A 1,1,1-trichloroethane-degrading anaerobic mixed microbial culture enhances biotransformation of mixtures of chlorinated ethenes and ethanes

Molecular techniques in the biotechnological fight against halogenated compounds in anoxic environments

Microbial treatment of environmental contamination by anthropogenic halogenated organic compounds has become popular in recent decades, especially in the subsurface environments. Molecular techniques such as polymerase chain reaction-based fingerprinting methods have been extensively used to closely monitor the presence and activities of dehalogenating microbes, which also lead to the discovery of new dehalogenating bacteria and novel functional genes. Nowadays, traditional molecular techniques are being further developed and optimized for higher sensitivity, specificity, and accuracy to better fit the contexts of dehalogenation. On the other hand, newly developed high throughput techniques, such as microarray and next-generation sequencing, provide unsurpassed detection ability, which has enabled large-scale comparative genomic and whole-genome transcriptomic analysis. The aim of this review is to summarize applications of various molecular tools in the field of microbially mediated dehalogenation of various halogenated organic compounds. It is expected that traditional molecular techniques and nucleic-acid-based biomarkers will still be favoured in the foreseeable future because of relative low costs and high flexibility. Collective analyses of metagenomic sequencing data are still in need of information from individual dehalogenating strains and functional reductive dehalogenase genes in order to draw reliable conclusions.

Temporal variations in natural attenuation of chlorinated aliphatic hydrocarbons in eutrophic river sediments impacted by a contaminated groundwater plume

Chlorinated aliphatic hydrocarbons (CAHs) often discharge into rivers as contaminated groundwater baseflow. Biotransformation, sorption and dilution of CAHs in the impacted river sediments have been reported to reduce discharge, but the effect of temporal variations in environmental conditions on the occurrence and extent of those processes in river sediments is largely unknown. We monitored the reduction of CAH discharge into the Zenne River during a 21-month period. Despite a relatively stable influx of CAHs from the groundwater, the total reduction in CAH discharge from 120 to 20 cm depth in the river sediments, on average 74 ± 21%, showed moderate to large temporal variations, depending on the riverbed location. High organic carbon and anaerobic conditions in the river sediments allowed microbial reductive dechlorination of both chlorinated ethenes and chlorinated ethanes. δ(13)C values of the CAHs showed that this biotransformation was remarkably stable over time, despite fluctuating pore water temperatures. Daughter products of the CAHs, however, were not detected in stoichiometric amounts and suggested the co-occurrence of a physical process reducing the concentrations of CAHs in the riverbed. This process was the main process causing temporal variations in natural attenuation of the CAHs and was most likely dilution by surface water-mixing. However, higher spatial resolution monitoring of flow transients in the riverbed is required to prove dilution contributions due to dynamic surface water-groundwater flow exchanges. δ(13)C values and a site-specific isotope enrichment factor for reductive dechlorination of the main groundwater pollutant vinyl chloride (VC) allowed assessment of changes over time in the extent of both biotransformation and dilution of VC for different scenarios in which those processes either occurred consecutively or simultaneously between 120 and 20 cm depth in the riverbed. The extent of reductive dechlorination of VC ranged from 27 to 89% and differed spatially but was remarkably stable over time, whereas the extent of VC reduction by dilution ranged from 6 to 94%, showed large temporal variations, and was often the main process contributing to the reduction of VC discharge into the river.

Quantifying the effects of 1,1,1-trichloroethane and 1,1-dichloroethane on chlorinated ethene reductive dehalogenases

Mixtures of chlorinated ethenes and ethanes are often found at contaminated sites. In this study, we undertook a systematic investigation of the inhibitory effects of 1,1,1-trichloroethane (1,1,1-TCA) and 1,1-dichloroethane (1,1-DCA) on chlorinated ethene dechlorination in three distinct Dehalococcoides-containing consortia. To focus on inhibition acting directly on the reductive dehalogenases, dechlorination assays used cell-free extracts prepared from cultures actively dechlorinating trichloroethene (TCE) to ethene. The dechlorination assays were initiated with TCE, cis-1,2-dichloroethene (cDCE), or vinyl chloride (VC) as substrates and either 1,1,1-TCA or 1,1-DCA as potential inhibitors. 1,1,1-TCA inhibited VC dechlorination similarly in cell suspension and cell-free extract assays, implicating an effect on the VC reductases associated with the dechlorination of VC to nontoxic ethene. Concentrations of 1,1,1-TCA in the range of 30-270 μg/L reduced VC dechlorination rates by approximately 50% relative to conditions without 1,1,1-TCA. 1,1,1-TCA also inhibited reductive dehalogenases involved in TCE and cDCE dechlorination. In contrast, 1,1-DCA had no pronounced inhibitory effects on chlorinated ethene reductive dehalogenases, indicating that removal of 1,1,1-TCA via reductive dechlorination to 1,1-DCA is a viable strategy to relieve inhibition.

Follow-up study on the effects on well chemistry from biological and chemical remediation of chlorinated solvents

The enduring effects of injected materials used for the remediation of chlorinated solvents were examined. Approximately two years previous to this study, four different remediation methods were tested in an area located southeast of Oklahoma City, OK. These methods included bioremediation under both anaerobic and aerobic conditions and chemical remediation using Fenton's reagent or KMnO(4). A series of water quality tests performed in this investigation revealed that the bioremediation processes did not introduce any unexpected chemistry. However, the wells that were treated anaerobically still had water with a negative oxidation-reduction potential and had no recontamination with migrating trichloroethylene as opposed to the aerobic wells that had both positive redox potentials and trichloroethylene present. Also, chemical treatment using Fenton's reagent did not result in any long-term changes in the well chemistry, with the exception of inducing a slight acidity. This is due to the facts that addition of iron into the aquifer that is already in contact with iron-rich clay soil had little long-term effects and the radical chemistry with hydrogen peroxide is short-lived due to its reactivity. KMnO(4)-based remediation results in deposition of new materials containing manganese in elevated oxidation states that may provide long-term protection against the build up of chlorinated organic compounds.

Natural and enhanced anaerobic degradation of 1,1,1-trichloroethane and its degradation products in the subsurface--a critical review

1,1,1-Trichloroethane (TCA) in groundwater is susceptible to a variety of natural degradation mechanisms. Evidence of intrinsic decay of TCA in aquifers is commonly observed; however, TCA remains a persistent pollutant at many sites and some of the daughter products that accumulate from intrinsic decay of TCA have been determined to be more toxic than the parent compound. Research advances from the past decade indicate that in situ enhanced reductive dechlorination (ERD) offers promise as a cost-effective solution toward the cleanup of groundwater contaminated with TCA and its transformation daughter products. Laboratory studies have demonstrated that pure or mixed cultures containing certain Dehalobacter (Dhb) bacteria can catalyze respiratory dechlorination of TCA and 1,1-dichloroethane (1,1-DCA) to monochloroethane (CA) in groundwater systems. 16S rRNA Dhb gene probes have been used as biomarkers in groundwater samples to both assess ERD potential and quantify growth of Dhb in ERD applications at TCA sites. Laboratory findings suggest that iron-bearing minerals and methanogenic bacteria that co-occur in reduced aquifers may synergistically affect dechlorination of TCA. Despite these advances, a number of significant challenges remain, including an inability of any known cultures to completely dechlorinate TCA to ethane. CA is commonly observed as a terminal product of the biological reductive dechlorination of TCA and 1,1-DCA. Also important is the lack of rigorous field studies demonstrating the utility of bioaugmentation with Dhb cultures for remediation of TCA in the field. In this paper we review the state-of-the-science of TCA degradation in aquifers, examining results from both laboratory experiments and twenty-two field case studies, focusing on the capabilities and limits of ERD technology, and identifying aspects of the technology that warrant further development.

Insights into enzyme kinetics of chloroethane biodegradation using compound specific stable isotopes

While compound specific isotope analysis (CSIA) has been used extensively to investigate remediation of chlorinated ethenes, to date considerably less information is available on its applicability to chlorinated ethanes. In this study, biodegradation of 1,1,1-trichloroethane (1,1,1-TCA) and 1,1-dichloroethane (1,1-DCA) was carried out by a Dehalobacter-containing mixed culture. Carbon isotope fractionation factors (ε) measured during whole cell degradation demonstrated that values for 1,1,1-TCA and 1,1-DCA (-1.8‰ and -10.5‰, respectively) were significantly smaller than values reported for abiotic reductive dechlorination of these same compounds. Similar results were found in experiments degrading these two priority pollutants by cell free extracts (CFE) where values of -0.8‰ and -7.9‰, respectively, were observed. For 1,1,1-TCA in particular, the large kinetic isotope effect expected for cleavage of a C-Cl bond was almost completely masked during biodegradation by both whole cells and CFE. Comparison to previous studies demonstrates that these patterns of isotopic fractionation are not attributable to transport effects across the cell membrane, as had been seen for other compounds such as PCE. In contrast these results reflect significant differences in the kinetics of the enzymes catalyzing chlorinated ethane degradation.

Chloroform respiration to dichloromethane by a Dehalobacter population

Chloroform (CF), or trichloromethane, is an ubiquitous environmental pollutant because of its widespread industrial use, historically poor disposal and recalcitrance to biodegradation. Chloroform is a potent inhibitor of metabolism and no known organism uses it as a growth substrate. We discovered that CF was rapidly and sustainably dechlorinated in the course of investigating anaerobic reductive dechlorination of 1,1,1-trichloroethane in a Dehalobacter-containing culture. Like 1,1,1-trichloroethane dechlorination in this culture, CF dechlorination was a growth-linked respiratory process, requiring H(2) as an electron donor and CF as an electron acceptor. Moreover, the same specific reductive dehalogenase likely catalyzed both reactions. This Dehalobacter population appears specialized for substrates with three halogen substituents on the same carbon atom, with widespread implications for bioremediation.

1,1,1-trichloroethane and 1,1-dichloroethane reductive dechlorination kinetics and co-contaminant effects in a Dehalobacter-containing mixed culture

1,1,1-Trichloroethane (1,1,1-TCA) is a common groundwater contaminant that can be reductively dechlorinated to 1,1-dichloroethane (1,1-DCA) and monochloroethane, and can support the growth of certain dehalorespiring strains of Dehalobacter We used reductive dehalogenase cell-free extract assays (with reduced methyl viologen) and whole cell suspension dechlorination assays (with hydrogen) and a Dehalobacter-containing enrichment culture to explore the kinetics of l,1,1-TCA and 1,1-DCA reductive dechlorination in the presence of the common co-contaminants trichloroethene (TCE), cis-dichloroethene (cDCE), and vinyl chloride (VC). These chlorinated ethenes were most significant inhibitors of 1,1,1-TCA dechlorination in cell-free extracts, indicating direct effects on the reductive dehalogenase enzyme(s). The inhibition was present but less pronounced in whole cell suspension assays. None of the chlorinated ethenes inhibited 1,1-DCA dechlorination in cell-free extract assays, yet cDCE and particularly VC were inhibitors in whole cell assays, indicating an effect on Dehalobacter, but not on the dehalogenase enzyme(s). Marked differences in kinetic parameters for 1,1,1-TCA and 1,1-DCA, and an uncoupling of these two activities in cultures grown on 1,1-DCA compared to those grown on 1,1,1-TCA was strong evidence for the existence of distinct 1,1,1-TCA and 1,1-DCA reductive dehalogenase enzymes.

Characterization of a Dehalobacter coculture that dechlorinates 1,2-dichloroethane to ethene and identification of the putative reductive dehalogenase gene

Dehalobacter and "Dehalococcoides" spp. were previously shown to be involved in the biotransformation of 1,1,2-trichloroethane (1,1,2-TCA) and 1,2-dichloroethane (1,2-DCA) to ethene in a mixed anaerobic enrichment culture. Here we report the further enrichment and characterization of a Dehalobacter sp. from this mixed culture in coculture with an Acetobacterium sp. Through a series of serial transfers and dilutions with acetate, H(2), and 1,2-DCA, a stable coculture of Acetobacterium and Dehalobacter spp. was obtained, where Dehalobacter grew during dechlorination. The isolated Acetobacterium strain did not dechlorinate 1,2-DCA. Quantitative PCR with specific primers showed that Dehalobacter cells did not grow in the absence of a chlorinated electron acceptor and that the growth yield with 1,2-DCA was 6.9 (+/-0.7) x 10(7) 16S rRNA gene copies/mumol 1,2-DCA degraded. PCR with degenerate primers targeting reductive dehalogenase genes detected three distinct Dehalobacter/Desulfitobacterium-type sequences in the mixed-parent culture, but only one of these was present in the 1,2-DCA-H(2) coculture. Reverse transcriptase PCR revealed the transcription of this dehalogenase gene specifically during the dechlorination of 1,2-DCA. The 1,2-DCA-H(2) coculture could dechlorinate 1,2-DCA but not 1,1,2-TCA, nor could it dechlorinate chlorinated ethenes. As a collective, the genus Dehalobacter has been show to dechlorinate many diverse compounds, but individual species seem to each have a narrow substrate range.