Reductive dechlorination of tetrachloroethene to cis-1, 2-dichloroethene by a thermophilic anaerobic enrichment culture

Effect of wine pomace extract on dechlorination of chloroethenes in soil suspension

Chloroethenes are widely used as solvent in the metal industry and the dry cleaning industry, but their spillage into soil and groundwater due to improper handling has negatively impacted human health. Bioremediation using microorganisms is one of the technologies to clean up soil and groundwater contaminated with chloroethenes. In this study, we examined the bioremediation of chloroethene-contaminated soil using wine pomace extract (WPE). WPE is a liquid containing seven major carboxylic acids and other substances extracted from grape pomace produced in winemaking. WPE clearly promoted the anaerobic bioremediation of chloroethenes. In the tetrachloroethene (PCE) degradation test that used fractions derived from WPE, the water-eluted fraction containing L-lactic acid, L-tartaric acid, and others promoted the dechlorination of PCE, whereas the methanol-eluted fraction containing mainly syringic acid did not. In another PCE degradation test that used L-lactic acid, L-tartaric acid, and syringic acid test solutions, L-lactic acid and L-tartaric acid enhanced the dechlorination of PCE, but syringic acid did not. The results suggest that L-lactic acid and L-tartaric acid in WPE function as hydrogen donors in the anaerobic microbial degradation of chloroethene. This technology realizes environmental remediation through the effective use of food by-products.

Microbiome reengineering by four environmental factors for the rapid biodegradation of trichloroethylene

Trichloroethylene (TCE) was once a widely applied industrial solvent, but is now an infamous contaminant in groundwater. Although anaerobic reductive dechlorination is considered a greener remediation approach, the accumulation of toxic intermediates, such as vinyl chloride (VC), and a longer remediation period are highly concerning. Biostimulation and bioaugmentation have been developed to solve these problems. The former method may not be effective, and the latter may introduce foreign genes. Here, we propose a new approach by applying environmental stresses to reshape the indigenous microbiome. In this study, by using the Taguchi method, the effects of heating, pH, salinity, and desiccation were systematically examined. The optimum conditions were defined as 50 °C, pH 9, 3.50% salinity (w/v), and 21% volumetric water content (θ_W). The top performing group, G7, can complete the conversion of 11.81 mg/L TCE into ethene in 3.0 days with a 1.23% abundance of Dehalococcoides mccartyi 195 (Dhc 195). Redundancy analysis confirmed that temperature and salinity were the predominant factors in reorganizing the microbiomes. The microbiome structure and its effectiveness can last for at least 90 d. The repetitive selection conditions and sustainable degradation capability strongly supported that microbiome reengineering is feasible for the rapid bioremediation of TCE-contaminated environmental matrices.

Mini-review: effect of temperature on microbial reductive dehalogenation of chlorinated ethenes: a review

Temperature is a key factor affecting microbial activity and ecology. An increase in temperature generally increases rates of microbial processes up to a certain threshold, above which rates decline rapidly. In the subsurface, temperature of groundwater is usually stable and related to the annual average temperature at the surface. However, anthropogenic activities related to the use of the subsurface, e.g. for thermal heat management, foremost heat storage, will affect the temperature of groundwater locally. This mini-review intends to summarize the current knowledge on reductive dehalogenation activities of the chlorinated ethenes, common urban groundwater contaminants, at different temperatures. This includes an overview of activity and dehalogenation extent at different temperatures in laboratory isolates and enrichment cultures, the effect of shifts in temperature in micro- and mesocosm studies as well as observed biotransformation at different natural and induced temperatures at contaminated field sites. Furthermore, we address indirect effects on biotransformation, e.g. changes in fermentation, methanogenesis and sulfate reduction as competing or synergetic microbial processes. Finally, we address the current gaps in knowledge regarding bioremediation of chlorinated ethenes, microbial community shifts and bottlenecks for active combination with thermal energy storage, and necessities for bioaugmentation and/or natural re-populations after exposure to high temperature.

Organohalide respiration in pristine environments: implications for the natural halogen cycle

Halogenated organic compounds, also termed organohalogens, were initially considered to be of almost exclusively anthropogenic origin. However, over 5000 naturally synthesized organohalogens are known today. This has also fuelled the hypothesis that the natural and ancient origin of organohalogens could have primed development of metabolic machineries for their degradation, especially in microorganisms. Among these, a special group of anaerobic microorganisms was discovered that could conserve energy by reducing organohalogens as terminal electron acceptor in a process termed organohalide respiration. Originally discovered in a quest for biodegradation of anthropogenic organohalogens, these organohalide-respiring bacteria (OHRB) were soon found to reside in pristine environments, such as the deep subseafloor and Arctic tundra soil with limited/no connections to anthropogenic activities. As such, accumulating evidence suggests an important role of OHRB in local natural halogen cycles, presumably taking advantage of natural organohalogens. In this minireview, we integrate current knowledge regarding the natural origin and occurrence of industrially important organohalogens and the evolution and spread of OHRB, and describe potential implications for natural halogen and carbon cycles.

Effects of elevated temperature on Dehalococcoides dechlorination performance and DNA and RNA biomarker abundance

Coupling thermal treatment with microbial reductive dechlorination is a promising remedy for tetrachloroethene (PCE) and trichloroethene (TCE) contaminated source zones. Laboratory experiments evaluated Dehalococcoides (Dhc) dechlorination performance, viability, and biomarker gene (DNA) and transcript (mRNA) abundances during exposure to elevated temperatures. The PCE-dechlorinating consortia BDI and OW produced ethene when incubated at temperatures of 30 °C, but vinyl chloride (VC) accumulated when cultures were incubated at 35 or 40 °C. Cultures incubated at 40 °C for less than 49 days resumed VC dechlorination following cooling; however, incubation at 45 °C resulted in complete loss of dechlorination activity. Dhc 16S rRNA, bvcA, and vcrA gene abundances in cultures showing complete dechlorination to ethene at 30 °C exceeded those measured in cultures incubated at higher temperatures, consistent with observed dechlorination activities. Conversely, biomarker gene transcript abundances per cell in cultures incubated at 35 and 40 °C were generally at least one order-of-magnitude greater than those measured in ethene-producing cultures incubated at 30 °C. Even in cultures accumulating VC, transcription of the vcrA gene, which is implicated in VC-to-ethene dechlorination, was up-regulated. Temperature stress caused the up-regulation of Dhc reductive dehalogenase gene expression indicating that Dhc gene expression measurements should be interpreted cautiously as Dhc biomarker gene transcript abundances may not correlate with dechlorination activity.

Aerobic biodegradation of dichloroethenes by indigenous bacteria isolated from contaminated sites in Africa

The widespread use of tetrachloroethene (PCE) and trichloroethene (TCE) as dry cleaning solvents and degreasing agents for military and industrial applications has resulted in significant environmental contamination worldwide. Anaerobic biotransformation of PCE and TCE through reductive dechlorination frequently lead to the accumulation of dichloroethenes (DCEs), thus limiting the use of reductive dechlorination for the biotransformation of the compounds. In this study, seven bacteria indigenous to contaminated sites in Africa were characterized for DCE degradation under aerobic conditions. The specific growth rate constants of the bacterial isolates ranged between 0.346-0.552 d(-1) and 0.461-0.667 d(-1) in cis-DCE and trans-DCE, respectively. Gas chromatographic analysis revealed that up to 75% of the compounds were degraded within seven days with the degradation rate constants ranging between 0.167 and 0.198 d(-1). The two compounds were also observed to be significantly degraded, simultaneously, rather than sequentially, when present as a mixture. Phylogenetic analysis of the 16S rRNA gene sequences of the bacterial isolates revealed their identity as well as their relation to other environmentally-important bacteria. The observed biodegradation of DCEs may contribute to PCE and TCE removal at the aerobic fringe of groundwater plumes undergoing reductive dechlorination in contaminated sites.

Temperature dependence of anaerobic TCE-dechlorination in a highly enriched Dehalococcoides-containing culture

Temperature dependence of reductive trichloroethene (TCE) dechlorination was investigated in an enrichment culture (KB-1), using lactate or propionate as electron donors at a temperature interval from 4 to 60 degrees C. Dechlorination was complete to ethene at temperatures between 10 and 30 degrees C (lactate-amended) and between 15 and 30 degrees C (propionate-amended). Dechlorination stalled at cis-1,2-dichloroethene (cDCE) at 4 degrees C (lactate-amended), at and below 10 degrees C (propionate-amended), and at 40 degrees C with both electron donors. No dechlorination of TCE was observed at 50 and 60 degrees C. Concentrations of Dehalococcoides had increased or remained constant after 15 days of incubation at temperatures involving complete dechlorination to ethene. Temperature dependence of dechlorination rates was compared using zero order degradation kinetics and a Monod growth-rate model for multiple electron acceptor usage with competition. Maximum growth rates (mu) and zero order degradation rates were highest for TCE dechlorination at 30 degrees C with lactate as substrate (mu(TCE) of 7.00+/-0.14 days(-1)). In general, maximum growth rates and dechlorination rates of TCE were up to an order of magnitude higher than rates for utilization of cis-dichloroethene (cDCE, mu(c)(DCE) up to 0.17+/-0.02 days(-1)) and vinyl chloride (VC, mu(VC) up to 0.52+/-0.09 days(-1)). Temperature dependence of maximum growth rates and degradation rates of cDCE and VC were similar and highest at 15-30 degrees C, with growth rates on cDCE being lower than on VC. This study demonstrates that bioaugmentation of chlorinated ethene sites may be more efficient at elevated temperatures.

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

1,1,1-trichloroethane (1,1,1-TCA) is a common groundwater pollutant as a result of improper disposal and accidental spills. It is often found as a cocontaminant with trichloroethene (TCE) and inhibits some TCE-degrading microorganisms. 1,1,1-TCA removal is therefore required for effective bioremediation of sites contaminated with mixed chlorinated organics. This study characterized MS, a 1,1,1-TCA-degrading, anaerobic, mixed microbial culture derived from a 1,1,1-TCA-contaminated site in the northeastern United States. MS reductively dechlorinated 1,1,1-TCA to 1,1-dichloroethane (1,1-DCA) and then to monochloroethane (CA) but not further. Cloning of bacterial 16S rRNA genes revealed among other organisms the presence of a Dehalobacter sp. and a Desulfovibrio sp., which are both phylogenetically related to known dehalorespiring strains. Monitoring of these populations with species-specific quantitative PCR during degradation of 1,1,1-TCA and 1,1-DCA showed that Dehalobacter proliferated during dechlorination. Dehalobacter growth was dechlorination dependent, whereas Desulfovibrio growth was dechlorination independent. Experiments were also performed to test whether MS could enhance TCE degradation in the presence of inhibiting levels of 1,1,1-TCA. Dechlorination of cis-dichloroethene (cDCE) and vinyl chloride (VC) in KB-1, a chloroethene-degrading culture used for bioaugmentation, was inhibited with 1,1,1-TCA present. When KB-1 and MS were coinoculated, degradation of cDCE and VC to ethene proceeded as soon as the 1,1,1-TCA was dechlorinated to 1,1-DCA by MS. This demonstrated the potential application of the MS and KB-1 cultures for cobioaugmentation of sites cocontaminated with 1,1,1-TCA and TCE.

Anaerobic microbial dehalogenation

The natural production and anthropogenic release of halogenated hydrocarbons into the environment has been the likely driving force for the evolution of an unexpectedly high microbial capacity to dehalogenate different classes of xenobiotic haloorganics. This contribution provides an update on the current knowledge on metabolic and phylogenetic diversity of anaerobic microorganisms that are capable of dehalogenating--or completely mineralizing--halogenated hydrocarbons by fermentative, oxidative, or reductive pathways. In particular, research of the past decade has focused on halorespiring anaerobes, which couple the dehalogenation by dedicated enzyme systems to the generation of energy by electron transport-driven phosphorylation. Significant advances in the biochemistry and molecular genetics of degradation pathways have revealed mechanistic and structural similarities between dehalogenating enzymes from phylogenetically distinct anaerobes. The availability of two almost complete genome sequences of halorespiring isolates recently enabled comparative and functional genomics approaches, setting the stage for the further exploitation of halorespiring and other anaerobic dehalogenating microbes as dedicated degraders in biological remediation processes.

Quantifying the effects of fumarate on in situ reductive dechlorination rates

In situ methods are needed to evaluate the effectiveness of chemical amendments at enhancing reductive dechlorination rates in groundwater that is contaminated with the priority pollutant, trichloroethene (TCE). In this communication, a method that utilizes single-well, "push-pull" tests to quantify the effects of chemical amendments on in situ reductive dechlorination rates is presented and demonstrated. Five push-pull tests were conducted in each of five monitoring wells located in a TCE-contaminated aquifer at the site of a former chemical manufacturing facility. Rates for the reductive dechlorination of the fluorinated TCE-surrogate, trichlorofluoroethene (TCFE), were measured before (test 1) and after (test 5) three successive additions (tests 2-4) of fumarate. Fumarate was selected to stimulate the growth and activity of indigenous microorganisms with the metabolic capability to reduce TCFE and TCE. In three wells, first-order rate constants for the reductive dechlorination of TCFE increased by 8.2-92 times following fumarate additions. In two wells, reductive dechlorination of TCFE was observed after fumarate additions but not before. The transformation behavior of fumarate was also monitored following each fumarate addition. Correlations between the reductive dechlorination of TCFE and the reduction of fumarate to succinate were observed, indicating that these reactions were supported by similar biogeochemical conditions at this site.

Phylogenetic analysis of bacterial populations in an anaerobic microbial consortium capable of degrading saturation concentrations of tetrachloroethylene

An anaerobic microbial consortium able to biodegrade saturation levels of perchloroethylene (PCE) in a column containing a source zone of PCE was examined phylogenetically to determine microbial community structure and spatial variation in relation to the PCE source. The consortium was comprised of at least 34 members with 7 organisms sharing affiliations with known respiratory or cometabolic dechlorinators. Seven other organisms had their closest phylogenetic relative detected in other environments containing chlorinated compounds. Based on denaturing gradient gel electrophoresis, significant Bacteria were Dehalococcoides ethenogenes, Shewanella putrefaciens, and an Acetobacterium species. Spatial variations in community structure of the consortium relative to the PCE source zone were observed. A Pseudomonas species was predominant in a zone 30 cm from the PCE source. A Methanothrix species was predominant at points over 85 cm from the source zone. A Trichlorobacter species was detected where PCE concentrations were highest, up to 85 cm from the PCE source, whereas D. ethenogenes was ubiquitous to over 128 cm from the PCE source.

Direct cloning from enrichment cultures, a reliable strategy for isolation of complete operons and genes from microbial consortia

Enrichment cultures of microbial consortia enable the diverse metabolic and catabolic activities of these populations to be studied on a molecular level and to be explored as potential sources for biotechnology processes. We have used a combined approach of enrichment culture and direct cloning to construct cosmid libraries with large (>30-kb) inserts from microbial consortia. Enrichment cultures were inoculated with samples from five environments, and high amounts of avidin were added to the cultures to favor growth of biotin-producing microbes. DNA was extracted from three of these enrichment cultures and used to construct cosmid libraries; each library consisted of between 6,000 and 35,000 clones, with an average insert size of 30 to 40 kb. The inserts contained a diverse population of genomic DNA fragments isolated from the consortia organisms. These three libraries were used to complement the Escherichia coli biotin auxotrophic strain ATCC 33767 Delta(bio-uvrB). Initial screens resulted in the isolation of seven different complementing cosmid clones, carrying biotin biosynthesis operons. Biotin biosynthesis capabilities and growth under defined conditions of four of these clones were studied. Biotin measured in the different culture supernatants ranged from 42 to 3,800 pg/ml/optical density unit. Sequencing the identified biotin synthesis genes revealed high similarities to bio operons from gram-negative bacteria. In addition, random sequencing identified other interesting open reading frames, as well as two operons, the histidine utilization operon (hut), and the cluster of genes involved in biosynthesis of molybdopterin cofactors in bacteria (moaABCDE).

Halorespiring bacteria-molecular characterization and detection

Recently, a rapidly increasing number of bacteria has been isolated that is able to couple the reductive dehalogenation of various halogenated aromatic and aliphatic compounds like chlorophenols and tetrachloroethene to energy conservation by electron-transport-coupled phosphorylation. The potential of these halorespiring bacteria for innovative clean-up strategies of polluted anoxic environments has greatly stimulated efforts to unravel the molecular basis of the novel respiratory chains they possess. The thorough characterization of halorespiratory key components at the physiological, biochemical and molecular genetic level has revealed both structural and functional similarity of chloroaryl- and chloroalkyl-respiratory chains from different phylogenetically distinct microorganisms. The reductive dehalogenases from halorespiring bacteria were found to comprise a novel class of corrinoid-containing Fe/S-proteins. Sensitive molecular methods for monitoring both presence and fate of halorespiring bacteria have been developed, which will be instrumental for the design and maintenance of optimised in situ bioremediation processes.