.; Moll, Karen M.; Lauchnor, Ellen G.; Gerlach, Robin; Peyton, Brent M.; Sims, R. C.Microalgal biofilms grown to evaluate potential nutrient removal options for wastewaters and feedstock for biofuels production were studied to determine the influence of bicarbonate amendment on their growth, nutrient uptake capacity, and lipid accumulation after nitrogen starvation. No significant differences in growth rates, nutrient removal, or lipid accumulation were observed in the algal biofilms with or without bicarbonate amendment. The biofilms possibly did not experience carbon-limited conditions because of the large reservoir of dissolved inorganic carbon in the medium. However, an increase in photosynthetic rates was observed in algal biofilms amended with bicarbonate. The influence of bicarbonate on photosynthetic and respiration rates was especially noticeable in biofilms that experienced nitrogen stress. Medium nitrogen depletion was not a suitable stimulant for lipid production in the algal biofilms and as such, focus should be directed toward optimizing growth and biomass productivities to compensate for the low lipid yields and increase nutrient uptake.