Transition from cometabolic to growth-linked biodegradation of vinyl chloride by a Pseudomonas sp. isolated on ethene

Contrasting regulatory effects of organic acids on aerobic vinyl chloride biodegradation in etheneotrophs

Vinyl chloride (VC) is a common groundwater pollutant generated during anaerobic biodegradation of chlorinated solvents (e.g., trichloroethene (TCE) or tetrachloroethene (PCE)). Aerobic VC biodegradation by etheneotrophs can support anaerobic PCE and TCE bioremediation to achieve complete removal in situ. However, anaerobic bioremediation strategies necessitate biostimulation with electron donors that are fermented in situ, generating organic acids that could influence aerobic VC biodegradation processes. We examined the effect of organic acids (lactate, acetate, propionate, and butyrate) on aerobic VC biodegradation by VC-assimilating etheneotrophs Mycobacterium strain JS60 and Nocardioides strain JS614. Strain JS60 grew on all organic acids tested, while strain JS614 did not respond to lactate. VC-grown strain JS60 fed VC and one or more organic acids showed carbon catabolite repression (CCR) behavior where VC biodegradation occurred only after organic acids were depleted. In contrast, CCR was not evident in VC-grown strain JS614, which degraded VC and organic acids simultaneously. Acetate-grown JS60 showed similar CCR behavior when fed VC and a single organic acid, except that extended lag periods (5-12 days) occurred before VC oxidation ensued. Acetate-grown JS614 fed VC and either acetate or butyrate displayed 5-8 day lag periods before simultaneous VC and organic acid biodegradation. In contrast, acetate-grown JS614 degraded VC and propionate without a significant lag, suggesting a regulatory link between propionate and VC oxidation in JS614. Different global regulatory mechanisms controlling VC biodegradation in the presence of organic acids in etheneotrophs have implications for developing combined anaerobic-aerobic bioremediation strategies at chlorinated ethene-contaminated sites. KEY POINTS: • With organic acids present, VC utilization was repressed in JS60, but not in JS614 • Strain JS60 grew readily on lactate, while strain JS614 did not • Propionate alleviated lag periods for VC utilization in acetate-grown JS614.

Natural Biodegradation of Vinyl Chloride and cis-Dichloroethene in Aerobic and Suboxic Conditions

Chlorinated ethene (CE) groundwater contamination is commonly treated through anaerobic biodegradation (i.e., reductive dechlorination) either as part of an engineered system or through natural attenuation. Aerobic biodegradation has also been recognized as a potentially significant pathway for the removal of the lower CEs cis-1,2-dichloroethene (cDCE) and vinyl chloride (VC). However, the role of aerobic biodegradation under low oxygen conditions typical of contaminated groundwater is unclear. Bacteria capable of aerobic VC biodegradation appear to be common in the environment, while aerobic biodegradation of cDCE is less common and little is known regarding the organisms responsible. In this study, we investigate the role of aerobic cDCE and VC biodegradation in a mixed contaminant plume (including CEs, BTEX, and ketones) at Naval Air Station North Island, Installation Restoration Site 9. Sediment and groundwater collected from the plume source area, mid-plume, and shoreline were used to prepare microcosms under fully aerobic (8 mg/L dissolved oxygen (DO)) and suboxic (< 1 mg/L DO) conditions. In the shoreline microcosms, VC and cDCE were rapidly degraded under suboxic conditions (100% and 77% removal in < 62 days). In the suboxic VC microcosms, biodegradation was associated with a > 5 order of magnitude increase in the abundance of functional gene etnE, part of the aerobic VC utilization pathway. VC and cDCE were degraded more slowly under fully aerobic conditions (74% and 30% removal) in 110 days. High-throughput 16S rRNA and etnE sequencing suggest the presence of novel VC- and cDCE-degrading bacteria. These results suggest that natural aerobic biodegradation of cDCE and VC is occurring at the site and provide new evidence that low (< 1 mg/L) DO levels play a significant role in natural attenuation of cDCE and VC.

Microbiome Composition and Dynamics of a Reductive/Oxidative Bioelectrochemical System for Perchloroethylene Removal: Effect of the Feeding Composition

Chlorinated solvents still represent an environmental concern that requires sustainable and innovative bioremediation strategies. This study describes the microbiome composition of a novel bioelectrochemical system (BES) based on sequential reductive/oxidative dechlorination for complete perchloroethylene (PCE) removal occurring in two separate but sequential chambers. The BES has been tested under various feeding compositions [i.e., anaerobic mineral medium (MM), synthetic groundwater (SG), and real groundwater (RG)] differing in presence of sulfate, nitrate, and iron (III). In addition, the main biomarkers of the dechlorination process have been monitored in the system under various conditions. Among them, Dehalococcoides mccartyi 16S rRNA and reductive dehalogenase genes (tceA, bvcA, and vcrA) involved in anaerobic dechlorination have been quantified. The etnE and etnC genes involved in aerobic dechlorination have also been quantified. The feeding composition affected the microbiome, in particular when the BES was fed with RG. Sulfuricurvum, enriched in the reductive compartment, operated with MM and SG, suggesting complex interactions in the sulfur cycle mostly including sulfur oxidation occurring at the anodic counter electrode (MM) or coupled to nitrate reduction (SG). Moreover, the known Mycobacterium responsible for natural attenuation of VC by aerobic degradation was found abundant in the oxidative compartment fed with RG, which was in line with the high VC removal observed (92 ± 2%). D. mccartyi was observed in all the tested conditions ranging from 8.78E + 06 (with RG) to 2.35E + 07 (with MM) 16S rRNA gene copies/L. tceA was found as the most abundant reductive dehalogenase gene in all the conditions explored (up to 2.46 E + 07 gene copies/L in MM). The microbiome dynamics and the occurrence of biomarkers of dechlorination, along with the kinetic performance of the system under various feeding conditions, suggested promising implications for the scale-up of the BES, which couples reductive with oxidative dechlorination to ensure the complete removal of highly chlorinated ethylene and mobile low-chlorinated by-products.

Biotic and abiotic reductive dechlorination of chloroethenes in aquitards

Chlorinated solvents occur as dense nonaqueous phase liquid (DNAPL) or as solutes when dissolved in water. They are present in many pollution sites in urban and industrial areas. They are toxic, carcinogenic, and highly recalcitrant in aquifers and aquitards. In the latter case, they migrate by molecular diffusion into the matrix. When aquitards are fractured, chlorinated solvents also penetrate as a free phase through the fractures. The main objective of this study was to analyze the biogeochemical processes occurring inside the matrix surrounding fractures and in the joint-points zones. The broader implications of this objective derive from the fact that, incomplete natural degradation of contaminants in aquitards generates accumulation of daughter products. This causes steep concentration gradients and back-diffusion fluxes between aquitards and high hydraulic conductivity layers. This offers opportunities to develop remediation strategies based, for example, on the coupling of biotic and reactive abiotic processes. The main results showed: 1) Degradation occurred especially in the matrix adjacent to the orthogonal network of fractures and textural heterogeneities, where texture contrasts favored microbial development because these zones constituted ecotones. 2) A dechlorinating bacterium not belonging to the Dehalococcoides genus, namely Propionibacterium acnes, survived under the high concentrations of dissolved perchloroethene (PCE) in contact with the PCE-DNAPL and was able to degrade it to trichloroethene (TCE). Dehalococcoides genus was able to conduct PCE reductive dechlorination at least up to cis-1,2-dichloroethene (cDCE), which shows again the potential of the medium to degrade chloroethenes in aquitards. 3) Degradation of PCE in the matrix resulted from the coupling of reactive abiotic and biotic processes-in the first case, promoted by Fe²⁺ sorbed to iron oxides, and in the latter case, related to dechlorinating microorganisms. The dechlorination resulting from these coupling processes is slow and limited by the need for an adequate supply of electron donors.

The role of ecotones in the dehalogenation of chloroethenes in alluvial fan aquifers

The presence of ecotones in transition zones between geological strata (e.g. layers of gravel and sand interbedded with layers of silt in distal alluvial fan deposits) in aquifers plays a significant role in regulating the flux of matter and energy between compartments. Ecotones are characterised by steep physicochemical and biological gradients and considerable biological diversity. However, the link between organic pollutants and degradation potential in ecotones has scarcely been studied. The aim of this study is to relate the presence of ecotones with the dehalogenation of chloroethenes. A field site was selected where chloroethene contamination occurs in a granular aquifer with geological heterogeneities. The site is monitored by multilevel and conventional wells. Groundwater samples were analysed by chemical, isotopic, and molecular techniques. The main results were as follows: (1) two ecotones were characterised in the source area, one in the upper part of the aquifer and the second in the transition zone to the bottom aquitard, where the aged pool is located; (2) the ecotone located in the transition zone to the bottom aquitard has greater microbial diversity, due to higher geological heterogeneities; (3) both ecotones show the reductive dehalogenation of perchloroethylene and trichloroethylene; and (4) these ecotones are the main zones of the reductive dehalogenation of the pollutants, given the more reductive conditions at the centre of the plume. These findings suggest that ecotones are responsible for natural attenuation, where oxic conditions prevailed at the aquifer and bioremediation strategies could be applied more effectively in these zones to promote complete reductive dehalogenation.

Examining aerobic degradation of chloroethenes mixture in consortium composed of Comamonas testosteroni RF2 and Mycobacterium aurum L1

An environmental isolate Comamonas testosteroni RF2 has been previously described to cometabolize trichloroethene (TCE), 1,2-cis-dichloroethene (cDCE), 1,2-trans-dichloroethene (tDCE), and 1,1-dichloroethene (1,1DCE) when grown on phenol and lactate sodium. In this study, three vinyl chloride (VC) degrading strains, Mycobacterium aurum L1, Pseudomonas putida PS, and Rhodococcus ruber Sm-1 were used to form consortia with the strain RF2 in terms to achieve the removal of VC along with above-mentioned chloroethenes. Degradation assays were performed for a binary mixture of cDCE and VC as well as for a mixture of TCE, all DCEs and VC. The consortium composed of C. testosteroni RF2 and M. aurum L1 showed to be the most efficient towards the removal of cDCE (6.01 mg L^-1) in the binary mixture with VC (10 mg L^-1) and was capable of efficiently removing chloroethenes in the mixture sample at the initial concentrations of 116 μg L^-1 for TCE, 662 μg L^-1 for cDCE, 42 μg L^-1 for tDCE, 16 μg L^-1 for 1,1DCE, and 7 mg L^-1 for VC with a removal efficiency of nearly 100% for all of the compounds. Although complete removal of VC took a significantly longer time than the removal of other chloroethenes, the consortium composed of C. testosteroni RF2 and M. aurum L1 displayed strong bioremediation potential for aquifers with downstream contamination characterized by the presence of less chlorinated ethenes.

Combining nanoscale zero-valent iron with electrokinetic treatment for remediation of chlorinated ethenes and promoting biodegradation: A long-term field study

Nanoscale zero-valent iron (nZVI) is recognized as a powerful tool for the remediation of groundwater contaminated by chlorinated ethenes (CEs). This long-term field study explored nZVI-driven degradation of CEs supported by electrokinetic (EK) treatment, which positively affects nZVI longevity and migration, and its impact on indigenous bacteria. In particular, the impact of combined nZVI-EK treatment on organohalide-respiring bacteria, ethenotrophs and methanotrophs (all capable of CE degradation) was assessed using molecular genetic markers detecting Dehalococcoides spp., Desulfitobacterium spp., the reductive dehalogenase genes vcrA and bvcA and ethenotroph and methanotroph functional genes. The remediation treatment resulted in a rapid decrease of the major pollutant cis-1,2-dichloroethene (cDCE) by 75% in the affected area, followed by an increase in CE degradation products methane, ethane and ethene. The newly established geochemical conditions in the treated aquifer not only promoted growth of organohalide-respiring bacteria but also allowed for the concurrent presence of vinyl chloride- and cDCE-oxidizing methanotrophs and (especially) ethenotrophs, which proliferated preferentially in the vicinity of an anode where low levels of oxygen were produced. The nZVI treatment resulted in a temporary negative impact on indigenous bacteria in the application well close to the cathode; but even there, the microbiome was restored within 15 days. The nZVI-EK treatment proved highly effective in reducing CE contamination and creating a suitable environment for subsequent biodegradation by changing groundwater conditions, promoting transport of nutrients and improving CE availability to soil and groundwater bacteria.

Cryogenic soil coring reveals coexistence of aerobic and anaerobic vinyl chloride degrading bacteria in a chlorinated ethene contaminated aquifer

Vinyl chloride (VC) is a common groundwater contaminant and known human carcinogen. Three major bacterial guilds are known to participate in VC biodegradation: aerobic etheneotrophs and methanotrophs, and anaerobic organohalide-respiring VC-dechlorinators. We investigated the spatial relationships between functional genes representing these three groups of bacteria (as determined by qPCR) with chlorinated ethene concentrations in a surficial aquifer at a contaminated site. We used cryogenic soil coring to collect high-resolution aquifer sediment samples and to preserve sample geochemistry and nucleic acids under field conditions. All samples appeared to be anaerobic (i.e., contained little to no dissolved oxygen). VC biodegradation associated functional genes from etheneotrophs (etnC and/or etnE), methanotrophs (mmoX and/or pmoA), and anaerobic VC-dechlorinators (bvcA and/or vcrA) coexisted in 48% of the samples. Transcripts of etnC/etnE and bvcA/vcrA were quantified in contemporaneous groundwater samples, indicating co-located gene expression. Functional genes from etheneotrophs and anaerobic VC-dechlorinators were correlated to VC concentrations in the lower surficial aquifer (p < 0.05). Methanotroph functional genes were not correlated to VC concentrations. Cryogenic soil coring proved to be a powerful tool for capturing high-spatial resolution trends in geochemical and nucleic acid data in aquifer sediments. We conclude that both aerobic etheneotrophs and anaerobic VC-dechlorinators may play a significant role in VC biodegradation in aquifers that have little dissolved oxygen.

Differences of cell surface characteristics between the bacterium Pseudomonas veronii and fungus Ophiostoma stenoceras and their different adsorption properties to hydrophobic organic compounds

The first step of microbial biodegradation is the adsorption of pollutants on the microorganisms' surface, which is determined by the microorganism type and pollutant hydrophobicity. One fungus Ophiostoma stenoceras LLC and one bacterium Pseudomonas veronii ZW were chosen for the investigation of cell surface hydrophobicity and adsorption abilities to various organic compounds. Results showed that the fungus could better capture and adsorb organic compounds in liquid and gas phases, and the adsorption was a physical monolayer adsorption process. Much smaller partition coefficient for gas-fungus suggested that direct gaseous adsorption was preferred. The XPS (X-ray photoelectron spectroscopy) characterization further confirmed that several functional groups changed after the adsorption of compounds. The time taken for complete degradation of hexane, tetrahydrofuran and chlorobenzene was shorter with the addition of O. stenoceras LLC. Such findings are useful in exploring the special cell surface of fungus in adsorption and bioenhancement for organic treatment of organic contaminants using bacteria.

Contrasting growth properties of Nocardioides JS614 on threedifferent vinyl halides

Ethene (ETH)-grown inocula of Nocardioides JS614 grow on vinyl chloride (VC), vinyl fluoride (VF), or vinyl bromide (VB) as the sole carbon and energy source, with faster growth rates and higher cell yields on VC and VF than on VB. However, whereas acetate-grown inocula of JS614 grow on VC and VF after a lag period, growth on VB did not occur unless supplemental ethene oxide (EtO) was present in the medium. Despite inferior growth on VB, the maximum rate of VB consumption by ETH-grown cells was ~ 50% greater than the rates of VC and VF consumption, but Br^- release during VB consumption was non-stoichiometric with VB consumption (~ 66%) compared to 100% release of Cl^- and F^- during VC and VF consumption. Evidence was obtained for VB turnover-dependent toxicity of cell metabolism in JS614 with both acetate-dependent respiration and growth being significantly reduced by VB turnover, but no VC or VF turnover-dependent toxicity of growth was detected. Reduced growth rate and cell yield of JS614 on VB probably resulted from a combination of inefficient metabolic processing of the highly unstable VB epoxide (t_0.5 = 45 s), accompanied by growth inhibitory effects of VB metabolites on acetate-dependent metabolism. The exact role(s) of EtO in promoting growth of alkene repressed JS614 on VB remains unresolved, with evidence of EtO inducing epoxide consuming activity prior to an increase in alkene oxidizing activity and supplementing reductant supply when VB is the growth substrate.

Natural attenuation of chlorinated ethenes in hyporheic zones: A review of key biogeochemical processes and in-situ transformation potential

Chlorinated ethenes (CEs) are legacy contaminants whose chemical footprint is expected to persist in aquifers around the world for many decades to come. These organohalides have been reported in river systems with concerning prevalence and are thought to be significant chemical stressors in urban water ecosystems. The aquifer-river interface (known as the hyporheic zone) is a critical pathway for CE discharge to surface water bodies in groundwater baseflow. This pore water system may represent a natural bioreactor where anoxic and oxic biotransformation process act in synergy to reduce or even eliminate contaminant fluxes to surface water. Here, we critically review current process understanding of anaerobic CE respiration in the competitive framework of hyporheic zone biogeochemical cycling fuelled by in-situ fermentation of natural organic matter. We conceptualise anoxic-oxic interface development for metabolic and co-metabolic mineralisation by a range of aerobic bacteria with a focus on vinyl chloride degradation pathways. The superimposition of microbial metabolic processes occurring in sediment biofilms and bulk solute transport delivering reactants produces a scale dependence in contaminant transformation rates. Process interpretation is often confounded by the natural geological heterogeneity typical of most riverbed environments. We discuss insights from recent field experience of CE plumes discharging to surface water and present a range of practical monitoring technologies which address this inherent complexity at different spatial scales. Future research must address key dynamics which link supply of limiting reactants, residence times and microbial ecophysiology to better understand the natural attenuation capacity of hyporheic systems.

Relationships between the Abundance and Expression of Functional Genes from Vinyl Chloride (VC)-Degrading Bacteria and Geochemical Parameters at VC-Contaminated Sites

Bioremediation of vinyl chloride (VC) contamination in groundwater could be mediated by three major bacterial guilds: anaerobic VC-dechlorinators, methanotrophs, and ethene-oxidizing bacteria (etheneotrophs) via metabolic or cometabolic pathways. We collected 95 groundwater samples across 6 chlorinated ethene-contaminated sites and searched for relationships among VC biodegradation gene abundance and expression and site geochemical parameters (e.g., VC concentrations). Functional genes from the three major VC-degrading bacterial guilds were present in 99% and expressed in 59% of the samples. Etheneotroph and methanotroph functional gene abundances ranged from 10² to 10⁹ genes per liter of groundwater among the samples with VC reductive dehalogenase gene (bvcA and vcrA) abundances reaching 10⁸ genes per liter of groundwater. Etheneotroph functional genes (etnC and etnE) and VC reductive dehalogenase genes (bvcA and vcrA) were strongly related to VC concentrations (p < 0.001). Methanotroph functional genes (mmoX and pmoA) were not related to VC concentration (p > 0.05). Samples from sites with bulk VC attenuation rates >0.08 year^-1 contained higher levels of etheneotroph and anaerobic VC-dechlorinator functional genes and transcripts than those with bulk VC attenuation rates <0.004 year^-1. We conclude that both etheneotrophs and anaerobic VC-dechlorinators have the potential to simultaneously contribute to VC biodegradation at these sites.

Cometabolic degradation of dichloroethenes by Comamonas testosteroni RF2

An environmental isolate Comamonas testosteroni strain RF2, which has been found to cometabolize trichloroethene (TCE) in the presence of phenol and sodium lactate as growth substrates, was tested to investigate its capacity for degrading 1,2-cis-dichloroethene (cDCE), 1,2-trans-dichlorothene (tDCE), and 1,1-dichloroethene (1,1DCE). Degradation assays were performed for single DCEs, as well as for a mixture of DCEs with TCE, which resembled contaminated plume in groundwater. RF2 was capable of efficiently removing all three dichloroethenes (DCEs) at the initial aqueous concentrations of 6.01 mg L^-1 for cDCE, 3.80 mg L^-1 for tDCE and 0.65 mg L^-1 for 1,1DCE, with a removal efficiency of 100% for cDCE, 65.8% for tDCE, and 46.8% for 1,1DCE. Furthermore, complete removal of TCE, cDCE and 1,1DCE (122.5 μg L^-1, 84.3 μg L^-1 and 51.4 μg L^-1, respectively) was observed in a mixture sample that also contained 72.33 μg L^-1 of tDCE, which was removed to the amount of 72.3%. Moreover, degradation of cDCE (6.01 mg L^-1) led to a 93.8% release of inorganic chloride, and 2,2-dichloroacetaldehyde was determined as the first intermediate of cDCE transformation. The findings of this study suggest that the strain RF2 exhibits the potential to remediate groundwater contaminated with less chlorinated ethenes.

Biodegradation of Volatile Organic Compounds and Their Effects on Biodegradability under Co-Existing Conditions

Volatile organic compounds (VOCs) are major pollutants that are found in contaminated sites, particularly in developed countries such as Japan. Various microorganisms that degrade individual VOCs have been reported, and genomic information related to their phylogenetic classification and VOC-degrading enzymes is available. However, the biodegradation of multiple VOCs remains a challenging issue. Practical sites, such as chemical factories, research facilities, and illegal dumping sites, are often contaminated with multiple VOCs. In order to investigate the potential of biodegrading multiple VOCs, we initially reviewed the biodegradation of individual VOCs. VOCs include chlorinated ethenes (tetrachloroethene, trichloroethene, dichloroethene, and vinyl chloride), BTEX (benzene, toluene, ethylbenzene, and xylene), and chlorinated methanes (carbon tetrachloride, chloroform, and dichloromethane). We also summarized essential information on the biodegradation of each kind of VOC under aerobic and anaerobic conditions, together with the microorganisms that are involved in VOC-degrading pathways. Interactions among multiple VOCs were then discussed based on concrete examples. Under conditions in which multiple VOCs co-exist, the biodegradation of a VOC may be constrained, enhanced, and/or unaffected by other compounds. Co-metabolism may enhance the degradation of other VOCs. In contrast, constraints are imposed by the toxicity of co-existing VOCs and their by-products, catabolite repression, or competition between VOC-degrading enzymes. This review provides fundamental, but systematic information for designing strategies for the bioremediation of multiple VOCs, as well as information on the role of key microorganisms that degrade VOCs.

Modeling aerobic biotransformation of vinyl chloride by vinyl chloride-assimilating bacteria, methanotrophs and ethenotrophs

Recent studies have investigated the potential of enhanced groundwater Vinyl Chloride (VC) remediation in the presence of methane and ethene through the interactions of VC-assimilating bacteria, methanotrophs and ethenotrophs. In this study, a mathematical model was developed to describe aerobic biotransformation of VC in the presence of methane and ethene for the first time. It examines the metabolism of VC by VC-assimilating bacteria as well as cometabolism of VC by both methanotrophs and ethenotrophs, using methane and ethene respectively, under aerobic conditions. The developed model was successfully calibrated and validated using experimental data from microcosms with different experimental conditions. The model satisfactorily describes VC, methane and ethene dynamics in all microcosms tested. Modeling results describe that methanotrophic cometabolism of ethene promotes ethenotrophic VC cometabolism, which significantly enhances aerobic VC degradation in the presence of methane and ethene. This model is expected to be a useful tool to support effective and efficient processes for groundwater VC remediation.

Microbial degradation of chloroethenes: a review

Contamination by chloroethenes has a severe negative effect on both the environment and human health. This has prompted intensive remediation activity in recent years, along with research into the efficacy of natural microbial communities for degrading toxic chloroethenes into less harmful compounds. Microbial degradation of chloroethenes can take place either through anaerobic organohalide respiration, where chloroethenes serve as electron acceptors; anaerobic and aerobic metabolic degradation, where chloroethenes are used as electron donors; or anaerobic and aerobic co-metabolic degradation, with chloroethene degradation occurring as a by-product during microbial metabolism of other growth substrates, without energy or carbon benefit. Recent research has focused on optimising these natural processes to serve as effective bioremediation technologies, with particular emphasis on (a) the diversity and role of bacterial groups involved in dechlorination microbial processes, and (b) detection of bacterial enzymes and genes connected with dehalogenation activity. In this review, we summarise the different mechanisms of chloroethene bacterial degradation suitable for bioremediation and provide a list of dechlorinating bacteria. We also provide an up-to-date summary of primers available for detecting functional genes in anaerobic and aerobic bacteria degrading chloroethenes metabolically or co-metabolically.

Temporal abundance and activity trends of vinyl chloride (VC)-degrading bacteria in a dilute VC plume at Naval Air Station Oceana

Assessment and monitoring of microbial community dynamics is useful when tracking the progress of vinyl chloride (VC) bioremediation strategies, particularly in dilute plumes where apparent VC attenuation rates are low. In a long-term field study, the abundance and the activity of microbial VC degraders were tracked in three monitoring wells (MW05, MW25, and MW19) along a dilute VC plume at Naval Air Station (NAS) Oceana. High-throughput sequencing of partial 16S ribosomal RNA (rRNA) genes and transcripts revealed diverse groundwater microbial communities and showed that methanotrophs and anaerobic respirers (e.g., methanogens, sulfate reducers, and iron reducers) were among the most active and abundant guilds. Quantitative PCR analysis showed that among bacterial guilds with a potential to contribute to VC biodegradation, methanotrophs were the most abundant and active microbial group. Ethene-oxidizing bacterial populations were less abundant and relatively inactive compared to methanotrophs. In MW19, expression of functional genes associated with both aerobic VC oxidation and anaerobic VC reduction was observed. Overall, our results reveal that the groundwater community contains various active bacterial guilds previously associated with metabolic and cometabolic VC degradation processes either under aerobic and anaerobic conditions that might have contributed to the slowly decreasing VC concentrations at the NAS Oceana site over the 6-year study period.

Geochemical Parameters and Reductive Dechlorination Determine Aerobic Cometabolic vs Aerobic Metabolic Vinyl Chloride Biodegradation at Oxic/Anoxic Interface of Hyporheic Zones

Hyporheic zones mediate vinyl chloride (VC) biodegradation in groundwater discharging into surface waters. At the oxic/anoxic interface (OAI) of hyporheic zones subjected to redox oscillations, VC is degraded via coexisting aerobic ethenotrophic and anaerobic reductive dechlorination pathways. However, the identity of aerobic VC degradation pathways (cometabolic vs metabolic) and their interactions with reductive dechlorination in relation to riverbed sediment geochemistry remain ill-defined. We addressed this using microcosms containing OAI sediments incubated under fluctuating oxic/anoxic atmosphere. Under oxic atmosphere, aerobic metabolic VC oxidation was absent in sediments with high total organic carbon (TOC) and VC was reductively dechlorinated to ethene. Ethene was oxidized by ethenotrophs that can degrade VC cometabolically. Contrastingly, VC was metabolically oxidized by ethenotrophs in low-TOC sediments with low reductive dechlorination potential. Accordingly, enrichment and isolation of metabolic VC-oxidizing ethenotrophs was successful only from the low-TOC sediment. Sequence analysis of etnE genes from the microcosms as well phylogenetic typing of the isolates showed that ethenotrophs in the sediments were facultative anaerobic Proteobacteria capable of coping with OAI-associated redox fluctuations. Our results suggest that local sediment heterogeneity supports/selects divergent VC degradation processes at the OAI and that high reductive dechlorination potential suppresses development of aerobic metabolic VC oxidation potential.

Epoxyalkane:Coenzyme M Transferase Gene Diversity and Distribution in Groundwater Samples from Chlorinated-Ethene-Contaminated Sites

Epoxyalkane:coenzyme M transferase (EaCoMT) plays a critical role in the aerobic biodegradation and assimilation of alkenes, including ethene, propene, and the toxic chloroethene vinyl chloride (VC). To improve our understanding of the diversity and distribution of EaCoMT genes in the environment, novel EaCoMT-specific terminal-restriction fragment length polymorphism (T-RFLP) and nested-PCR methods were developed and applied to groundwater samples from six different contaminated sites. T-RFLP analysis revealed 192 different EaCoMT T-RFs. Using clone libraries, we retrieved 139 EaCoMT gene sequences from these samples. Phylogenetic analysis revealed that a majority of the sequences (78.4%) grouped with EaCoMT genes found in VC- and ethene-assimilating Mycobacterium strains and Nocardioides sp. strain JS614. The four most-abundant T-RFs were also matched with EaCoMT clone sequences related to Mycobacterium and Nocardioides strains. The remaining EaCoMT sequences clustered within two emergent EaCoMT gene subgroups represented by sequences found in propene-assimilating Gordonia rubripertincta strain B-276 and Xanthobacter autotrophicus strain Py2. EaCoMT gene abundance was positively correlated with VC and ethene concentrations at the sites studied.

IMPORTANCE

The EaCoMT gene plays a critical role in assimilation of short-chain alkenes, such as ethene, VC, and propene. An improved understanding of EaCoMT gene diversity and distribution is significant to the field of bioremediation in several ways. The expansion of the EaCoMT gene database and identification of incorrectly annotated EaCoMT genes currently in the database will facilitate improved design of environmental molecular diagnostic tools and high-throughput sequencing approaches for future bioremediation studies. Our results further suggest that potentially significant aerobic VC degraders in the environment are not well represented in pure culture. Future research should aim to isolate and characterize aerobic VC-degrading bacteria from these underrepresented groups.

Kinetics of aerobic cometabolic biodegradation of chlorinated and brominated aliphatic hydrocarbons: A review

This review analyses kinetic studies of aerobic cometabolism (AC) of halogenated aliphatic hydrocarbons (HAHs) from 2001-2015 in order to (i) compare the different kinetic models proposed, (ii) analyse the estimated model parameters with a focus on novel HAHs and the identification of general trends, and (iii) identify further research needs. The results of this analysis show that aerobic cometabolism can degrade a wide range of HAHs, including HAHs that were not previously tested such as chlorinated propanes, highly chlorinated ethanes and brominated methanes and ethanes. The degree of chlorine mineralization was very high for the chlorinated HAHs. Bromine mineralization was not determined for studies with brominated aliphatics. The examined research period led to the identification of novel growth substrates of potentially high interest. Decreasing performance of aerobic cometabolism were found with increasing chlorination, indicating the high potential of aerobic cometabolism in the presence of medium- and low-halogenated HAHs. Further research is needed for the AC of brominated aliphatic hydrocarbons, the potential for biofilm aerobic cometabolism processes, HAH-HAH mutual inhibition and the identification of the enzymes responsible for each aerobic cometabolism process. Lastly, some indications for a possible standardization of future kinetic studies of HAH aerobic cometabolism are provided.

Aerobic Vinyl Chloride Metabolism in Groundwater Microcosms by Methanotrophic and Etheneotrophic Bacteria

Vinyl chloride (VC) is a carcinogen generated in groundwater by reductive dechlorination of chloroethenes. Under aerobic conditions, etheneotrophs oxidize ethene and VC, while VC-assimilators can use VC as their sole source of carbon and energy. Methanotrophs utilize only methane but can oxidize ethene to epoxyethane and VC to chlorooxirane. Microcosms were constructed with groundwater from the Carver site in MA containing these three native microbial types. Methane, ethene, and VC were added to the microcosms singly or as mixtures. In the absence of VC, ethene degraded faster when methane was also present. We hypothesized that methanotroph oxidation of ethene to epoxyethane competed with their use of methane, and that epoxyethane stimulated the activity of starved etheneotrophs by inducing the enzyme alkene monooxygenase. We then developed separate enrichment cultures of Carver methanotrophs and etheneotrophs, and demonstrated that Carver methanotrophs can oxidize ethene to epoxyethane, and that starved Carver etheneotrophs exhibit significantly reduced lag time for ethene utilization when epoxyethane is added. In our groundwater microcosm tests, when all three substrates were present, the rate of VC removal was faster than with either methane or ethene alone, consistent with the idea that methanotrophs stimulate etheneotroph destruction of VC.

Evaluating alternate biokinetic models for trace pollutant cometabolism

Mathematical models of cometabolic biodegradation kinetics can improve our understanding of the relevant microbial reactions and allow us to design in situ or in-reactor applications of cometabolic bioremediation. A variety of models are available, but their ability to describe experimental data has not been systematically evaluated for a variety of operational/experimental conditions. Here five different models were considered: first-order; Michaelis-Menten; reductant; competition; and combined models. The models were assessed on their ability to fit data from simulated batch experiments covering a realistic range of experimental conditions. The simulated observations were generated by using the most complex model structure and parameters based on the literature, with added experimental error. Three criteria were used to evaluate model fit: ability to fit the simulated experimental data, identifiability of parameters using a colinearity analysis, and suitability of the model size and complexity using the Bayesian and Akaike Information criteria. Results show that no single model fits data well for a range of experimental conditions. The reductant model achieved best results, but required very different parameter sets to simulate each experiment. Parameter nonuniqueness was likely to be due to the parameter correlation. These results suggest that the cometabolic models must be further developed if they are to reliably simulate experimental and operational data.

Degradation of dichloromethane by an isolated strain Pandoraea pnomenusa and its performance in a biotrickling filter

A strain Pandoraea pnomenusa LX-1 that uses dichloromethane (DCM) as sole carbon and energy source has been isolated and identified in our laboratory. The optimum aerobic biodegradation of DCM in batch culture was evaluated by response surface methodology. Maximum biodegradation (5.35 mg/(L·hr)) was achieved under cultivation at 32.8°C, pH 7.3, and 0.66% NaCl. The growth and biodegradation processes were well fitted by Haldane's kinetic model, yielding maximum specific growth and degradation rates of 0.133 hr(-1) and 0.856 hr(-1), respectively. The microorganism efficiently degraded a mixture of DCM and coexisting components (benzene, toluene and chlorobenzene). The carbon recovery (52.80%-94.59%) indicated that the targets were predominantly mineralized and incorporated into cell materials. Electron acceptors increased the DCM biodegradation rate in the following order: mixed > oxygen > iron > sulfate > nitrate. The highest dechlorination rate was 0.365 mg Cl(-)/(hr·mg biomass), obtained in the presence of mixed electron acceptors. Removal was achieved in a continuous biotrickling filter at 56%-85% efficiency, with a mineralization rate of 75.2%. Molecular biology techniques revealed the predominant strain as P. pnomenusa LX-1. These results clearly demonstrated the effectiveness of strain LX-1 in treating DCM-containing industrial effluents. As such, the strain is a strong candidate for remediation of DCM coexisting with other organic compounds.

Biodegradation of benzene, toluene, ethylbenzene, and o-xylene by the bacterium Mycobacterium cosmeticum byf-4

A new strain Mycobacterium cosmeticum byf-4 able to simultaneously degrade benzene, toluene, ethylbenzene, and o-xylene (BTE(o-)X) compounds has been isolated and identified previously in our laboratory. We further report here the extent of degradation of every BTE(o-)X component, and unravel the initial mechanism involved in BTE(o-)X degradation. This organism efficiently degrades all the BTE(o-)X components when these compounds are added either individually or as a composite mixture, and has a preference for toluene followed by benzene, ethylbenzene and then o-xylene. The significantly high carbon recovery indicated that the predominant fate for BTE(o-)X compounds was mineralization and incorporation into cell materials. The presence of BTE compounds in binary or ternary mixtures consistently had a negative effect on o-xylene degradation. The initial steps involved in the degradation of BTE(o-)X were investigated by isolation of metabolites and assay of reverse transcription RT-PCR. Isolation of metabolites suggested that the BTE(o-)X compounds were initially converted by a dioxygenase to their respective catechols. The gene sequence of the PCR amplicons revealed that this isolate contained a 454-bp toluene dioxygenase (TOD) fragment. The BTE(o-)X-specific induction of the genes encoding TOD was confirmed by RT-PCR analysis. These results indicated that TOD was possibly responsible for the initial steps of BTE(o-)X catabolism in M. cosmeticum byf-4.

Vinyl chloride removal from an air stream by biotrickling filter

A biofiltration process was used for degradation of vinyl chloride as a hazardous material in the air stream. Three biotrickling filters in series-parallel allowing uniform feed and moisture distribution all over the bed were used. Granular activated carbon mixed with compost was employed as carrier bed. The biological culture consisted of mixture of activated sludge from PVC wastewater treatment plant. Concurrent flow of gas and liquid was used in the bed. Results indicated that during the operation period of 110 days, the biotrickling bed was able to remove over 35% of inlet vinyl chloride. Maximum elimination capacity was calculated to be 0.56 g.m(-3).hr(-1). The amount of chlorine accumulated in the circulating liquid due to the degradation of vinyl chloride was measured to be equal to the vinyl chloride removed from the air stream.

Assessment and modification of degenerate qPCR primers that amplify functional genes from etheneotrophs and vinyl chloride-assimilators

AIMS

Degenerate qPCR primer sets that target the functional genes etnC and etnE in etheneotrophs and vinyl chloride-assimilating bacteria were assessed and modified in an effort to improve performance.

METHODS AND RESULTS

Functional gene abundance in four pure cultures was estimated by qPCR using novel (MRTC and MRTE) and existing (RTC and RTE) degenerate primer sets and compared to abundances estimated with nondegenerate gene-specific primers (GSPs). Functional gene abundance in groundwater DNA extracted from several contaminated sites was also estimated with MRTC and MRTE primers.

CONCLUSIONS

MRTC primers displayed significantly improved etnC quantification in both pure cultures and environmental samples.

SIGNIFICANCE AND IMPACT OF THE STUDY

Application of MRTC and MRTE primer sets will enhance microbial ecology studies involving etheneotrophs and qPCR analyses that support vinyl chloride bioremediation strategies.

Sequential reductive and oxidative biodegradation of chloroethenes stimulated in a coupled bioelectro-process

This article for the first time demonstrates successful application of electrochemical processes to stimulate sequential reductive/oxidative microbial degradation of perchloroethene (PCE) in mineral medium and in contaminated groundwater. In a flow-through column system, hydrogen generation at the cathode supported reductive dechlorination of PCE to cis-dichloroethene (cDCE), vinyl chloride (VC), and ethene (ETH). Electrolytically generated oxygen at the anode allowed subsequent oxidative degradation of the lower chlorinated metabolites. Aerobic cometabolic degradation of cDCE proved to be the bottleneck for complete metabolite elimination. Total removal of chloroethenes was demonstrated for a PCE load of approximately 1.5 μmol/d. In mineral medium, long-term operation with stainless steel electrodes was demonstrated for more than 300 days. In contaminated groundwater, corrosion of the stainless steel anode occurred, whereas DSA (dimensionally stable anodes) proved to be stable. Precipitation of calcareous deposits was observed at the cathode, resulting in a higher voltage demand and reduced dechlorination activity. With DSA and groundwater from a contaminated site, complete degradation of chloroethenes in groundwater was obtained for two months thus demonstrating the feasibility of the sequential bioelectro-approach for field application.

A quantitative PCR assay for aerobic, vinyl chloride- and ethene-assimilating microorganisms in groundwater

Vinyl chloride (VC) is a known human carcinogen that is primarily formed in groundwater via incomplete anaerobic dechlorination of chloroethenes. Aerobic, ethene-degrading bacteria (etheneotrophs), which are capable of both fortuitous and growth-linked VC oxidation, could be important in natural attenuation of VC plumes that escape anaerobic treatment. In this work, we developed a quantitative, real-time PCR (qPCR) assay for etheneotrophs in groundwater. We designed and tested degenerate qPCR primers for two functional genes involved in aerobic, growth-coupled VC- and ethene-oxidation (etnC and etnE). Primer specificity to these target genes was tested by comparison to nucleotide sequence databases, PCR analysis of template DNA extracted from isolates and environmental samples, and sequencing of qPCR products obtained from VC-contaminated groundwater. The assay was made quantitative by constructing standard curves (threshold cycle vs log gene copy number) with DNA amplified from Mycobacterium strain JS60, an etheneotrophic isolate. Analysis of groundwater samples from three different VC-contaminated sites revealed that etnC abundance ranged from 1.6 × 10(3) - 1.0 × 10(5) copies/L groundwater while etnE abundance ranged from 4.3 × 10(3) - 6.3 × 10(5) copies/L groundwater. Our data suggest this novel environmental measurement method will be useful for supporting VC bioremediation strategies, assisting in site closure, and conducting microbial ecology studies involving etheneotrophs.

Association of missense mutations in epoxyalkane coenzyme M transferase with adaptation of Mycobacterium sp. strain JS623 to growth on vinyl chloride

Vinyl chloride (VC) is a toxic groundwater pollutant associated with plastic manufacture and chlorinated solvent use. Aerobic bacteria that grow on VC as a carbon and energy source can evolve in the laboratory from bacteria that grow on ethene, but the genetic changes involved are unknown. We investigated VC adaptation in two variants (JS623-E and JS623-T) of the ethene-oxidizing Mycobacterium strain JS623. Missense mutations in the EtnE gene developed at two positions (W243 and R257) in cultures exposed to VC but not in cultures maintained on ethene. Epoxyalkane-coenzyme M transferase (EaCoMT) activities in cell extracts of JS623-E and JS623-T (150 and 645 nmol/min/mg protein, respectively) were higher than that of wild-type JS623 (74 nmol/min/mg protein), and in both variant cultures epoxyethane no longer accumulated during growth on ethene. The heterologous expression of two variant etnE alleles (W243G [etnE1] and R257L [etnE2]) from strain JS623 in Mycobacterium smegmatis showed that they had 42 to 59% higher activities than the wild type. Recombinant JS623 cultures containing mutant EtnE genes cloned in the vector pMV261 adapted to growth on VC more rapidly than the wild-type JS623 strain, with incubation times of 60 days (wild type), 1 day (pMVetnE1), and 35 days (pMVetnE2). The JS623(pMVetnE) culture did not adapt to VC after more than 60 days of incubation. Adaptation to VC in strain JS623 is consistently associated with two particular missense mutations in the etnE gene that lead to higher EaCoMT activity. This is the first report to pinpoint a genetic change associated with the transition from cometabolic to growth-linked VC oxidation in bacteria.

Inhibition of aerobic metabolic cis-1,2-di-chloroethene biodegradation by other chloroethenes

The presence of other chloroethenes influences aerobic metabolic biodegradation of cis-1,2-dichloroethene (cDCE). A new metabolically cDCE degrading enrichment culture was identified as also being capable of degrading vinyl chloride (VC), but not 1,1-dichloroethene (1,1DCE), trans-1,2-dichloroethene (tDCE), trichloroethene (TCE), or tetrachloroethene (PCE). The fastest degradation of cDCE was observed in the absence of any other chloroethene. In the presence of a second chloroethene (40-90 microM), the rate of cDCE (60 microM) degradation decreased in the following order: cDCE (+PCE) > cDCE (+tDCE) > cDCE (+VC)>cDCE (+1,1DCE) approximately cDCE (+TCE). With increasing concentrations of VC, ranging from 10 to 110 microM, the rate of cDCE (60 microM) degradation decreased. This study demonstrates that the inhibiting effects of chloroethene mixtures have to be considered during laboratory studies and bioremediation approaches based on metabolic cDCE degradation.

Proteomic analysis of ethene-enriched groundwater microcosms from a vinyl chloride-contaminated site

Contamination of groundwater with vinyl chloride (VC), a known human carcinogen, is a common environmental problem at plastics manufacturing, dry cleaning, and military sites. At many sites, there is the potential to cleanup VC groundwater plumes with aerobic VC-oxidizing microorganisms (e.g., methanotrophs, etheneotrophs, and VC-assimilating bacteria). Environmental biotechnologies that reveal the presence and activity of VC-oxidizing bacteria in contaminated groundwater samples would provide valuable lines of evidence that bioremediation of VC is occurring at a site. We applied targeted shotgun mass spectrometry-based proteomic methods to ethene-enriched groundwater microcosms from a VC-contaminated site. Polypeptides from the enzymes alkene monooxygenase (EtnC) and epoxyalkane:CoM transferase (EtnE), both of which are expressed by aerobic etheneotrophs and VC-assimilating bacteria, were identified in 7 of the 14 samples analyzed. Bioinformatic analysis revealed that 2 EtnC and 5 EtnE peptides were unique to deduced EtnC and EtnE sequences from two different cultivated strains. In addition, several partial EtnE genes sequenced from microcosms matched with observed EtnE peptides. Our results have revealed broader etheneotroph functional gene diversity and demonstrate the feasibility, speed, and accuracy of applying a targeted metaproteomics approach to identifying protein biomarkers from etheneotrophs in complex environmental samples.

Evaluating the fate of chlorinated ethenes in streambed sediments by combining stable isotope, geochemical and microbial methods

The occurrence of chlorinated ethene transformation in a streambed was investigated using concentration and carbon isotope data from water samples taken at different locations and depths within a 15 x 25 m study area across which a tetrachloroethene (PCE) plume discharges. Furthermore, it was evaluated how the degree of transformation is related to groundwater discharge rates, redox conditions, solid organic matter content (SOM) and microbial factors. Groundwater discharge rates were quantified based on streambed temperatures, and redox conditions using concentrations of dissolved redox-sensitive species. The degree of chlorinated ethene transformation was highly variable in space from no transformation to transformation beyond ethene. Complete reductive dechlorination to ethane and ethene occurred at locations with at least sulfate-reducing conditions and with a residence time in the samples streambed zone (80 cm depth) of at least 10 days. Among these locations, Dehalococcoides was detected using a PCR method where SOM contents were >2% w/w and where transformation proceeded beyond ethene. However, it was not detected at locations with low SOM, which may cause an insufficient H(2) supply to sustain a detectably dense Dehalococcoides population. Additionally, it is possible that other organisms are responsible for the biodegradation. A microcosm study with streambed sediments demonstrated the potential of VC oxidation throughout the site even at locations without a pre-exposure to VC, consistent with the detection of the epoxyalkane:coenzyme M transferase (EaCoMT) gene involved in the degradation of chlorinated ethenes via epoxidation. In contrast, no aerobic transformation of cDCE in microcosms over a period of 1.5 years was observed. In summary, the study demonstrated that carbon isotope analysis is a sensitive tool to identify the degree of chlorinated ethene transformation even in hydrologically and geochemically complex streambed systems. In addition, it was observed that the degree of transformation is related to redox conditions, which in turn depend on groundwater discharge rates.

Adaptation of aerobic, ethene-assimilating Mycobacterium strains to vinyl chloride as a growth substrate

Contamination of drinking water source zones by vinyl chloride (VC), a known human carcinogen and common groundwater contaminant, poses a public health risk. Bioremediation applications involving aerobic, VC-assimilating bacteria could be useful in alleviating environmental VC cancer risk, but their evolution and activity in the environment are poorly understood. In this study, adaptation of ethene-assimilating Mycobacterium strains JS622, JS623, JS624, and JS625 to VC as a growth substrate was investigated to test the hypothesis that VC-assimilating bacteria arise from naturally occurring ethene-assimilating bacteria. VC consumption in the absence of microbial growth was initially observed in cultures grown in both ethene and 1/10-strength trypticase soy agar + 1% (w/v) glucose. After extended incubations (55-476 days), all strains commenced growth-coupled VC consumption patterns. VC-adapted cultures grown on 20 mM acetate subsequently retained their ability to assimilate VC. Three independent purity check methods (streak plates, 16S rRNA gene sequencing, and repetitive extragenic palindromic polymerase chain reaction) verified culture purity prior to and following VC adaptation. Overall, our results suggest that ethene-assimilating mycobacteria have a widespread ability to adapt to VC as a growth substrate.

Soluble di-iron monooxygenase gene diversity in soils, sediments and ethene enrichments

Soluble di-iron monooxygenases (SDIMOs) are key enzymes in the bacterial oxidation of hydrocarbons, and have applications in environmental and industrial biotechnology. SDIMOs from pure cultures are unlikely to represent the total diversity of this enzyme family, so we used polymerase chain reaction to survey the diversity of SDIMO alpha subunit genes in environmental samples, ethene enrichments and ethene-degrading bacterial isolates. From 178 cloned amplicons, 98 restriction fragment length polymorphism types were seen, from which 75 representative SDIMO sequences were obtained; 45 from environmental samples, 25 from enrichments and seven from isolates. The sequences were diverse, including genes similar to ethene (etnC), propene (amoC, pmoC), propane (prmA) and butane (bmoX) monooxygenases, in addition to many novel sequences comprising a new SDIMO group (group 6). Environmental samples showed the highest diversity, with strong representation of group 6 SDIMOs and prmA-like genes. Ethene stimulation of samples resulted in increased frequencies of group 4 SDIMOs (etnC-like). Four ethene-utilizing Mycobacterium isolates (NBB1-NBB4) from enrichments all contained etnC; one isolate (NBB4) also contained three additional SDIMO genes (bmoX-like, amoC-like and group 6). The primers, database, clone libraries and strains reported here provide a resource for future bioremediation and biocatalysis studies, with particular relevance for chlorinated alkene and alkane compounds.

Biodegradation of vinyl chloride and cis-dichloroethene by a Ralstonia sp. strain TRW-1

An aerobic bacterium, Ralstonia sp. strain TRW-1, that assimilates vinyl chloride (VC) or ethene (ETH) as the sole carbon source was isolated from a chloroethene-degrading enrichment culture. Phylogenetic analysis of 16S rDNA sequence of the isolate revealed almost 99% sequence similarity to Ralstonia pickettii. To our knowledge, this is the first report describing the isolation of a member of Ralstonia that can degrade VC as the growth substrate. The measured growth yield values for VC and ETH were 11.27 and 18.90 g protein/mole, respectively. The estimated half-velocity constant K (m) values for VC and ETH were 9.09+/-2.97 and 5.73+/-2.96 muM, respectively. These values are almost three- to tenfold higher than for other VC-assimilating Mycobacterium sp. The strain also degrades cis-dichloroethene (cis-DCE) in mineral salts medium containing yeast-extract, beef-extract, casamino acids, or peptone. This ability of the strain TRW-1 to degrade cis-DCE in the presence of a nontoxic, water-soluble substrate is relevant to in-situ remediation of cis-DCE-contaminated aquifers.

Bioaugmentation potential of a vinyl chloride-assimilatingMycobacteriumsp., isolated from a chloroethene-contaminated aquifer

An aerobic bacterium, Mycobacterium sp. strain TRW-2 that assimilated vinyl chloride (VC) or ethene (ETH) as the sole carbon source was isolated from a chloroethene-degrading enrichment culture. The strain TRW-2 also degraded cis-dichloroethene (cis-DCE) in mineral salts medium, but only when VC was present as the primary carbon source. However, no degradation of trans-dichloroethene or trichloroethene occurred in either the presence or absence of added VC. The measured growth yield values were 6.53 and 14.1g protein/mol of VC and ETH utilized, respectively. Inoculation by strain TRW-2 in microcosms prepared with aquifer samples resulted in rapid degradation of VC, whereas native bacteria degraded negligible amounts of VC within the same time period, thus suggesting bioaugmentation potential of the isolate. Phylogenetic analysis of the 16S rDNA sequence of the isolate revealed 98% sequence similarity to the members of the genus Mycobacterium. In summary, the isolate's ability to degrade VC, cis-DCE, and ETH and also its ability to survive and degrade VC in the presence of other microorganisms is relevant to the remediation of VC-impacted aquifers.

Coupling aggressive mass removal with microbial reductive dechlorination for remediation of DNAPL source zones: a review and assessment

The infiltration of dense non-aqueous-phase liquids (DNAPLs) into the saturated subsurface typically produces a highly contaminated zone that serves as a long-term source of dissolved-phase groundwater contamination. Applications of aggressive physical-chemical technologies to such source zones may remove > 90% of the contaminant mass under favorable conditions. The remaining contaminant mass, however, can create a rebounding of aqueous-phase concentrations within the treated zone. Stimulation of microbial reductive dechlorination within the source zone after aggressive mass removal has recently been proposed as a promising staged-treatment remediation technology for transforming the remaining contaminant mass. This article reviews available laboratory and field evidence that supports the development of a treatment strategy that combines aggressive source-zone removal technologies with subsequent promotion of sustained microbial reductive dechlorination. Physical-chemical source-zone treatment technologies compatible with posttreatment stimulation of microbial activity are identified, and studies examining the requirements and controls (i.e., limits) of reductive dechlorination of chlorinated ethenes are investigated. Illustrative calculations are presented to explore the potential effects of source-zone management alternatives. Results suggest that, for the favorable conditions assumed in these calculations (i.e., statistical homogeneity of aquifer properties, known source-zone DNAPL distribution, and successful bioenhancement in the source zone), source longevity may be reduced by as much as an order of magnitude when physical-chemical source-zone treatment is coupled with reductive dechlorination.

Carbon isotopic fractionation during aerobic vinyl chloride degradation

Vinyl chloride (VC) is a carcinogenic contaminant commonly found in groundwater. Much research has focused on anaerobic reductive dechlorination of VC, and recently on aerobic VC degradation. In this study, the stable carbon isotope enrichment factor associated with aerobic VC assimilation was determined for Mycobacterium sp. strains JS60, JS61, and JS617 and Nocardioides sp. strain JS614. The enrichment factors ranged from -8.2+/-0.1 to -7.0+/-0.3 % and did not change as a function of biomass concentration. The measured enrichment factors for aerobic VC degradation were smaller than those reported for anaerobic VC degradation. Enrichment factors can also be expressed in terms of kinetic isotope effects (KIEs), 12k/13k, which result from the difference in reaction rates of bonds containing light and heavy isotopes. The KIEs for aerobic VC degradation (1.01+/-0.001) were smaller than those for anaerobic VC degradation (1.03+/-0.007). From the perspective of bond breakage during a chemical reaction, the larger KIE associated with anaerobic VC degradation as compared to aerobic VC degradation agrees with KIE theory. This theory predicts that larger fractionations can be expected in reactions where heavier atoms are involved (i.e., C-Cl bond for anaerobic versus C=C for aerobic) and in reactions involving large changes in vibrational frequencies of the molecule between its ground state and transition state (i.e., C-Cl cleavage versus C=C epoxidation). The significant fractionation observed during aerobic VC degradation suggests that stable carbon isotope measurements may be used as a tool to distinguish between biodegraded and nonbiodegraded VC.

Involvement of linear plasmids in aerobic biodegradation of vinyl chloride

Pseudomonas putida strain AJ and Ochrobactrum strain TD were isolated from hazardous waste sites based on their ability to use vinyl chloride (VC) as the sole source of carbon and energy under aerobic conditions. Strains AJ and TD also use ethene and ethylene oxide as growth substrates. Strain AJ contained a linear megaplasmid (approximately 260 kb) when grown on VC or ethene, but it contained no circular plasmids. While strain AJ was growing on ethylene oxide, it was observed to contain a 100-kb linear plasmid, and its ability to use VC as a substrate was retained. The linear plasmids in strain AJ were cured, and the ability of strain AJ to consume VC, ethene, and ethylene oxide was lost following growth on a rich substrate (Luria-Bertani broth) through at least three transfers. Strain TD contained three linear plasmids, ranging in size from approximately 90 kb to 320 kb, when growing on VC or ethene. As with strain AJ, the linear plasmids in strain TD were cured following growth on Luria-Bertani broth and its ability to consume VC and ethene was lost. Further analysis of these linear plasmids may help reveal the pathway for VC biodegradation in strains AJ and TD and explain why this process occurs at many but not all sites where groundwater is contaminated with chloroethenes. Metabolism of VC and ethene by strains AJ and TD is initiated by an alkene monooxygenase. Their yields during growth on VC (0.15 to 0.20 mg of total suspended solids per mg of VC) are similar to the yields reported for other isolates (i.e., Mycobacterium sp., Nocardioides sp., and Pseudomonas sp.).

Biodegradation of chloromethane by Pseudomonas aeruginosa strain NB1 under nitrate-reducing and aerobic conditions

Pseudomonas aeruginosa strain NB1 uses chloromethane (CM) as its sole source of carbon and energy under nitrate-reducing and aerobic conditions. The observed yield of NB1 was 0.20 (+/-0.06) (mean +/- standard deviation) and 0.28 (+/-0.01) mg of total suspended solids (TSS) mg of CM(-1) under anoxic and aerobic conditions, respectively. The stoichiometry of nitrate consumption was 0.75 (+/-0.10) electron equivalents (eeq) of NO(3)(-) per eeq of CM, which is consistent with the yield when it is expressed on an eeq basis. Nitrate was stoichiometrically converted to dinitrogen (0.51 +/- 0.05 mol of N(2) per mol of NO(3)(-)). The stoichiometry of oxygen use with CM (0.85 +/- 0.21 eeq of O(2) per eeq of CM) was also consistent with the aerobic yield. Stoichiometric release of chloride and minimal accumulation of soluble metabolic products (measured as chemical oxygen demand) following CM consumption, under anoxic and aerobic conditions, indicated complete biodegradation of CM. Acetylene did not inhibit CM use under aerobic conditions, implying that a monooxygenase was not involved in initiating aerobic CM metabolism. Under anoxic conditions, the maximum specific CM utilization rate (k) for NB1 was 5.01 (+/-0.06) micromol of CM mg of TSS(-1) day(-1), the maximum specific growth rate (micro(max)) was 0.0506 day(-1), and the Monod half-saturation coefficient (K(s)) was 0.067 (+/-0.004) microM. Under aerobic conditions, the values for k, micro(max), and K(s) were 10.7 (+/-0.11) micromol of CM mg of TSS(-1) day(-1), 0.145 day(-1), and 0.93 (+/-0.042) microM, respectively, indicating that NB1 used CM faster under aerobic conditions. Strain NB1 also grew on methanol, ethanol, and acetate under denitrifying and aerobic conditions, but not on methane, formate, or dichloromethane.

Distribution of the coenzyme M pathway of epoxide metabolism among ethene- and vinyl chloride-degrading Mycobacterium strains

An epoxyalkane:coenzyme M (CoM) transferase (EaCoMT) enzyme was recently found to be active in the aerobic vinyl chloride (VC) and ethene assimilation pathways of Mycobacterium strain JS60. In the present study, EaCoMT activity and genes were investigated in 10 different mycobacteria isolated on VC or ethene from diverse environmental samples. In all cases, epoxyethane metabolism in cell extracts was dependent on CoM, with average specific activities of EaCoMT between 380 and 2,910 nmol/min/mg of protein. PCR with primers based on conserved regions of EaCoMT genes from Mycobacterium strain JS60 and the propene oxidizers Xanthobacter strain Py2 and Rhodococcus strain B-276 yielded fragments (834 bp) of EaCoMT genes from all of the VC- and ethene-assimilating isolates. The Mycobacterium EaCoMT genes form a distinct cluster and are more closely related to the EaCoMT of Rhodococcus strain B-276 than that of Xanthobacter strain Py2. The incongruence of the EaCoMT and 16S rRNA gene trees and the fact that isolates from geographically distant locations possessed almost identical EaCoMT genes suggest that lateral transfer of EaCoMT among the Mycobacterium strains has occurred. Pulsed-field gel electrophoresis revealed large linear plasmids (110 to 330 kb) in all of the VC-degrading strains. In Southern blotting experiments, the strain JS60 EaCoMT gene hybridized to many of the plasmids. The CoM-mediated pathway of epoxide metabolism appears to be universal in alkene-assimilating mycobacteria, possibly because of plasmid-mediated lateral gene transfer.

Epoxyalkane: coenzyme M transferase in the ethene and vinyl chloride biodegradation pathways of mycobacterium strain JS60

Mycobacterium strains that grow on ethene and vinyl chloride (VC) are widely distributed in the environment and are potentially useful for biocatalysis and bioremediation. The catabolic pathway of alkene assimilation in mycobacteria is not well characterized. It is clear that the initial step is a monooxygenase-mediated epoxidation that produces epoxyethane from ethene and chlorooxirane from VC, but the enzymes involved in subsequent transformation of the epoxides have not been identified. We investigated epoxyethane metabolism in Mycobacterium strain JS60 and discovered a coenzyme M (CoM)-dependent enzyme activity in extracts from VC- and ethene-grown cells. PCR amplifications using primers targeted at epoxyalkane:CoM transferase (EaCoMT) genes yielded part of the JS60 EaCoMT gene, which was used to clone an 8.4-kb genomic DNA fragment. The complete EaCoMT gene (etnE) was recovered, along with genes (etnABCD) encoding a four-component monooxygenase and two genes possibly involved in acyl-CoA ester metabolism. Reverse transcription-PCR indicated that the etnE and etnA genes were cotranscribed and inducible by ethene and VC. Heterologous expression of the etnE gene in Mycobacterium smegmatis mc(2)155 using the pMV261 vector gave a recombinant strain capable of transforming epoxyethane, epoxypropane, and chlorooxirane. A metabolite identified by mass spectrometry as 2-hydroxyethyl-CoM was produced from epoxyethane. The results indicate that the EaCoMT and monooxygenase enzymes encoded by a single operon (etnEABCD) catalyze the initial reactions in both the VC and ethene assimilation pathways. CoM-mediated reactions appear to be more widespread in bacteria than was previously believed.