Phylogenetic and kinetic diversity of aerobic vinyl chloride-assimilating bacteria from contaminated sites

Natural Attenuation Potential of Vinyl Chloride and Butyl Acrylate Released in the East Palestine, Ohio Train Derailment Accident

The East Palestine, Ohio train derailment released toxic vinyl chloride (VC) and butyl acrylate (BA), which entered the watershed. Streambed sediment, surface water, and private well water samples were collected 128 and 276 days postaccident to assess the natural attenuation potential of VC and BA by quantifying biodegradation biomarker genes and conducting microcosm treatability studies. qPCR detected the aerobic VC degradation biomarkers etnC in ∼40% and etnE in ∼27% of sediments collected in both sampling campaigns in abundances reaching 105 gene copies g-1. The 16S rRNA genes of organohalide-respiring Dehalococcoides and Dehalogenimonas were, respectively, detected in 50 and 64% of sediment samples collected 128 days postaccident and in 63 and 88% of sediment samples collected 276 days postaccident, in abundances reaching 107 cells g-1. Elevated detection frequencies of VC degradation biomarker genes were measured immediately downstream of the accident site (i.e., Sulphur Run). Aerobic VC degradation occurred in all sediment microcosms and coincided with increases of etnC/etnE genes and Mycobacterium, a genus comprising aerobic VC degraders. The conversion of VC to ethene and an increased abundance of VC reductive dechlorination biomarker genes were observed in microcosms established with sediments collected from Sulphur Run. All anoxic microcosms rapidly degraded BA to innocuous products with intermediate formation of n-butanol and acrylate. The results indicate that microbiomes in the East Palestine watershed have natural attenuation capacity for VC and BA. Recommendations are made to improve first-response actions in future contaminant release accidents of this magnitude.

Ethylene and epoxyethane metabolism in methanotrophic bacteria: comparative genomics and physiological studies using Methylohalobius crimeensis

The genome of the methanotrophic bacterium Methylohalobius crimeensis strain 10Ki contains a gene cluster that encodes a putative coenzyme-M (CoM)-dependent pathway for oxidation of epoxyethane, based on homology to genes in bacteria that grow on ethylene and propylene as sole substrates. An alkene monooxygenase was not detected in the M. crimeensis genome, so epoxyethane is likely produced from co-oxidation of ethylene by the methane monooxygenase enzyme. Similar gene clusters were detected in about 10% of available genomes from aerobic methanotrophic bacteria, primarily strains grown from rice paddies and other wetlands. The sparse occurrence of the gene cluster across distant phylogenetic groups suggests that multiple lateral gene transfer events have occurred in methanotrophs. In support of this, the gene cluster in M. crimeensis was detected within a large genomic island predicted using multiple methods. Growth studies, reverse transcription-quantitative PCR (RT-qPCR) and proteomics were performed to examine the expression of these genes in M. crimeensis. Growth and methane oxidation activity were completely inhibited by the addition of >0.5% (v/v) ethylene to the headspace of cultures, but at 0.125% and below, the inhibition was only partial, and ethylene was gradually oxidized. The etnE gene encoding epoxyalkane:CoM transferase was strongly upregulated in ethylene-exposed cells based on RT-qPCR. Proteomics analysis confirmed that EtnE and nine other proteins encoded in the same gene cluster became much more predominant after cells were exposed to ethylene. The results suggest that ethylene is strongly inhibitory to M. crimeensis, but the bacterium responds to ethylene exposure by expressing an epoxide oxidation system similar to that used by bacteria that grow on alkenes. In the obligate methanotroph M. crimeensis, this system does not facilitate growth on ethylene but likely alleviates toxicity of epoxyethane formed through ethylene co-oxidation by particulate methane monooxygenase. The presence of predicted epoxide detoxification systems in several other wetland methanotrophs suggests that co-oxidation of ambient ethylene presents a stress for methanotrophic bacteria in these environments and that epoxyethane removal has adaptive value.

Aerobic co-metabolic cis-Dichloroethene degradation with Trichloroethene as primary substrate and effects of concentration ratios

Pollution with chloroethenes threaten groundwater resources worldwide. Cis-Dichloroethene (cDCE) and Trichloroethene (TCE) are widespread pollutants that often occur together at contaminated sites, either as primary discharges or as degradation products of anaerobic dechlorination. In this study, comprehensive microcosm experiments were conducted with groundwater samples of seven sites contaminated with chloroethenes. In total, twelve wells with different pollutant concentrations and chloroethene compositions were sampled, and aerobic microcosms including sterile controls were set up. The results revealed interactions as well as interferences between cDCE and TCE. First, co-metabolic cDCE degradation with TCE as growth substrate was detected for the first time in this work. Transformation yields Ty' (molar ratio of co-substrate degraded to primary substrate degraded) of the degradation process were determined and showed a linear relationship with the cDCE/TCE concentration ratio. At low cDCE/TCE ratio, aerobic metabolic TCE degradation can result in complete cDCE removal due to co-metabolic degradation. Secondly, interfering effects were detected at notable cDCE levels resulting in deceleration of TCE degradation and residual concentrations which were also correlating linearly with the cDCE/TCE concentration ratio. These findings are significant for investigating chloroethene contaminated sites and planning remediation strategies. In particular, the efficiency biological remediation methods in the presence of both pollutants can be evaluated more precisely through the knowledge of interactions and interferences. Our study emphasizes that co-contaminants and possible effects of contaminant mixtures on the degradation rates of individual substances should be considered in general.

Critical Role of Monooxygenase in Biodegradation of 2,4,6-Trinitrotoluene by Buttiauxella sp. S19-1

2,4,6-Trinitrotoluene (TNT) is an aromatic pollutant that is difficult to be degraded in the natural environment. The screening of efficient degrading bacteria for bioremediation of TNT has received much attention from scholars. In this paper, transcriptome analysis of the efficient degrading bacterium Buttiauxella sp. S19-1 revealed that the monooxygenase gene (BuMO) was significantly up-regulated during TNT degradation. S-ΔMO (absence of BuMO gene in S19-1 mutant) degraded TNT 1.66-fold less efficiently than strain S19-1 (from 71.2% to 42.9%), and E-MO mutant (Escherichia coli BuMO-expressing strain) increased the efficiency of TNT degradation 1.33-fold (from 52.1% to 69.5%) for 9 h at 180 rpm at 27 °C in LB medium with 1.4 µg·mL^-1 TNT. We predicted the structure of BuMO and purified recombinant BuMO (rBuMO). Its specific activity was 1.81 µmol·min^-1·mg^-1 protein at pH 7.5 and 35 °C. The results of gas chromatography mass spectrometry (GC-MS) analysis indicated that 4-amino-2,6-dinitrotoluene (ADNT) is a metabolite of TNT biodegradation. We speculate that MO is involved in catalysis in the bacterial degradation pathway of TNT in TNT-polluted environment.

Intrinsic and bioaugmented aerobic trichloroethene degradation at seven sites

Trichloroethene (TCE) is one of the most prevalent contaminants in groundwater pollution worldwide. Aerobic-metabolic degradation of TCE has only recently been discovered at one field site. It has significant advantages over aerobic co-metabolism because no auxiliary substrates are required, and the oxygen demand is considerably lower. This study investigated the intrinsic degradation potential as well as the stimulation potential by bioaugmentation in microcosm experiments with groundwater from seven different sites contaminated with chloroethenes. An enrichment culture metabolizing TCE aerobically served as inoculum. The groundwater samples were inoculated with liquid culture in mineral salts medium as well as with immobilized culture on silica sand. Additionally, some samples were inoculated with groundwater from the site where the enrichment culture originated. The microcosms without inoculum proved the occurrence of aerobic TCE-metabolizing bacteria stimulated by the supply of oxygen in 54% of the groundwater samples. TCE degradation started in most cases after adaptation times of up to 92 d. The doubling time of 24 d indicated comparatively slow growth of the aerobic TCE degrading microorganisms. Bioaugmentation triggered or accelerated TCE-degradation in all microcosms with chlorothene concentrations below 100 mg L^-1. All inoculation strategies (liquid and immobilized enrichment culture or addition of groundwater from the active field site) were successful. Our study demonstrates that aerobic-metabolic TCE degradation can occur and be stimulated across a broad hydrogeologic spectrum and should be considered as a viable option for groundwater remediation at TCE-contaminated sites.

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.

Nocardioides alcanivorans sp. nov., a novel hexadecane-degrading species isolated from plastic waste

Strain NGK65T, a novel hexadecane degrading, non-motile, Gram-positive, rod-to-coccus shaped, aerobic bacterium, was isolated from plastic polluted soil sampled at a landfill. Strain NGK65T hydrolysed casein, gelatin, urea and was catalase-positive. It optimally grew at 28 °C, in 0–1% NaCl and at pH 7.5–8.0. Glycerol, d-glucose, arbutin, aesculin, salicin, potassium 5-ketogluconate, sucrose, acetate, pyruvate and hexadecane were used as sole carbon sources. The predominant membrane fatty acids were iso-C16:0 followed by iso-C17:0 and C18:1 ω9c. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and hydroxyphosphatidylinositol. The cell-wall peptidoglycan type was A3γ, with ll-diaminopimelic acid and glycine as the diagnostic amino acids. MK 8 (H4) was the predominant menaquinone. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NGK65T belongs to the genus Nocardioides (phylum Actinobacteria ), appearing most closely related to Nocardioides daejeonensis MJ31T (98.6%) and Nocardioides dubius KSL-104T (98.3%). The genomic DNA G+C content of strain NGK65T was 68.2%. Strain NGK65T and the type strains of species involved in the analysis had average nucleotide identity values of 78.3–71.9% as well as digital DNA–DNA hybridization values between 22.5 and 19.7%, which clearly indicated that the isolate represents a novel species within the genus Nocardioides . Based on phenotypic and molecular characterization, strain NGK65T can clearly be differentiated from its phylogenetic neighbours to establish a novel species, for which the name Nocardioides alcanivorans sp. nov. is proposed. The type strain is NGK65T (=DSM 113112T=NCCB 100846T).

Direct aerobic oxidation (DAO) of chlorinated aliphatic hydrocarbons: A review of key DAO bacteria, biometabolic pathways and in-situ bioremediation potential

Contamination of aquifers and vadose zones with chlorinated aliphatic hydrocarbons (CAH) is a world-wide issue. Unlike other reactions, direct aerobic oxidation (DAO) of CAHs does not require growth substrates and avoids the generation of toxic by-products. Here, we critically review the current understanding of chlorinated aliphatic hydrocarbons-DAO and its application in bioreactors and at the field scale. According to reports on chlorinated aliphatic hydrocarbons-DAO bacteria, isolates mainly consisted of Methylobacterium and Proteobacterium. Chlorinated aliphatic hydrocarbons-DAO bacteria are characterized by tolerance to a high concentration of CAHs and highly efficient removal of CAHs. Trans-1,2-dichloroethylene (t-DCE) is easily transformed biomass for bacteria, followed by 1,2-dichloroethane (1,2-DCA), dichloromethane (DCM), vinyl chloride (VC) and cis-1,2-dichloroethylene (c-DCE). Significant differences in the maximum specific growth rates were observed with different CAHs and biometabolic pathways for DCM, 1,2-DCA, VC and c-DCE degradation have been successfully parsed. Detection of the functional genes etnC and etnE is useful for the determination of active VC DAO bacteria. Additionally, DAO bacteria have been successfully applied to CAHs in new types of bioreactors with satisfactory results. To the best of the authors' knowledge, only one study on DAO-CAHs was conducted in-situ and resulted in 99% CAH removal. Lastly, we put forward future development prospect of chlorinated aliphatic hydrocarbons-DAO.

Comparative Genomic Study of Vinyl Chloride Cluster and Description of Novel Species, Mycolicibacterium vinylchloridicum sp. nov

Advanced physicochemical and chemical absorption methods for chlorinated ethenes are feasible but incur high costs and leave traces of pollutants on the site. Biodegradation of such pollutants by anaerobic or aerobic bacteria is emerging as a potential alternative. Several mycobacteria including Mycolicibacterium aurum L1, Mycolicibacterium chubuense NBB4, Mycolicibacterium rhodesiae JS60, Mycolicibacterium rhodesiae NBB3 and Mycolicibacterium smegmatis JS623 have previously been described as assimilators of vinyl chloride (VC). In this study, we compared nucleotide sequence of VC cluster and performed a taxogenomic evaluation of these mycobacterial species. The results showed that the complete VC cluster was acquired by horizontal gene transfer and not intrinsic to the genus Mycobacterium sensu lato. These results also revealed the presence of an additional xcbF1 gene that seems to be involved in Coenzyme M biosynthesis, which is ultimately used in the VC degradation pathway. Furthermore, we suggest for the first time that S/N-Oxide reductase encoding gene was involved in the dissociation of the SsuABC transporters from the organosulfur, which play a crucial role in the Coenzyme M biosynthesis. Based on genomic data, M. aurum L1, M. chubuense NBB4, M. rhodesiae JS60, M. rhodesiae NBB3 and M. smegmatis JS623 were misclassified and form a novel species within the genus Mycobacterium sensu lato. Mycolicibacterium aurum L1^T (CECT 8761^T = DSM 6695^T) was the subject of polyphasic taxonomic studies and showed ANI and dDDH values of 84.7 and 28.5% with its close phylogenetic neighbour, M. sphagni ATCC 33027^T. Phenotypic, chemotaxonomic and genomic data considering strain L1^T (CECT 8761^T = DSM 6695^T) as a type strain of novel species with the proposed name, Mycolicibacterium vinylchloridicum sp. nov.

Detection of an alkene monooxygenase in vinyl chloride-oxidizing bacteria with GeneFISH

Fluorescence in situ hybridization (FISH) can provide information on the morphology, spatial arrangement, and local environment of individual cells enabling the investigation of intact microbial communities. GeneFISH uses polynucleotide probes and enzymatic signal amplification to detect genes that are present in low copy numbers. Previously, this technique has only been applied in a small number of closely related organisms. However, many important functional genes, such as those involved in xenobiotic degradation or pathogenesis, are present in diverse microbial strains. Here, we present a geneFISH method for the detection of the functional gene etnC, which encodes the alpha subunit of an alkene monooxygenase used by aerobic ethene and vinyl chloride oxidizing bacteria (etheneotrophs). The probe concentration was optimized and found to be 100 pg/μl, similar to previous geneFISH reports. Permeabilization was necessary for successful geneFISH labeling of Mycobacteria; sequential treatment with lysozyme and achromopeptidase was the most effective treatment. This method was able to detect etnC in several organisms including Mycobacteria and Nocardioides, demonstrating for the first time that a single geneFISH probe can detect a variety of alleles (>80% sequence similarity) across multiple species. Detection of etnC with geneFISH has practical applications for bioremediation. This method can be readily adapted for other functional genes and has broad applications for investigating microbial communities in natural and engineered systems.

Bioaugmenting the poplar rhizosphere to enhance treatment of 1,4-dioxane

1,4-Dioxane is a highly mobile and persistent groundwater pollutant that often forms large dilute plumes. Because of this, utilizing aggressive pump-and-treat and ex-situ technologies such as advanced oxidation can be prohibitively expensive. In this study, we bioaugmented the poplar rhizosphere with dioxane-degrading bacteria Mycobacterium dioxanotrophicus PH-06 or Pseudonocardia dioxanivorans CB1190 to enhance treatment of 1,4-dioxane in bench-scale experiments. All treatments tested removed 10 mg/L dioxane to near health advisory levels (<4 μg/L). However, PH-06-bioaugmented poplar significantly outperformed all other treatments, reaching <4 μg/L in only 13 days. Growth curve experiments confirmed that PH-06 could not utilize root extract as an auxiliary carbon source for growth. Despite this limitation, our findings suggest that PH-06 is a strong bioaugmentation candidate to enhance the treatment of dioxane by phytoremediation. In addition, we confirmed that CB1190 could utilize both 1,4-dioxane and root extract as substrates. Finally, we demonstrated the large-scale production of these two strains for use in the field. Overall, this study shows that combining phytoremediation and bioaugmentation is an attractive strategy to treat dioxane-contaminated groundwater to low risk-based concentrations (~1 μg/L).

Vapor Intrusion Investigations and Decision-Making: A Critical Review

At sites impacted by volatile organic compounds (VOCs), vapor intrusion (VI) is the pathway with the greatest potential to result in actual human exposure. Since sites with VI were first widely publicized in late 1990s, the scientific understanding of VI has evolved considerably. The VI conceptual model has been extended beyond relatively simple scenarios to include nuances, such as biological and hydrogeological factors that may limit the potential for VI and alternative pathways, such as preferential pathways and direct building contact/infiltration that may enhance VI in some cases. Regulatory guidance documents typically recommend initial concentration- or distance-based screening to evaluate whether VI may be a concern, followed by a multiple-lines-of-evidence (MLE) investigation approach for sites that do not screen out. These recommendations for detailed evaluation of VI currently focus on monitoring of VOC concentrations in groundwater, soil gas, and indoor air and can be supplemented by other lines of evidence. In this Critical Review, we summarize key elements important to VI site characterization, provide the status and current understanding, and highlight data interpretation challenges, as well as innovative tools developed to help overcome the challenges. Although there have been significant advances in the understanding of VI in the past 20 years, limitations and knowledge gaps in screening, investigation methods, and modeling approaches still exist. Potential areas for further research include improved initial screening methods that account for the site-specific role of barriers, improved understanding of preferential pathways, and systematic study of buildings and infrastructure other than single-family residences.

Hydrochemical Conditions for Aerobic/Anaerobic Biodegradation of Chlorinated Ethenes—A Multi-Site Assessment

A stall of cis-1,2-DCE and vinyl chloride (VC) is frequently observed during bioremediation of groundwater chloroethenes via reductive dechlorination. These chloroethenes may be oxidised by aerobic methanotrophs or ethenotrophs co-metabolically and/or metabolically. We assessed the potential for such oxidation at 12 sites (49 groundwater samples) using hydrochemical and molecular biological tools. Both ethenotroph (etnC and etnE) and methanotroph (mmoX and pmoA) functional genes were identified in 90% of samples, while reductive dehalogenase functional genes (vcrA and bvcA) were identified in 82%. All functional genes were simultaneously detected in 78% of samples, in actively biostimulated sites in 88% of samples. Correlation analysis revealed that cis-1,2-DCE concentration was positively correlated with vcrA, etnC and etnE, while VC concentration was correlated with etnC, etnE, vcrA and bvcA. However, feature selection based on random forest classification indicated a significant relationship for the vcrA in relation to cis-1,2-DCE, and vcrA, bvcA and etnE for VC and no prove of relationship between cis-1,2-DCE or VC and the methanotroph functional genes. Analysis of hydrochemical parameters indicated that aerobic oxidation of chloroethenes by ethenotrophs may take place under a range of redox conditions of aquifers and coincide with high ethene and VC concentrations.

Do CSIA data from aquifers inform on natural degradation of chlorinated ethenes in aquitards?

Back-diffusion of chlorinated ethenes (CEs) from low-permeability layers (LPLs) causes contaminant persistence long after the primary spill zones have disappeared. Naturally occurring degradation in LPLs lowers remediation time frames, but its assessment through sediment sampling is prohibitive in conventional remediation projects. Scenario simulations were performed with a reactive transport model (PHT3D in FloPy) accounting for isotope effects associated with degradation, sorption, and diffusion, to evaluate the potential of CSIA data from aquifers in assessing degradation in aquitards. The model simulated a trichloroethylene (TCE) DNAPL and its pollution plume within an aquifer-aquitard-aquifer system. Sequential reductive dechlorination to ethene and sorption were uniform in the aquitard and did not occur in the aquifer. After 10 years of loading the aquitard through diffusion from the plume, subsequent source removal triggered release of TCE by back-diffusion. In the upper aquifer, during the loading phase, δ¹³C-TCE was slightly enriched (up to 2‰) due to diffusion effects stimulated by degradation in the aquitard. In the upper aquifer, during the release phase, (i) source removal triggered a huge δ¹³C increase especially for higher CEs, (ii) moreover, downstream decreasing isotope ratios (caused by downgradient later onset of the release phase) with temporal increasing isotope ratios reflect aquitard degradation (as opposed to downstream increasing and temporally constant isotope ratios in reactive aquifers), and (iii) the carbon isotope mass balance (CIMB) enriched up to 4‰ as lower CEs (more depleted, less sorbing) have been transported deeper into the aquitard. Thus, enriched CIMB does not indicate oxidative transformation in this system. The CIMB enrichment enhanced with more sorption and lower aquitard thickness. Thin aquitards are quicker flushed from lower CEs leading to faster CIMB enrichment over time. CIMB enrichment is smaller or nearly absent when daughter products accumulate. Aquifer CSIA patterns indicative of aquitard degradation were similar in case of linear decreasing rate constants but contrasted with previous simulations assuming a thin bioactive zone. The Rayleigh equation systematically underestimates the extent of TCE degradation in aquifer samples especially during the loading phase and for conditions leading to long remediation time frames (low groundwater flow velocity, thicker aquitards, strong sorption in the aquitard). The Rayleigh equation provides a good and useful picture on aquitard degradation during the release phase throughout the sensitivity analysis. This modelling study provides a framework on how aquifer CSIA data can inform on the occurrence of aquitard degradation and its pitfalls.

Dissipation, dehalogenation, and denitration of chloroaromatic compounds by Nocardioides sp. strain PD653: Characterization of the substrate specificity

The substrate range of Nocardioides sp. strain PD653, capable of mineralizing hexachlorobenzene, was investigated based on the dissipation of substrates and the liberation of halogen ions. Strain PD653 dehalogenated 10 out of 18 halophenol congeners; however, it could dehalogenate only hexachlorobenzene out of seven halobenzene congeners tested. Moreover, dehalogenation activities were shown for chloronitrobenzenes, along with an increase in the number of substituted chlorine atoms except for 2,3,4,5-tetrachloro-1-nitrobenzene. These results suggested that this strain might be applicable to remediate soil contaminated with these persistent chloroaromatic compounds.

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.

Aerobic metabolic trichloroethene biodegradation under field-relevant conditions

Chloroethenes belong to the most widely distributed groundwater contaminants. Since 2014, it has been known that trichloroethene (TCE) can be degraded aerobically and metabolically as growth substrate by a mixed bacterial enrichment culture (named SF culture). In this study, the degradation capabilities under a range of field-relevant conditions were investigated in fixed-bed reactors as well as in batch experiments. Aerobic metabolic TCE degradation was stable over the long term, with degradation optima at 22 °C and pH 7. Degradation of up to 400 μM TCE was observed. The longest starvation period after which degradation of TCE was regained was 112 days. The possible co-contaminants perchloroethene, trans-1,2-dichloroethene, and cis-1,2-dichloroethene did not inhibit TCE degradation, even though they were not degraded themselves. The presence of equimolar amounts of 1,1-dichloroethene and vinyl chloride inhibited TCE degradation. Experiments with groundwater from different chloroethene-contaminated field sites proved the potential of the SF culture for bioaugmentation. Thus, aerobic metabolic TCE degradation should be considered as a promising method for the bioremediation of field sites with TCE as the main contaminant.

Microbial Synthesis and Transformation of Inorganic and Organic Chlorine Compounds

Organic and inorganic chlorine compounds are formed by a broad range of natural geochemical, photochemical and biological processes. In addition, chlorine compounds are produced in large quantities for industrial, agricultural and pharmaceutical purposes, which has led to widespread environmental pollution. Abiotic transformations and microbial metabolism of inorganic and organic chlorine compounds combined with human activities constitute the chlorine cycle on Earth. Naturally occurring organochlorines compounds are synthesized and transformed by diverse groups of (micro)organisms in the presence or absence of oxygen. In turn, anthropogenic chlorine contaminants may be degraded under natural or stimulated conditions. Here, we review phylogeny, biochemistry and ecology of microorganisms mediating chlorination and dechlorination processes. In addition, the co-occurrence and potential interdependency of catabolic and anabolic transformations of natural and synthetic chlorine compounds are discussed for selected microorganisms and particular ecosystems.

Heterologous Expression of Mycobacterium Alkene Monooxygenases in Gram-Positive and Gram-Negative Bacterial Hosts

Alkene monooxygenases (MOs) are soluble di-iron-containing enzymes found in bacteria that grow on alkenes. Here, we report improved heterologous expression systems for the propene MO (PmoABCD) and ethene MO (EtnABCD) from Mycobacterium chubuense strain NBB4. Strong functional expression of PmoABCD and EtnABCD was achieved in Mycobacterium smegmatis mc2155, yielding epoxidation activities (62 and 27 nmol/min/mg protein, respectively) higher than any reported to date for heterologous expression of a di-iron MO system. Both PmoABCD and EtnABCD were specialized for the oxidation of gaseous alkenes (C2 to C4), and their activity was much lower on liquid alkenes (C5 to C8). Despite intensive efforts to express the complete EtnABCD enzyme in Escherichia coli, this was not achieved, although recombinant EtnB and EtnD proteins could be purified individually in soluble form. The biochemical function of EtnD as an oxidoreductase was confirmed (1.36 μmol cytochrome c reduced/min/mg protein). Cloning the EtnABCD gene cluster into Pseudomonas putida KT2440 yielded detectable epoxidation of ethene (0.5 nmol/min/mg protein), and this could be stimulated (up to 1.1 nmol/min/mg protein) by the coexpression of cpn60 chaperonins from either Mycobacterium spp. or E. coli Successful expression of the ethene MO in a Gram-negative host was validated by both whole-cell activity assays and peptide mass spectrometry of induced proteins seen on SDS-PAGE gels.IMPORTANCE Alkene MOs are of interest for their potential roles in industrial biocatalysis, most notably for the stereoselective synthesis of epoxides. Wild-type bacteria that grow on alkenes have high activities for alkene oxidation but are problematic for biocatalysis, since they tend to consume the epoxide products. Using recombinant biocatalysts is the obvious alternative, but a major bottleneck is the low activities of recombinant alkene MOs. Here, we provide new high-activity recombinant biocatalysts for alkene oxidation, and we provide insights into how to further improve these systems.

Coenzyme M biosynthesis in bacteria involves phosphate elimination by a functionally distinct member of the aspartase/fumarase superfamily

For nearly 30 years, coenzyme M (CoM) was assumed to be present solely in methanogenic archaea. In the late 1990s, CoM was reported to play a role in bacterial propene metabolism, but no biosynthetic pathway for CoM has yet been identified in bacteria. Here, using bioinformatics and proteomic approaches in the metabolically versatile bacterium Xanthobacter autotrophicus Py2, we identified four putative CoM biosynthetic enzymes encoded by the xcbB1, C1, D1, and E1 genes. Only XcbB1 was homologous to a known CoM biosynthetic enzyme (ComA), indicating that CoM biosynthesis in bacteria involves enzymes different from those in archaea. We verified that the ComA homolog produces phosphosulfolactate from phosphoenolpyruvate (PEP), demonstrating that bacterial CoM biosynthesis is initiated similarly as the phosphoenolpyruvate-dependent methanogenic archaeal pathway. The bioinformatics analysis revealed that XcbC1 and D1 are members of the aspartase/fumarase superfamily (AFS) and that XcbE1 is a pyridoxal 5'-phosphate-containing enzyme with homology to d-cysteine desulfhydrases. Known AFS members catalyze β-elimination reactions of succinyl-containing substrates, yielding fumarate as the common unsaturated elimination product. Unexpectedly, we found that XcbC1 catalyzes β-elimination on phosphosulfolactate, yielding inorganic phosphate and a novel metabolite, sulfoacrylic acid. Phosphate-releasing β-elimination reactions are unprecedented among the AFS, indicating that XcbC1 is an unusual phosphatase. Direct demonstration of phosphosulfolactate synthase activity for XcbB1 and phosphate β-elimination activity for XcbC1 strengthened their hypothetical assignment to a CoM biosynthetic pathway and suggested functions also for XcbD1 and E1. Our results represent a critical first step toward elucidating the CoM pathway in 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.

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.

Grape pomace compost harbors organohalide-respiring Dehalogenimonas species with novel reductive dehalogenase genes

Organohalide-respiring bacteria have key roles in the natural chlorine cycle; however, most of the current knowledge is based on cultures from contaminated environments. We demonstrate that grape pomace compost without prior exposure to chlorinated solvents harbors a Dehalogenimonas (Dhgm) species capable of using chlorinated ethenes, including the human carcinogen and common groundwater pollutant vinyl chloride (VC) as electron acceptors. Grape pomace microcosms and derived solid-free enrichment cultures were able to dechlorinate trichloroethene (TCE) to less chlorinated daughter products including ethene. 16S rRNA gene amplicon and qPCR analyses revealed a predominance of Dhgm sequences, but Dehalococcoides mccartyi (Dhc) biomarker genes were not detected. The enumeration of Dhgm 16S rRNA genes demonstrated VC-dependent growth, and 6.55±0.64 × 10⁸ cells were measured per μmole of chloride released. Metagenome sequencing enabled the assembly of a Dhgm draft genome, and 52 putative reductive dehalogenase (RDase) genes were identified. Proteomic workflows identified a putative VC RDase with 49 and 56.1% amino acid similarity to the known VC RDases VcrA and BvcA, respectively. A survey of 1,173 groundwater samples collected from 111 chlorinated solvent-contaminated sites in the United States and Australia revealed that Dhgm 16S rRNA genes were frequently detected and outnumbered Dhc in 65% of the samples. Dhgm are likely greater contributors to reductive dechlorination of chlorinated solvents in contaminated aquifers than is currently recognized, and non-polluted environments represent sources of organohalide-respiring bacteria with novel RDase genes.

Complete genome sequence of the sand-sediment actinobacterium Nocardioides dokdonensis FR1436T

Nocardioides dokdonensis, belonging to the class Actinobacteria, was first isolated from sand sediment of a beach in Dokdo, Korea, in 2005. In this study, we determined the genome sequence of FR1436, the type strain of N. dokdonensis, and analyzed its gene contents. The genome sequence is the second complete one in the genus Nocardioides after that of Nocardioides sp. JS614. It is composed of a 4,376,707-bp chromosome with a G + C content of 72.26%. From the genome sequence, 4,104 CDSs, three rRNA operons, 51 tRNAs, and one tmRNA were predicted, and 71.38% of the genes were assigned putative functions. Through the sequence analysis, dozens of genes involved in steroid metabolism, especially its degradation, were detected. Most of the identified genes were located in large gene clusters, which showed high similarities with the gene clusters in Pimelobacter simplex VKM Ac-2033D. Genomic features of N. dokdonensis associated with steroid catabolism indicate that it could be used for research and application of steroids in science and industry.

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.

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.

Nocardioides, Sediminibacterium, Aquabacterium, Variovorax, and Pseudomonas linked to carbon uptake during aerobic vinyl chloride biodegradation

Vinyl chloride (VC) is a frequent groundwater contaminant and a known human carcinogen. Bioremediation is a potential cleanup strategy for contaminated sites; however, little is known about the bacteria responsible for aerobic VC degradation in mixed microbial communities. In attempts to address this knowledge gap, the microorganisms able to assimilate labeled carbon ((13)C) from VC within a mixed culture capable of rapid VC degradation (120 μmol in 7 days) were identified using stable isotope probing (SIP). For this, at two time points during VC degradation (days 3 and 7), DNA was extracted from replicate cultures initially supplied with labeled or unlabeled VC. The extracted DNA was ultracentrifuged, fractioned, and the fractions of greater buoyant density (heavy fractions, 1.758 to 1.780 g mL(-1)) were subject to high-throughput sequencing. Following this, specific primers were designed for the most abundant phylotypes in the heavy fractions. Then, quantitative PCR (qPCR) was used across the buoyant density gradient to confirm label uptake by these phylotypes. From qPCR and/or sequencing data, five phylotypes were found to be dominant in the heavy fractions, including Nocardioides (∼40 %), Sediminibacterium (∼25 %), Aquabacterium (∼17 %), Variovorax (∼6 %), and Pseudomonas (∼1 %). The abundance of two functional genes (etnC and etnE) associated with VC degradation was also investigated in the SIP fractions. Peak shifts of etnC and etnE gene abundance toward heavier fractions were observed, indicating uptake of (13)C into the microorganisms harboring these genes. Analysis of the total microbial community indicated a significant dominance of Nocardioides over the other label-enriched phylotypes. Overall, the data indicate Nocardioides is primarily responsible for VC degradation in this mixed culture, with the other putative VC degraders generating a small growth benefit from VC degradation. The specific primers designed toward the putative VC degraders may be of use for investigating VC degradation potential at contaminated sites.

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.

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.

Organohalide Respiring Bacteria and Reductive Dehalogenases: Key Tools in Organohalide Bioremediation

Organohalides are recalcitrant pollutants that have been responsible for substantial contamination of soils and groundwater. Organohalide-respiring bacteria (ORB) provide a potential solution to remediate contaminated sites, through their ability to use organohalides as terminal electron acceptors to yield energy for growth (i.e., organohalide respiration). Ideally, this process results in non- or lesser-halogenated compounds that are mostly less toxic to the environment or more easily degraded. At the heart of these processes are reductive dehalogenases (RDases), which are membrane bound enzymes coupled with other components that facilitate dehalogenation of organohalides to generate cellular energy. This review focuses on RDases, concentrating on those which have been purified (partially or wholly) and functionally characterized. Further, the paper reviews the major bacteria involved in organohalide breakdown and the evidence for microbial evolution of RDases. Finally, the capacity for using ORB in a bioremediation and bioaugmentation capacity are discussed.

Gene and whole genome analyses reveal that the mycobacterial strain JS623 is not a member of the species Mycobacterium smegmatis

Unexpected differences were found between the genome of strain JS623, used in bioremediation studies, and the genome of strain mc²155, a model organism for investigating basic biology of mycobacteria. Both strains are currently assigned in the databases to the species Mycobacterium smegmatis and, consequently, the environmental isolate JS623 is increasingly included as a representative of that species in comparative genome‐based approaches aiming at identifying distinctive traits of the different members of the genus Mycobacterium. We applied traditional molecular taxonomic procedures – inference of single and concatenated gene trees – to re‐evaluate the membership of both strains to the same species, adopting the latest accepted cut‐off values for species delimitation. Additionally, modern whole genome‐based in silico methods where performed in a comprehensive molecular phylogenetic analysis of JS623 and other members of the genus Mycobacterium. These analyses showed that all relevant genome parameters of JS623 clearly separate this strain from M. smegmatis. The strain JS623 should be corrected as Mycobacterium sp. not only in the literature but, even more importantly, in the database entries, as inclusion of the genome wrongly attributed to the M. smegmatis species in comparative studies will result in misleading conclusions.

Biochemical and biophysical characterisation of haloalkane dehalogenases DmrA and DmrB in Mycobacterium strain JS60 and their role in growth on haloalkanes

Haloalkane dehalogenases (HLDs) catalyse the hydrolysis of haloalkanes to alcohols, offering a biological solution for toxic haloalkane industrial wastes. Hundreds of putative HLD genes have been identified in bacterial genomes, but relatively few enzymes have been characterised. We identified two novel HLDs in the genome of Mycobacterium rhodesiae strain JS60, an isolate from an organochlorine-contaminated site: DmrA and DmrB. Both recombinant enzymes were active against C2-C6 haloalkanes, with a preference for brominated linear substrates. However, DmrA had higher activity against a wider range of substrates. The kinetic parameters of DmrA with 4-bromobutyronitrile as a substrate were Km  = 1.9 ± 0.2 mM, kcat  = 3.1 ± 0.2 s(-1) . DmrB showed the highest activity against 1-bromohexane. DmrA is monomeric, whereas DmrB is tetrameric. We determined the crystal structure of selenomethionyl DmrA to 1.7 Å resolution. A spacious active site and alternate conformations of a methionine side-chain in the slot access tunnel may contribute to the broad substrate activity of DmrA. We show that M. rhodesiae JS60 can utilise 1-iodopropane, 1-iodobutane and 1-bromobutane as sole carbon and energy sources. This ability appears to be conferred predominantly through DmrA, which shows significantly higher levels of upregulation in response to haloalkanes than DmrB.

Biodegradation of cis-dichloroethene and vinyl chloride in the capillary fringe

Volatile chlorinated compounds are major pollutants in groundwater, and they pose a risk of vapor intrusion into buildings. Vapor intrusion can be prevented by natural attenuation in the vadose zone if biodegradation mechanisms can be established. In this study, we tested the hypothesis that bacteria can use cis-dichloroethene (cis-DCE) or vinyl chloride (VC) as an electron donor in the vadose zone. Anoxic water containing cis-DCE or VC was pumped continuously beneath laboratory columns that represented the vadose zone. Columns were inoculated with Polaromonas sp. strain JS666, which grows aerobically on cis-DCE, or with Mycobacterium sp. JS60 and Nocardiodes sp. JS614 that grow on VC. Complete biodegradation with fluxes of 84 ± 15 μmol of cis-DCE · m(-2) · hr(-1) and 218 ± 25 μmole VC·m(-2) · h(-1) within the 23 cm column indicated that microbial activities can prevent the migration of cis-DCE and VC vapors. Oxygen and volatile compound profiles along with enumeration of bacterial populations indicated that most of the biodegradation took place in the first 10 cm above the saturated zone within the capillary fringe. The results revealed that cis-DCE and VC can be biodegraded readily at the oxic/anoxic interfaces in the vadose zone if appropriate microbes are present.

Mutagenesis of the hydrocarbon monooxygenase indicates a metal centre in subunit-C, and not subunit-B, is essential for copper-containing membrane monooxygenase activity

The hydrocarbon monooxygenase (HMO) of Mycobacterium NBB4 is a member of the copper-containing membrane monooxygenase (CuMMO) superfamily, which also contains particulate methane monooxygenases (pMMOs) and ammonia monooxygenases (AMOs). CuMMOs have broad applications due to their ability to catalyse the oxidation of difficult substrates of environmental and industrial relevance. Most of our understanding of CuMMO biochemistry is based on pMMOs and AMOs as models. All three available structures are from pMMOs. These share two metal sites: a dicopper centre coordinated by histidine residues in subunit-B and a 'variable-metal' site coordinated by carboxylate and histidine residues from subunit-C. The exact nature and role of these sites is strongly debated. Significant barriers to progress have been the physiologically specialized nature of methanotrophs and autotrophic ammonia-oxidizers, lack of a recombinant expression system for either enzyme and difficulty in purification of active protein. In this study we use the newly developed HMO model system to perform site-directed mutagenesis on the predicted metal-binding residues in the HmoB and HmoC of NBB4 HMO. All mutations of predicted HmoC metal centre ligands abolished enzyme activity. Mutation of a predicted copper-binding residue of HmoB (B-H155V) reduced activity by 81 %. Mutation of a site that shows conservation within physiologically defined subgroups of CuMMOs was shown to reduce relative HMO activity towards larger alkanes. The study demonstrates that the modelled dicopper site of subunit-B is not sufficient for HMO activity and that a metal centre predicted to be coordinated by residues in subunit-C is essential for activity.

Application of polycolloid-releasing substrate to remediate trichloroethylene-contaminated groundwater: a pilot-scale study

The objectives of this pilot-scale study were to (1) evaluate the effectiveness of bioremediation of trichloroethylene (TCE)-contaminated groundwater with the supplement of slow polycolloid-releasing substrate (SPRS) (contained vegetable oil, cane molasses, surfactants) under reductive dechlorinating conditions, (2) apply gene analyses to confirm the existence of TCE-dechlorinating genes, and (3) apply the real-time polymerase chain reaction (PCR) to evaluate the variations in TCE-dechlorinating bacteria (Dehalococcoides spp.). Approximately 350L of SPRS solution was supplied into an injection well (IW) and groundwater samples were collected and analyzed from IW and monitor wells periodically. Results show that the SPRS caused a rapid increase of the total organic carbon concentration (up to 5794mg/L), and reductive dechlorination of TCE was significantly enhanced. TCE dechlorination byproducts were observed and up to 99% of TCE removal (initial TCE concentration=1872μg/L) was observed after 50 days of operation. The population of Dehalococcoides spp. increased from 4.6×10(1) to 3.41×10(7)cells/L after 20 days of operation. DNA sequencing results show that there were 31 bacterial species verified, which might be related to TCE biodegradation. Results demonstrate that the microbial analysis and real-time PCR are useful tools to evaluate the effectiveness of TCE reductive dechlorination.

Anaerobic oxidation of ethene coupled to sulfate reduction in microcosms and enrichment cultures

Ethene is considered recalcitrant under anaerobic conditions, but biological reduction to ethane and oxidation to CO2 have been reported; however, little is known about these processes or the organisms carrying them out. In this report we describe sulfate dependent ethene consumption in microcosms prepared with sediments from a freshwater canal. A first dose of 0.6 mmol/L ethene was consumed within 77 days, and a second dose was largely consumed twelve days later. Material from this microcosm was transferred into growth medium with ethene as the only electron donor (except for trace amounts of vitamins) and sulfate as the electron acceptor. Four doses of ethene were consumed at increasing rates, and the cultures have been transferred at least eight times in this medium. Conversion of [(14)C]ethene primarily to (14)CO2 was demonstrated in fifth and sixth generation cultures, as well as production of sulfide in other cultures, confirming the ethene/sulfate couple. Ovoid cells 1-2 μm in diameter were found in cultures containing ethene and sulfate, and quantitative PCR showed large increases in bacterial 16S rRNA gene copy number. Over half of a 16S rRNA gene clone library from a sixth-generation culture was a phylotype with a sequence ca. 90% identical with a clade of Deltaproteobacteria that includes Desulfovirga adipica and several Syntrophobacter spp. These studies have solidified the concept that deficits in mass balances for chloroethene fate in sulfate reducing zones of contaminated groundwater sites may be due to ethene oxidation, and suggest a unique phylotype is involved in this process.

RubisCO-based CO2 fixation and C1 metabolism in the actinobacterium Pseudonocardia dioxanivorans CB1190

Pseudonocardia is an actinobacterial genus of interest due to its potential biotechnological, medical and environmental remediation applications, as well as for the ecologically relevant symbiotic relationships it forms with attine ants. Some Pseudonocardia spp. can grow autotrophically, but the genetic basis of this capability has not previously been reported. In this study, we examined autotrophy in Pseudonocardia dioxanivorans CB1190, which can grow using H2 and CO2, as well as heterotrophically. Genomic and transcriptomic analysis of CB1190 cells grown with H2/bicarbonate implicated the Calvin-Benson-Bassham (CBB) cycle in growth-supporting CO2 fixation, as well as a [NiFe] hydrogenase-encoding gene cluster in H2 oxidation. The CBB cycle genes are evolutionarily most related to actinobacterial homologues, although synteny has not been maintained. Ribulose-1,5-bisphosphate carboxylase activity was confirmed in H2/bicarbonate-grown CB1190 cells and was detected in cells grown with the C1 compounds formate, methanol and carbon monoxide. We also demonstrated the upregulation of CBB cycle genes upon exposure of CB1190 to these C1 substrates, and identified genes putatively involved in generating CO2 from the C1 substrates by using RT-qPCR. Finally, the potential for autotrophic growth of other Pseudonocardia spp. was explored, and the ecological implications of autotrophy in attine ant- and plant root-associated Pseudonocardia discussed.

Cytochrome P450 initiates degradation of cis-dichloroethene by Polaromonas sp. strain JS666

Polaromonas sp. strain JS666 grows on cis-1,2-dichoroethene (cDCE) as the sole carbon and energy source under aerobic conditions, but the degradation mechanism and the enzymes involved are unknown. In this study, we established the complete pathway for cDCE degradation through heterologous gene expression, inhibition studies, enzyme assays, and analysis of intermediates. Several lines of evidence indicate that a cytochrome P450 monooxygenase catalyzes the initial step of cDCE degradation. Both the transient accumulation of dichloroacetaldehyde in cDCE-degrading cultures and dichloroacetaldehyde dehydrogenase activities in cell extracts of JS666 support a pathway for degradation of cDCE through dichloroacetaldehyde. The mechanism minimizes the formation of cDCE epoxide. The molecular phylogeny of the cytochrome P450 gene and the organization of neighboring genes suggest that the cDCE degradation pathway recently evolved in a progenitor capable of degrading 1,2-dichloroethane either by the recruitment of the cytochrome P450 monooxygenase gene from an alkane catabolic pathway or by selection for variants of the P450 in a preexisting 1,2-dichloroethane catabolic pathway. The results presented here add yet another role to the broad array of productive reactions catalyzed by cytochrome P450 enzymes.

Kinetics of 1,2-dichloroethane and 1,2-dibromoethane biodegradation in anaerobic enrichment cultures

1,2-Dichloroethane (1,2-DCA) and 1,2-dibromoethane (ethylene dibromide [EDB]) contaminate groundwater at many hazardous waste sites. The objectives of this study were to measure yields, maximum specific growth rates (μ), and half-saturation coefficients (K(S)) in enrichment cultures that use 1,2-DCA and EDB as terminal electron acceptors and lactate as the electron donor and to evaluate if the presence of EDB has an effect on the kinetics of 1,2-DCA dehalogenation and vice versa. Biodegradation was evaluated at the high concentrations found at some industrial sites (>10 mg/liter) and at lower concentrations found at former leaded-gasoline sites (1.9 to 3.7 mg/liter). At higher concentrations, the Dehalococcoides yield was 1 order of magnitude higher when bacteria were grown with 1,2-DCA than when they were grown with EDB, while μ's were similar for the two compounds, ranging from 0.19 to 0.52 day(-1) with 1,2-DCA to 0.28 to 0.36 day(-1) for EDB. K(S) was larger for 1,2-DCA (15 to 25 mg/liter) than for EDB (1.8 to 3.7 mg/liter). In treatments that received both compounds, EDB was always consumed first and adversely impacted the kinetics of 1,2-DCA utilization. Furthermore, 1,2-DCA dechlorination was interrupted by the addition of EDB at a concentration 100 times lower than that of the remaining 1,2-DCA; use of 1,2-DCA did not resume until the EDB level decreased close to its maximum contaminant level (MCL). In lower-concentration experiments, the preferential consumption of EDB over 1,2-DCA was confirmed; both compounds were eventually dehalogenated to their respective MCLs (5 μg/liter for 1,2-DCA, 0.05 μg/liter for EDB). The enrichment culture grown with 1,2-DCA has the advantage of a more rapid transition to 1,2-DCA after EDB is consumed.