Groundwater contamination is of environmental and human health concern. Bioremediation is a nature-based method for contaminant treatment. Bioremediation, which relies on the ability of microorganisms to destroy or transform contaminants, must be reliable and cost-competitive in comparison to more traditional treatment methods. Two hurdles must be overcome to enhance bioremediation’s effectiveness and competitiveness: i) being able to degrade recalcitrant compounds, and ii) being able to control the growth rate and location of microorganisms involved in bioremediation in the subsurface. My dissertation adds foundational knowledge and engineering application on how to biodegrade recalcitrant emerging and legacy halogenated compounds. Generating biotransformation knowledge on the recalcitrant emerging contaminants called per- and polyfluoroalkyl substances (PFAS) may lead to solutions for protecting both people and the planet. In my dissertation, I analyzed PFAS biotransformation and microbial defluorination literature via meta-analytical and bibliometric methods to identify unexplored topics and experimental conditions. The metanalytical work identified trends in PFAS microbial biotransformation science to inform future experimental design. The second hurdle which must be overcome is being able to control bacterial growth in the subsurface. During bioremediation implementation microbial overgrowth may clog injection wells and the subsurface, leading to reduced porosity and treatment efficacy. Contaminant treatment schemes based on aerobic cometabolism frequently exhibit overgrowth at subsurface injection points for O2 (the electron acceptor) and a labile hydrocarbon (e.g., propane). My dissertation work experimentally evaluated acetylene as a microbial inhibitor for use in controlling microbial overgrowth during trichloroethene (TCE) aerobic cometabolism. I demonstrated that acetylene reduces the likelihood of microbial overgrowth of TCE-degrading microorganisms in soil-free microcosms and aquifer soil columns while retaining TCE degradation capacity. Cumulatively, my dissertation provides foundational knowledge for academics and bioremediation practitioners to develop robust and reliable bioremediation technologies.

Selenium oxyanions (i.e., selenate and selenite) can be released into the environment from surface mining. Selenium is an essential micronutrient, but high selenium in water has adverse health effects for aquatic animals and humans. Mine-influenced water is often co-contaminated with high concentrations of nitrate, selenium oxyanions, and sulfate. The Saturated Rock Fill (SRF) is a treatment technology that utilizes waste rocks from surface mining to create a biological treatment system that can be effective at removing nitrate and selenium-oxyanions from the mine-influenced water. The Selenium, Sulfur, and Nitrogen species (SeSANS) model can be used to estimate the respiration, synthesis, and endogenous decay of biomass in an SRF. The goal of this thesis is to simulate SRF biofilms using a biofilm version of SeSANS. Three nitrate loads (100, 250, and 450 kg NO3-N/day) with a low flow rate (1000 m3/d) or a high flow rate (5000 m3/d) -- a total of six scenarios -- were simulated for 5000 days of operation. The influent water contained 0.18 g Se/m3 of selenate, 0.02 Se/m3 selenite, and 800 S/m3 of sulfate; the input nitrate concentration was 100, 250, and 450 g N/m3 for the low flow rate and 20, 50, and 90 g N/m3 for the high flow rate. Methanol was injected as the electron donor. These criteria were used to define a successful simulation: effluent nitrate < 3 mg N/L and total dissolved Se < 0.029 mg Se/L, minimal sulfate reduction, and an average biofilm-biomass density of 96 kg TS/m3. To achieve those criteria, the following model parameters were adjusted: rate for methanol addition, biofilm thickness, SRF volumes, and biofilm-detachment rates. The most important parameter for achieving all the goals was the methanol addition ratio: 3.56 g COD/g NO3-N. Another important outcome was that the high-flow-rate scenarios required a larger total SRF volume to achieve target nitrate and Se-oxyanion reductions. The results of the simulations can be used to estimate biofilm characteristics and optimize the SRF configuration and treatment operation.

The world currently faces hundreds of millions of cubic meters of soil contaminated with petroleum crude oil residuals. The application of ozone gas (O3) to contaminated soil is an effective means to oxidize petrogenic compounds and, when used with bioremediation, remove the oxidized byproducts. The overarching goal of this dissertation was to evaluate two areas of potential concern to large-scale O3 deployment: the capacity of O3-treated petroleum contaminated soils to support seed germination before bioremediation and the transport characteristics of O3 in soil columns. A matched study comparing the germination outcomes of radish (Raphanus sativus L.), grass (Lagurus ovatus), and lettuce (Lactuca sativa) in soils contaminated with three crude oils at various O3 total-dose levels showed that radish germination was sensitive to the soluble byproducts of oxidized petroleum (assayed as dissolved organic carbon [DOC]), but not sensitive to the unreacted petroleum (total petroleum hydrocarbon [TPH]). A multivariable logistic regression model based on the radish results showed that adverse germination outcomes varied with the DOC concentration and that DOC ecotoxicity decreased with increasing O3 dose-level and background organic material. The model was used to create a risk management map of conditions that created 10%, 25%, and 50% extra risks of adverse radish germination. Thus, while O3 effectively lowered TPH in soils, the byproducts exhibited ecotoxicity that inhibited radish germination. On the other hand, the sensitivity of radish germination to oxidized petroleum byproducts could be utilized to assess ecological risk. The feasibility of gas transport in the soil matrix is also of paramount concern to field-scale utilization of O3. A matched study comparing TPH removal at three field-relevant loading rates (4, 12, or 36 mgozone/ gsoil/ hr) and various total dose-levels showed an anisotropic pattern along the axial distance favoring the column inlet end. The asymmetry decreased as loading rate decreased and with concurrent improvements in O3-transport distance, O3 utilization, and heat balance. Overall, a low O3 loading rate significantly improved O3 transport and utilization efficiency, while also better distributing reaction-generated heat along the gas flow path for a depth typically utilized in bioremediation field settings.

The increasing concentrations of greenhouse gases into the atmosphere call for urgent measures to use non-fossil feedstock for fuels and chemicals. Synthesis gas (or syngas) is a mixture of three gases: hydrogen (H2), carbon monoxide (CO), and carbon dioxide (CO2). Syngas already is widely used as a non-fossil fuel and a building block for a variety of chemicals using the Fischer-Tropsch process. Recently, syngas fermentation has attracted attention as a more sustainable way for the conversion of syngas to chemicals, since its biocatalysts are self-generating, are resilient, and can utilize a wide range of syngas compositions. However, syngas fermentation has technical and economic limitations. This dissertation, by contributing to the understanding of syngas fermentation, helps to overcome the limitations. A bibliometric analysis showed the topic’s landscape and identified that mass transfer is the biggest challenge for the process. One means to improve syngas mass transfer is to use the membrane biofilm reactor, or MBfR, to deliver syngas to the microorganisms. MBfR experiments delivering pure H2 demonstrated that the H2:IC ratio (IC is inorganic carbon) controlled the overall production rate of organic compounds and their carbon-chain length. Organic chemicals up to eight carbons could be produced with a high H2:IC ratio. A novel asymmetric membrane dramatically improved mass transfer rates for all syngas components, and its low selectivity among them made it ideal for high-rate syngas fermentation. MBfR experiments using syngas and the asymmetric membrane, as well as a conventional symmetric membrane, confirmed that the key parameter for generating long-chain products was a high H2:IC ratio. The fast mass transfer rate of the asymmetric membrane allowed a very high areal production rate of acetate: 253 g.m-2.d-1, the highest reported to date. Since the membrane delivered H2 and C from the syngas feed, the relatively low selectivity of the asymmetric membrane favored acetogenesis over microbial chain elongation. A techno-economic analysis of the MBfR showed that the cost to produce acetate was less than its market price. All results presented in this dissertation support the potential of syngas fermentation using the MBfR as a means to produce commodity chemicals and biofuels from syngas.

Water is a vital resource, and its protection is a priority world-wide. One widespread threat to water quality is contamination by chlorinated solvents. These dry-cleaning and degreasing agents entered the watershed through spills and improper disposal and now are detected in 4% of U.S. aquifers and 4.5-18% of U.S. drinking water sources. The health effects of these contaminants can be severe, as they are associated with damage to the nervous, liver, kidney, and reproductive systems, developmental issues, and possibly cancer. Chlorinated solvents must be removed or transformed to improve water quality and protect human and environmental health. One remedy, bioaugmentation, the subsurface addition of microbial cultures able to transform contaminants, has been implemented successfully at hundreds of sites since the 1990s. Bioaugmentation uses the bacteria Dehalococcoides to transform chlorinated solvents with hydrogen, H2, as the electron donor. At advection limited sites, bioaugmentation can be combined with electrokinetics (EK-Bio) to enhance transport. However, challenges for successful bioremediation remain. In this work I addressed several knowledge gaps surrounding bioaugmentation and EK-Bio. I measured the H2 consuming capacity of soils, detailed the microbial metabolisms driving this demand, and evaluated how these finding relate to reductive dechlorination. I determined which reactions dominated at a contaminated site with mixed geochemistry treated with EK-Bio and compared it to traditional bioaugmentation. Lastly, I assessed the effect of EK-Bio on the microbial community at a field-scale site. Results showed the H2 consuming capacity of soils was greater than that predicted by initial measurements of inorganic electron acceptors and primarily driven by carbon-based microbial metabolisms. Other work demonstrated that, given the benefits of some carbon-based metabolisms to microbial reductive dechlorination, high levels of H2 consumption in soils are not necessarily indicative of hostile conditions for Dehalococcoides. Bench-scale experiments of EK-Bio under mixed geochemical conditions showed EK-Bio out-performed traditional bioaugmentation by facilitating biotic and abiotic transformations. Finally, results of microbial community analysis at a field-scale implementation of EK-Bio showed that while there were significant changes in alpha and beta diversity, the impact of EK-Bio on native microbial communities was minimal.