The findings of this study demonstrate that Dehalococcoides species are intimately involved in complete reductive detoxification of chlorinated ethenes and are widely distributed in anoxic sediments and aquifers, including non-contaminated (pristine) environments. Careful examination of enrichment culture dechlorination kinetics, 16S rRNA gene based analyses, and reductive dehalogenase gene targeted PCR approaches revealed that complete reductive dechlorination is carried out by multiple dechlorinators. Two new dechlorinating species were isolated from contaminated and non-contaminated site materials. The first new isolate, designated strain SZ, was isolated from PCE-to-ethene dechlorinating microcosms established with creek sediment. 16S rRNA gene sequence of the strain SZ indicates that the new isolate is affiliated with the genus Geobacter most closely related to G. thiogenes. Strain SZ is capable of stepwise dechlorination of PCE to cis-DCE, while the closest relatives were not able to dechlorinate PCE or TCE. Dechlorination of PCE or TCE by strain SZ was supported by acetate, hydrogen or pyruvate as electron donor. Chloroethene-dechlorinating populations have been shown to have distinct electron donor requirements. However, none of previously described chlorinated ethene degrading population can use both, acetate and hydrogen, as electron donors. PCE dechlorination by strain SZ uses both acetate and hydrogen as electron donors suggesting that the ability to versatile electron donor utilization may increase the efficiency of bioremediation approaches. Importantly, strain SZ reduced two environmental priority pollutants, PCE and U(VI) concomitantly and detected from both bio-stimulated chloroethene and uranium contaminated sites, strongly suggesting that strain SZ play a important roles in in-situ bioremediation of chloroethene and U(VI) contaminated sites. The second, a new Dehalococcoides species designated strain GT, was isolated from contaminated site materials. Strain GT uses trichloroethene (TCE), cis-DCE, 1,1-dichloroethene (1,1-DCE), and the human carcinogen vinyl chloride (VC) as growth supporting electron acceptors producing products ethene and inorganic chloride. The new isolate shares common traits of Dehalococcoides such as ampicillin resistance, strict hydrogen-dependent metabolism, and a low hydrogen consumption threshold concentration. Culture-dependent and independent, 16S rRNA gene and reductive dehalogenase gene targeted PCR approaches suggested culture purity.

Trichloroethene (TCE) and tetrachloroethene (PCE) are among the most commonly detected groundwater contaminants, and are often difficult to remediate due to their presence as dense non-aqueous phase liquids (DNAPLs) in the subsurface. The objective of this study was to assess the potential of using a passive in situ carbon/hydrogen releasing barrier system to bioremediate TCE-contaminated groundwater. The slow carbon/hydrogen releasing material would cause the aerobic cometabolism and reductive dechlorination of TCE in aquifer. The carbon/hydrogen releasing materials would release carbon when contacts with groundwater and release hydrogen after the anaerobic biodegradation of released carbon, thus cause the reductive dechlorination of TCE. Results from the microcosm study indicate that the addition of emulsified substrate, cane molasses, Simple GreenTM (a biodegradable surfactant), or lecithin would enhance the biodegradation rate of TCE under anaerobic conditions. However, addition of multivitamin would increase the bacterial population in the media but would not be able to enhance the TCE degradation rate. Results show that a significant pH drop was observed due to the production of organic acids after the aerobic biodegradation process of cane molasses and lecithin. This also caused the inhibition of microbial growth in microcosms. Results reveal that higher TCE removal efficiency was observed in microcosms with Simple GreenTM addition followed by the addition of cane molasses, lecithin, multivitamin, emulsified substrate, groundwater (without substrate addition). Results from the microcosm study indicate that the addition of emulsified substrate would enhance the biodegradation rate of TCE under anaerobic conditions. However, appearance of high nitrate concentration would inhibit the TCE degradation process due to the occurrence of denitrification. Compared with nitrate, high sulfate concentration would not have significant impact on the reductive dechlorination of TCE. Results reveal that higher TCE removal efficiency was observed in microcosms with emulsified substrate addition followed by the addition of high sulfate concentration, high nitriate concentration, groundwater (without substrate addition). Results from the gene analysis show that phenol monooxygenase, toluene monooxygenase, and toluene dioxygenase were observed in the microcosms with lecithin, cane molasses, Simple GreenTM, and emulsified substrate. This indicates that the addition of substrates would induce the potential of TCE-degrading enzyme. Addition of emulsified substrate and emulsified substrate in nitrate or sulfate-rich media would stimulate Dehalococcoides sp. to induce tceA, bvcA, and vcrA, enzymes for TCE reductive dechlorination.

The Port of Houston and the Houston Ship Channel (HSC) are highly industrialized areas along Galveston Bay, Texas. The HSC is highly polluted with a host of persistent organic pollutants, including dioxins. The main objective of this study was to determine the potential for in situ bioremediation in the HSC sediments. Our study focused on the bacterial group Dehalococcoides, since it is the only known group to reductively dechlorinate dioxins. Culture independent methods were used to determine the presence or absence of Dehalococcoides in HSC sediments. Molecular methods including PCR, cloning, restriction enzyme digest, and sequencing were used to determine the diversity of Dehalococcoides as well as total bacterial diversity in HSC sediments. The metabolically active members of the microbial community in HSC sediments were also determined using the same molecular methods as described above. Dehalococcoides was detected in every sediment core and at various depths within each core. Depths ranged from 1cm (SG-6) to 30cm (11261). Dehalococcoides diversity was centered on Dehalococcoides ethenogenes strain 195 and Dehalococcoides sp. strain CBDB1. Overall bacterial diversity in HSC sediments was dominated by Proteobacteria, especially Deltaproteobacteria, and Chloroflexi, which include Dehalococcoides. Total bacterial diversity at a wetlands control site was dominated by Betaproteobacteria and Acidobacteria. Deltaproteobacteria and Chloroflexi were determined to be the major metabolically active groups within the HSC sediments. These findings indicate that the HSC sediments have great potential for successful in situ bioremediation. These results also support the use of Dehalococcoides as a biological proxy for dioxin contamination.

Fe(II)-based degradative solidification/stabilization (Fe(II)-DS/S) technology is the modification of conventional solidification/stabilization (S/S). Inorganic pollutants are immobilized by Fe(II)-DS/S while organic pollutants are destroyed. Experimental studies were conducted to identify the active agents for Tetrachloroethylene (PCE) degradation as well as the conditions that enhance the formation of the active agents in the Fe(II)-DS/S system. PCE was chosen as a model chlorinated aliphatic hydrocarbon in this study. First, the conditions that lead to maximizing production of the active agents were identified by measuring the ability of various chemical mixtures to degrade PCE. Results showed that Fe(II), Fe(III), Ca, and Cl were the the important elements that affect degradation activity. Elemental compositions of the mixtures and the conditions affecting solid formation might be the important factors in determining how active solids are formed. Second, instrumental analyses (XRD, SEM, SEM-EDS) were used to identify minerals in chemical mixtures that have high activities. Results indicate that active agents for PCE degradation in Portland cement slurries and in cement extracts might be one of several AFm phases. However, systems without cement did not form the same solids as those with cement or cement extract. Ferrous hydroxide was identified as a major solid phase formed in systems without cement. Finally, the effect of using different types of ordinary Portland cement (OPC) on PCE degradation rate during Fe(II)-DS/S was examined and the solids were examined by instrumental analyses (XRD, SEM, SEM-EDS). Four different OPC (Txi, Lehigh, Quikrete, and Capitol) showed different PCE degradation behaviors. Pseudo first-order kinetics was observed for Capitol and Txi OPC and second-order kinetics was observed for Quikrete. In the case of Lehigh cement, pseudo first-order kinetics was observed in cement slurry and second-order kinetics in cement extract. Calcium aluminum hydroxide hydrates dominated solids made with Txi, Quikrete, and Lehigh cements and Friedel’s salt was the major phase found in solids made with Capitol cements. Fe tended to be associated with hexagonal thin plate particles, which were supposed to be a LDH.

For sites contaminated with chloroethene non-aqueousphase liquids, designing a remediation system that couples in situ chemical oxidation (ISCO) with potassium permanganate (KMnO4) and microbial dechlorination may be complicated because of the potentially adverse effects of ISCO on anaerobic bioremediation processes. Therefore, one-dimensional column studies were conducted to understand the effect of permanganate oxidation on tetrachloroethene (PCE) dechlorination by the anaerobic mixed culture KB-1. Following the confirmation of PCE dechlorination, KMnO4 was applied to all columns at a range of concentrations and application velocities to simulate varied distances from oxidant injection. Immediately following oxidation, reductive dechlorination was inhibited; however, after passing several pore volumes of sterile growth medium through the columns after oxidation, a rebound of PCE dechlorination activity was observed in every inoculated column without the need to reinoculate. The volume of medium required for a rebound of dechlorination activity differed from 1.1 to 8.1 pore volumes (at a groundwater velocity of 4 cm/d), depending on the specific condition of oxidant application.

Numerical models (GMS MODFLOW, SEAM3D, and SEAM3D Interface) were applied to simulate groundwater flow, petroleum hydrocarbon compound (PHC) transport and biodegradation, and the transport and biotransformation of chlorinated ethenes at Site FT-002 Plattsburgh Air Force Base (PAFB), NY. Site FT-002 was contaminated with waste jet fuel and chlorinated ethenes used as a fire source during fire fighting training. The results of groundwater analysis indicated that the aquifer exhibited aerobic, nitrate reducing, ferrogenic, sulfate reducing and methanogenic conditions due to the biodegradation of the PHCs. Additional groundwater analysis showed the biotransformation of TCE to DCE, VC, and ethene. A numerical model was developed to simulate and assess the extent to which reductive dechlorination and direct anaerobic oxidation were responsible for the biotransformation of the chlorinated ethenes. Reductive dechlorination accounted for the 100%, 98.3%, and 97.5% of the biotransformation of TCE, DCE, and VC respectively. Direct anaerobic oxidation accounted for 1.7% and 2.5% of the biotransformation of DCE and VC respectively. Though direct anaerobic oxidation only accounted for a small percentage of total biotransformation it was necessary to fully develop the biotransformation of the DCE and VC in the ferrogenic zone. This study focused on the mechanisms responsible for the biotransformation of chlorinated ethenes, specifically reductive dechlorination and direct anaerobic oxidation. By further defining the NAPL source and initial conditions it could be used as a tool to accurately predict the monitored natural attenuation (MNA) of the FT-002 contaminant plume. / Master of Science

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.

During the Fukushima Daiichi power plant incident sea water was used in an attempt to cool reactor Unit 3. Since sea water contains an excessive amount of chloride, 36Cl has likely been formed and spread in the environment. Because of the long residence time and the presumed high mobility in water there is an increased interest to learn more about the biogeochemical cycle of chlorine from a radiation risk assessment perspective. Chlorine occurs in inorganic form as chloride (Clin) or bound to organic matter as organic chlorine (Clorg) and is commonly found in the environment due to both anthropogenic and natural processes. Though there are still uncertainties regarding all of the components of the chlorine cycle in soil, the chlorination of organic matter has been exemplified by research. The reverse process, Clorg mineralizing into Clin, has however not been thoroughly investigated. For this study the objective was to observe at what rate Clorg mineralizes into Clin, this by using 36Cl as a tracer in forest soil. 36Cl was added to the soil and 36Clorg was formed over a period of approximately 100 days. After chlorination the samples were incubated in different conditions and the amount of 36Clorg was observed over a period of time (180 days). The result showed no evident dechlorination during the experiment period which indicates that Clorg can be stable in the organic horizon in forest soil.

abstract: Trichloroethene (TCE) is a ubiquitous soil and groundwater contaminant. The most common bioremediation approach for TCE relies on the process of reductive dechlorination by Dehalococcoides mccartyi. D. mccartyi use TCE, dichloroethene, and vinyl chloride as electron acceptors and hydrogen as an electron donor. At contaminated sites, reductive dechlorination is typically promoted by adding a fermentable substrate, which is broken down to short chain fatty acids, simple alcohols, and hydrogen. This study explored microbial chain elongation (MCE), instead of fermentation, to promote TCE reductive dechlorination. In MCE, microbes use simple substrates (e.g., acetate, ethanol) to build medium chain fatty acids and also produce hydrogen during this process. Soil microcosm using TCE and acetate and ethanol as MCE substrates were established under anaerobic conditions. In soil microcosms with synthetic groundwater and natural groundwater, ethene was the main product from TCE reductive dechlorination and butyrate and hydrogen were the main products from MCE. Transfer microcosms using TCE and either acetate and ethanol, ethanol, or acetate were also established. The transfers with TCE and ethanol showed the faster rates of reductive dechlorination and produced more elongated products (i.e., hexanoate). The microbial groups enriched in the soil microcosms likely responsible for chain elongation were most similar to Clostridium genus. These investigations showed the potential for synergistic microbial chain elongation and reductive dechlorination of chlorinated ethenes. / Dissertation/Thesis / Masters Thesis Civil, Environmental and Sustainable Engineering 2019

The goal of this study was to use molecular biology techniques to access and monitor the efficacy of bioremediation on a trichloroethene (TCE) polluted site. We added emulsified hydrogen releasing materials to stimulate onsite microbial growth and the biodegradation of TCE. This process was known as enhanced bioremediation. In this study, there were two bioremediation sites had been treated anaerobically. Groundwater samples were taken periodically for microbial analysis. Denaturing gradient gel electrophoresis (DGGE) was used to evaluate the variations in microbial community structures during the in situ groundwater remediation. The DGGE DNA bandings were sequenced to determine the 16S rRNA gene sequences and identify the dominate bacterial species. In addition, we used Dehalococcoides spp. 16S rRNA genes as the targets to do real-time PCR. Results show that the emulsified hydrogen releasing materials could enhance anaerobic reductive dechlorination. After addition of emulsified hydrogen releasing materials, we found that the volatile organic compounds concentrations (i.e., TCE, 1, 1-DCE and VC) were decreased. In microbial analysis, the diversities of the microbial community were increased after nutrient supplement. According to the DNA sequencing results, there were 31 bacterial species had been found that related to TCE degradation (i.e., Acidovorax sp., Burkholderiales, Pseudomonas sp., £]-proteobacterium, Comamonadaceae, Iron-reducing bacterium, Hydrogenophilaceae, Clostridium sp., Geobacter sp., Rhodoferax ferrireducens, Dehalospirillum multivorans and Dehalococcoides spp.). Dehalococcoides spp. can be used as a biomarker to evaluate the efficacy of anaerobic bioremediation on a TCE contaminated site. Therefore, we quantified Dehalococcoides populations to explain the capacity of bioremediation after addition of emulsified hydrogen releasing materials to groundwater. Results reveal that Dehalococcoides cell numbers of site A were 4.47¡Ñ103-8.26¡Ñ104 CFU/liter, site B were 4.60¡Ñ102-9.31¡Ñ107 CFU/liter. This data indicated that the addition of emulsified substrate would increase the growth of total Dehalococcoides population under anaerobic conditions. Overall, results from this study demonstrated that the microbial analysis and quantities of Dehalococcoides at different time points can provide useful information to proceed with bioremediation methods.