Bioremediation of chlorinated contaminants in groundwater can be achieved by reductive dechlorination by anaerobic dechlorinating cultures. However, at sites impacted with multiple different chlorinated contaminants, reductive dechlorination is often inhibited by co-contaminants. The inhibitory effects of trichloroethene, cis-dichloroethene and vinyl chloride on chloroform dechlorination were studied using a Dehalobacter-containing chloroform dechlorinating mixed culture (ACT-3). The inhibitory effect of chloroform on chlorinated ethene dechlorination was studied in a Dehalococcoides-containing trichloroethene dechlorinating mixed culture (KB-1). Vinyl chloride was found to be the strongest inhibitor of chloroform in ACT-3. Chloroform exerted a complex and strong inhibitory effect on chlorinated ethene dechlorination in KB-1. The potential for microbial reductive defluorination was also examined in the enrichment cultures. Quantifying the substrates and substrate interactions in dechlorinating cultures is necessary to most efficiently use these cultures to remediate contaminated sites.

The purpose of this research was to investigate the microorganisms, genetics and biochemistry of anaerobic dechlorination of chlorinated ethanes, which are common groundwater contaminants. Specifically, this project used mixed microbial cultures to study the dechlorination of 1,2-dichloroethane (1,2-DCA), 1,1,2-trichloroethane (1,1,2-TCA) and 1,1,1-trichloroethane (1,1,1-TCA). A mixed microbial culture enriched from a contaminated multilayered aquifer in West Louisiana dechlorinated 1,2-DCA, 1,1,2-TCA, tetrachloroethene, trichloroethene, cis-dichloroethene and vinyl chloride (VC) to non-toxic ethene when amended with ethanol as the electron donor. 16S rRNA gene sequence analysis revealed the presence of the putative dechlorinating organisms Dehalobacter and Dehalococcoides spp. Denaturing gradient gel electrophoresis analysis and quantitative PCR (qPCR) with species-specific primers demonstrated that both organisms grew during the dichloroelimination of 1,2-DCA to ethene. Conversely, during the dichloroelimination of 1,1,2-TCA to VC only Dehalobacter grew, while during the reductive dechlorination of VC to ethene only Dehalococcoides grew. Further enrichment with 1,2-DCA, H2 and acetate yielded a co-culture of Dehalobacter and Acetobacterium spp. that did not dechlorinate other chlorinated ethanes or ethenes. Dehalobacter grew in the presence but not in the absence of 1,2-DCA, while Acetobacterium growth was not affected by 1,2-DCA. A novel putative Dehalobacter-associated 1,2-DCA reductive dehalogenase gene was identified and was shown to be transcribed only in the presence of 1,2-DCA. An enrichment microbial culture derived from a 1,1,1-TCA-contaminated site in the northeastern United States was also studied. This culture, referred to as MS, reductively dechlorinated 1,1,1-TCA to 1,1-dichloroethane (1,1-DCA) and then to monochloroethane (CA) when amended with methanol, ethanol, acetate and lactate. 16S rRNA gene sequence analysis revealed the presence of the putative dechlorinating organism Dehalobacter sp., whose growth during 1,1,1-TCA and 1,1-DCA dechlorination was confirmed by qPCR. In the presence of chlorinated ethenes, dechlorination 1,1,1-TCA by the culture MS was slowed, while dechlorination of 1,1-DCA was completely inhibited. Experiments with cell-free extracts and whole cell suspensions of culture MS suggested that chlorinated ethenes have direct inhibitory effects on 1,1,1-TCA reductive dehalogenase(s), while the inhibition of 1,1-DCA dechlorination may be due to effects on non-dehalogenase components of Dehalobacter sp. cells. Additionally, two novel reductive dehalogenase genes associated with 1,1,1-TCA reductive dechlorination were identified.

KB-1 is an anaerobic Dehalococcoides-containing microbial culture used industrially to bioremediate sites impacted with chlorinated solvents. The culture is typically grown at pH 7. However, lower pH is often encountered and therefore the effect of pH was investigated. Both sudden and stepwise decreases in pH from 7 to 6 and 5.5 were investigated over a period of 450 days. An electron balance was also calculated to look at the flow of electrons for dechlorination. More than 95% of the reducing equivalents went towards methanogenesis and acetogenesis. Select microorganisms were compared by quantitative Polymerase Chain Reaction. It was found that lower rates of dechlorination correspond to low Dehalococcoides numbers and that different methanogens were enriched on different electron donors.

Bioremediation of chlorinated contaminants in groundwater can be achieved by reductive dechlorination by anaerobic dechlorinating cultures. However, at sites impacted with multiple different chlorinated contaminants, reductive dechlorination is often inhibited by co-contaminants. The inhibitory effects of trichloroethene, cis-dichloroethene and vinyl chloride on chloroform dechlorination were studied using a Dehalobacter-containing chloroform dechlorinating mixed culture (ACT-3). The inhibitory effect of chloroform on chlorinated ethene dechlorination was studied in a Dehalococcoides-containing trichloroethene dechlorinating mixed culture (KB-1). Vinyl chloride was found to be the strongest inhibitor of chloroform in ACT-3. Chloroform exerted a complex and strong inhibitory effect on chlorinated ethene dechlorination in KB-1. The potential for microbial reductive defluorination was also examined in the enrichment cultures. Quantifying the substrates and substrate interactions in dechlorinating cultures is necessary to most efficiently use these cultures to remediate contaminated sites.

abstract: Contamination by chlorinated ethenes is widespread in groundwater aquifers, sediment, and soils worldwide. The overarching objectives of my research were to understand how the bacterial genus Dehalococcoides function optimally to carry out reductive dechlorination of chlorinated ethenes in a mixed microbial community and then apply this knowledge to manage dechlorinating communities in the hydrogen-based membrane biofilm reactor (MBfR). The MBfR is used for the biological reduction of oxidized contaminants in water using hydrogen supplied as the electron donor by diffusion through gas-transfer fibers. First, I characterized a new anaerobic dechlorinating community developed in our laboratory, named DehaloR^2, in terms of chlorinated ethene turnover rates and assessed its microbial community composition. I then carried out an experiment to correlate performance and community structure for trichloroethene (TCE)-fed microbial consortia. Fill-and-draw reactors inoculated with DehaloR^2 demonstrated a direct correlation between microbial community function and structure as the TCE-pulsing rate was increased. An electron-balance analysis predicted the community structure based on measured concentrations of products and constant net yields for each microorganism. The predictions corresponded to trends in the community structure based on pyrosequencing and quantitative PCR up to the highest TCE pulsing rate, where deviations to the trend resulted from stress by the chlorinated ethenes. Next, I optimized a method for simultaneous detection of chlorinated ethenes and ethene at or below the Environmental Protection Agency maximum contaminant levels for groundwater using solid phase microextraction in a gas chromatograph with a flame ionization detector. This method is ideal for monitoring biological reductive dechlorination in groundwater, where ethene is the ultimate end product. The major advantage of this method is that it uses a small sample volume of 1 mL, making it ideally suited for bench-scale feasibility studies, such as the MBfR. Last, I developed a reliable start-up and operation strategy for TCE reduction in the MBfR. Successful operation relied on controlling the pH-increase effects of methanogenesis and homoacetogenesis, along with creating hydrogen limitation during start-up to allow dechlorinators to compete against other microorgansims. Methanogens were additionally minimized during continuous flow operation by a limitation in bicarbonate resulting from strong homoacetogenic activity. / Dissertation/Thesis / Ph.D. Civil and Environmental Engineering 2012

Polaromonas sp. strain JS666 is the only isolated bacterium capable of aerobic growth using the groundwater pollutant cis-1,2-dichloroethene (cDCE) as a sole carbon source. Its genome has a wealth of evidence of recent gene acquisition through horizontal gene transfer, and contains gene clusters predicted to encode enzymes allowing the metabolism of a wide variety of xenobiotic compounds. Culture growth using each of these hypothesized substrates was tested experimentally, and many were confirmed as sole carbon sources for strain JS666. In addition to pollutant degradation, many of these metabolic pathways have applicability in the field of biocatalysis, as does the genome-assisted pathway prediction approach to biocatalyst discovery. During (or immediately following) growth on cDCE, cultures of Polaromonas sp. strain JS666 oxidize ethene to epoxyethane at an increased rate, and also cometabolically oxidize several other chlorinated ethenes. Given the involvement of a monooxygenase in other species' 1-chloroethene (vinyl chloride) oxidation, it was hypothesized that alkene oxidation in strain JS666 was due to the activity of a monooxygenase that also was responsible for the first step in cDCE oxidation. The alkene oxidation activity of strain JS666 was investigated using gene expression analysis, proteomics, and whole-cell kinetic assays. Results of these experiments pointed to the upregulation of a cyclohexanone monooxygenase (CHMO) during growth on cDCE and during oxidation of ethene. To determine the activity of this cyclohexanone monooxygenase, its gene was cloned and heterologously expressed in an E. coli host. Our CHMO expression system exhibited activity on cyclohexanone, but not cDCE or ethene, disproving our hypothesis about its involvement in alkene oxidation. The heterologously expressed monooxygenase was also investigated for enantioselective oxidation of racemic cyclic ketones to chiral lactones, and was discovered to have very high enantioselectivity with the tested compounds. Chiral lactones and other single-enantiomer oxidation products are valuable for fine chemical synthesis, and their biocatalytic production is more environmentally sustainable and often less expensive than traditional techniques. The research described in the following chapters illustrates the many opportunities that arise when the fields of bioremediation and biocatalysis converge. The shared research goals and methods of these two areas lend themselves to interdisciplinary research, and increased communication and crossover between them should provide benefits for both environmental remediation and sustainable chemical synthesis.

In recent years, due to the continuous development of machinery, electronics, leather, chemical companies and dry-cleaning industry, more and more chlorinated hydrocarbons accumulate in the soil, causing serious harm to the environment. The accumulation of chlorinated hydrocarbons and the teratogenic, carcinogenic, and mutagenic hazards seriously threaten human health. Therefore, the remediation of chlorinated hydrocarbons is imminent. Under this premise, in-situ bioremediation has gradually received attention. For in situ bioremediation of soil contaminated with chlorinated hydrocarbons, the most commonly used methods are biostimulation alone, bioaugmentation alone, and a combination with biostimulation and bioaugmentation. The removal rate of trichloroethylene in the case of using biostimulation products alone is significantly lower than that of using bioaugmentation products alone. The removal rate of trichloroethylene by biostimulation products alone does not exceed 60%, and “DCE pause” occurred, but did not occur in the case of using bioaugmentation products. The removal rate of trichloroethylene by bioaugmentation products is generally higher than 98%, and it will promote the degradation of trichloroethylene or tetrachloroethylene to non-toxic ethylene. Therefore, only cases containing bioaugmentation can achieve non-toxic degradation of chlorinated hydrocarbons and take into account the high removal rate of them. In addition, the biostimulation duration is significantly shorter.

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Natural Attenuation Software (NAS) was developed as a screening tool to estimate remediation timeframes for monitored natural attenuation (MNA) to lower groundwater contaminant concentrations to regulatory limits, and to assist in decision-making on the level of source zone treatment in conjunction with MNA using site-specific remediation objectives. In addition, NAS facilitates the combined use of MNA with engineered remedial actions (ERAs) so that the benefits of each technology can be maximized while minimizing costs of remediation. The primary expected benefit of NAS is to increase regulatory acceptance of MNA, thereby decreasing overall remediation costs. NAS is designed for application to ground-water systems consisting of porous, relatively homogeneous, saturated media, and assumes that groundwater flow is uniform and unidirectional. NAS consists of a combination of analytical and numerical solute transport models implemented in three main interactive modules to provide estimates for: (1) target source concentration required for a plume extent to contract to regulatory limits, (2) time required for NAPL contaminants in the source area to attenuate to a predetermined target source concentration, and (3) time required for a plume extent to contract to regulatory limits after source reduction. Natural attenuation processes that NAS models include advection, dispersion, sorption, non-aqueous phase liquid (NAPL) dissolution, and biodegradation. NAS determines redox zonation, and estimates and applies varied biodegradation rates from one redox zone to the next. Recently, NAS was enhanced to include petroleum hydrocarbons, chlorinated ethenes, chlorinated ethanes, chlorinated methanes, and chlorinated benzenes, or any user-defined contaminants (e.g., heavy metals, radioisotopes), and has included the capability to model co-mingled plumes. To enable comparison of remediation timeframe estimates between MNA and specific ERAs, NAS was modified to incorporate an estimation technique for timeframes associated with pump-and-treat remediation technology for comparison to, or in conjunction with, MNA. NAS also expanded analysis tools for improved performance assessment, as well as the assessment of sustainability of natural attenuation processes over time. A Department of Defense (DoD) Environmental Security Technology Certification Program (ESTCP) demonstration was undertaken to evaluate the capability of the NAS software to provide reasonable estimates of MNA cleanup timeframes in a variety of environments and sites throughout the United States. Overall, results suggest that NAS was satisfactory in meeting performance objectives set forth in the demonstration, and that because NAS is based on sound science, it can serve as an effective tool for decision-making and data analysis at a wide range of contaminated sites and is not limited to a small subset of “simple sites” because of its simplicity. At some sites, NAS-estimated timeframes were crucial for winning regulatory acceptance of MNA, with cost-benefit analyses providing estimates of savings associated with using MNA as a final remediation strategy. / Ph. D.