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

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.

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.

Diversity of bacteria and archaea in the groundwater contaminated by chlorinated solvents undergoing natural attenuation

Chlorinated solvents (CS)-contaminated groundwater poses serious risks to the environment and public health. Microorganisms play a vital role in efficient remediation of CS. In this study, the microbial community (bacterial and archaeal) composition of three CS-contaminated groundwater wells located at an abandoned chemical factory which covers three orders of magnitude in concentration (0.02-16.15 mg/L) were investigated via 16S rRNA gene high-throughput sequencing. The results indicated that Proteobacteria and Thaumarchaeota were the most abundant bacterial and archaeal groups at the phylum level in groundwater, respectively. The major bacterial genera (Flavobacterium sp., Mycobacterium sp. and unclassified Parcubacteria taxa, etc.) and archaeal genera (Thaumarchaeota Group C3, Miscellaneous Crenarchaeotic Group and Miscellaneous Euryarchaeotic Group, etc.) might be involved in the dechlorination processes. In addition, Pearson's correlation analyses showed that alpha diversity of the bacterial community was not significantly correlated with CS concentration, while alpha diversity of archaeal community greatly decreased with the increased contamination of CS. Moreover, partial Mantel test indicated that oxidation-reduction potential, dissolved oxygen, temperature and methane concentration were major drivers of bacterial and archaeal community composition, whereas CS concentration had no significant impact, indicating that both indigenous bacterial and archaeal community compositions are capable of withstanding elevated CS contamination. This study improves our understanding of how the natural microbial community responds to high CS-contaminated groundwater.

Genetic and Physiological Characteristics of a Novel Marine Propylene-Assimilating Halieaceae Bacterium Isolated from Seawater and the Diversity of Its Alkene and Epoxide Metabolism Genes

The Gram-negative marine propylene-assimilating bacterium, strain PE-TB08W, was isolated from surface seawater. A structural gene analysis using the 16S rRNA gene showed 96, 94, and 95% similarities to Halioglobus species, Haliea sp. ETY-M, and Haliea sp. ETY-NAG, respectively. A phylogenetic tree analysis showed that strain PE-TB08W belonged to the EG19 (Chromatocurvus)-Congregibacter-Haliea cluster within the Halieaceae (formerly Alteromonadaceae) family. Thus, strain PE-TB08W was characterized as a newly isolated Halieaceae bacterium; we suggest that this strain belongs to a new genus. Other bacterial characteristics were investigated and revealed that strain PE-TB08W assimilated propylene, n-butane, 1-butene, propanol, and 1-butanol (C3 and C4 gaseous hydrocarbons and primary alcohols), but not various other alcohols, including methane, ethane, ethylene, propane, and i-butane. The putative alkene monooxygenase (amo) gene in this strain was a soluble methane monooxygenase-type (sMMO) gene that is ubiquitous in alkene-assimilating bacteria for the initial oxidation of alkenes. In addition, two epoxide carboxylase systems containing epoxyalkane, the co-enzyme M transferase (EaCoMT) gene, and the co-enzyme M biosynthesis gene, were found in the upstream region of the sMMO gene cluster. Both of these genes were similar to those in Xanthobacter autotrophicus Py2 and were inductively expressed by propylene. These results have a significant impact on the genetic relationship between terrestrial and marine alkene-assimilating 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.

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.

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.

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.

Selection for growth on 3-nitrotoluene by 2-nitrotoluene-utilizing Acidovorax sp. strain JS42 identifies nitroarene dioxygenases with altered specificities

Acidovorax sp. strain JS42 uses 2-nitrotoluene as a sole source of carbon and energy. The first enzyme of the degradation pathway, 2-nitrotoluene 2,3-dioxygenase, adds both atoms of molecular oxygen to 2-nitrotoluene, forming nitrite and 3-methylcatechol. All three mononitrotoluene isomers serve as substrates for 2-nitrotoluene dioxygenase, but strain JS42 is unable to grow on 3- or 4-nitrotoluene. Using both long- and short-term selections, we obtained spontaneous mutants of strain JS42 that grew on 3-nitrotoluene. All of the strains obtained by short-term selection had mutations in the gene encoding the α subunit of 2-nitrotoluene dioxygenase that changed isoleucine 204 at the active site to valine. Those strains obtained by long-term selections had mutations that changed the same residue to valine, alanine, or threonine or changed the alanine at position 405, which is just outside the active site, to glycine. All of these changes altered the regiospecificity of the enzymes with 3-nitrotoluene such that 4-methylcatechol was the primary product rather than 3-methylcatechol. Kinetic analyses indicated that the evolved enzymes had enhanced affinities for 3-nitrotoluene and were more catalytically efficient with 3-nitrotoluene than the wild-type enzyme. In contrast, the corresponding amino acid substitutions in the closely related enzyme nitrobenzene 1,2-dioxygenase were detrimental to enzyme activity. When cloned genes encoding the evolved dioxygenases were introduced into a JS42 mutant lacking a functional dioxygenase, the strains acquired the ability to grow on 3-nitrotoluene but with significantly longer doubling times than the evolved strains, suggesting that additional beneficial mutations occurred elsewhere in the genome.

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.

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.