Physiological and molecular genetic analyses of vinyl chloride and ethene biodegradation in Nocardioides sp. strain JS614

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.

Amaranth Plants with Various Color Phenotypes Recruit Different Soil Microorganisms in the Rhizosphere

To explore and utilize the abundant soil microorganisms and their beneficial functions, high-throughput sequencing technology was used to analyze soil microbial compositions in the rhizosphere of red and green amaranth varieties. The results showed that significant differences in soil microbial composition could be found in the rhizosphere of amaranth plants with different color phenotypes. Firstly, soil bacterial compositions in the rhizosphere were significantly different between red and green amaranths. Among them, Streptomyces, Pseudonocardia, Pseudolabrys, Acidibacter, norank_ f_ Micropepsaceae, Bradyrhizobium, and Nocardioides were the unique dominant soil bacterial genera in the rhizosphere of red amaranth. In contrast, Conexibacter, norank_f_norank_o_norank_c_TK10, and norank_f_ norank_o_ norank_ c_AD3 were the special dominant soil bacterial genera in the rhizosphere of green amaranth. Additionally, even though the soil fungal compositions in the rhizosphere were not significantly different between red and green amaranths, the abundance of the dominant soil fungal genera in the rhizosphere showed significant differences between red and green amaranths. For example, unclassified_k__Fungi, Fusarium, Cladophialophora, unclassified_c__Sordariomycetes and unclassified_p__Chytridiomycota significantly enriched as the dominant soil fungal genera in the rhizosphere of the red amaranth. In contrast, Aspergillues only significantly enriched as the dominant soil fungal genus in the rhizosphere of green amaranth. All of the above results indicated that amaranth with various color phenotypes exactly recruited different microorganisms in rhizosphere, and the enrichments of soil microorganisms in the rhizosphere could be speculated in contributing to amaranth color formations.

Development of a whole-cell biosensor for ethylene oxide and ethylene

Ethylene and ethylene oxide are widely used in the chemical industry, and ethylene is also important for its role in fruit ripening. Better sensing systems would assist risk management of these chemicals. Here, we characterise the ethylene regulatory system in Mycobacterium strain NBB4 and use these genetic parts to create a biosensor. The regulatory genes etnR1 and etnR2 and cognate promoter Petn were combined with a fluorescent reporter gene (fuGFP) in a Mycobacterium shuttle vector to create plasmid pUS301-EtnR12P. Cultures of M. smegmatis mc2-155(pUS301-EtnR12P) gave a fluorescent signal in response to ethylene oxide with a detection limit of 0.2 μM (9 ppb). By combining the epoxide biosensor cells with another culture expressing the ethylene monooxygenase, the system was converted into an ethylene biosensor. The co-culture was capable of detecting ethylene emission from banana fruit. These are the first examples of whole-cell biosensors for epoxides or aliphatic alkenes. This work also resolves long-standing questions concerning the regulation of ethylene catabolism in bacteria.

A novel soluble di-iron monooxygenase from the soil bacterium Solimonas soli

Soluble di-iron monooxygenase (SDIMO) enzymes enable insertion of oxygen into diverse substrates and play significant roles in biogeochemistry, bioremediation and biocatalysis. An unusual SDIMO was detected in an earlier study in the genome of the soil organism Solimonas soli, but was not characterized. Here, we show that the S. soli SDIMO is part of a new clade, which we define as 'Group 7'; these share a conserved gene organization with alkene monooxygenases but have only low amino acid identity. The S. soli genes (named zmoABCD) could be functionally expressed in Pseudomonas putida KT2440 but not in Escherichia coli TOP10. The recombinants made epoxides from C2 C8 alkenes, preferring small linear alkenes (e.g. propene), but also epoxidating branched, carboxylated and chlorinated substrates. Enzymatic epoxidation of acrylic acid was observed for the first time. ZmoABCD oxidised the organochlorine pollutants vinyl chloride (VC) and cis-1,2-dichloroethene (cDCE), with the release of inorganic chloride from VC but not cDCE. The original host bacterium S. soli could not grow on any alkenes tested but grew well on phenol and n-octane. Further work is needed to link ZmoABCD and the other Group 7 SDIMOs to specific physiological and ecological roles.

Nocardioides: "Specialists" for Hard-to-Degrade Pollutants in the Environment

Nocardioides, a genus belonging to Actinomycetes, can endure various low-nutrient conditions. It can degrade pollutants using multiple organic materials such as carbon and nitrogen sources. The characteristics and applications of Nocardioides are described in detail in this review, with emphasis on the degradation of several hard-to-degrade pollutants by using Nocardioides, including aromatic compounds, hydrocarbons, haloalkanes, nitrogen heterocycles, and polymeric polyesters. Nocardioides has unique advantages when it comes to hard-to-degrade pollutants. Compared to other strains, Nocardioides has a significantly higher degradation rate and requires less time to break down substances. This review can be a theoretical basis for developing Nocardioides as a microbial agent with significant commercial and application potential.

The 2-methylpropene degradation pathway in Mycobacteriaceae family strains

Mycolicibacterium gadium IBE100 and Mycobacterium paragordonae IBE200 are aerobic, chemoorganoheterotrophic bacteria isolated from activated sludge from a wastewater treatment plant. They use 2-methylpropene (isobutene, 2-MP) as the sole source of carbon and energy. Here, we postulate a degradation pathway of 2-methylpropene derived from whole genome sequencing, differential expression analysis and peptide-mass fingerprinting. Key genes identified are coding for a 4-component soluble diiron monooxygenase with epoxidase activity, an epoxide hydrolase, and a 2-hydroxyisobutyryl-CoA mutase. In both strains, involved genes are arranged in clusters of 61.0 and 58.5 kbp, respectively, which also contain the genes coding for parts of the aerobic pathway of adenosylcobalamin synthesis. This vitamin is essential for the carbon rearrangement reaction catalysed by the mutase. These findings provide data for the identification of potential 2-methylpropene degraders.

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.

Different rhizosphere soil microbes are recruited by tomatoes with different fruit color phenotypes

Background

To explore and utilize abundant soil microbes and their beneficial functions, the bacterial and fungal compositions in rhizospheres between red- and yellow-fruited tomato varieties were analyzed using high-throughput sequencing technique.

Result

Our results indicated that different soil microbes in rhizospheres of tomatoes were exactly recruited by different color fruit tomatoes. For the reasons as not only soil bacterial community, but also soil fungal compositions were all different between red and yellow fruit tomatoes. For example, Nocardioides, norank_f_norank_o_Vicinamibacterales, norank_f_norank_o_norank_c_KD4-96, norank_f_Birii41, norank_f_norank_o_S085 and Bradyrhizobium were the specific dominant soil bacterial genera, and Lecythophora, Derxomyces and unclassified_f_Pyronemataceae were the dominant soil fungal genera in the rhizospheres of red tomato varieties. By contrast, unclassified_f__Micromonsporaceae, Acidipila, Roseisolibacter, Gaiella and norank_f_Xanthobacteraceae were the unique dominant soil bacterial genera in the rhizospheres of yellow tomato varieties. And unclassified_o__Onygenales, Trichocladium, unclassified_c__Sordariomycetes, Pseudogymnoascus, Acremonium, Oidiodendron, Phialemonium, Penicillium, Phialosimplex were the unique dominant soil fungal genera in rhizospheres of yellow tomato varieties. Moreover, a higher abundance of specific soil bacterial and fungal genera in the rhizosphere was found in rhizospheres of the yellow than those of the red tomato varieties.

Conclusion

Soil bacterial and fungal compositions in rhizospheres between red- and yellow-fruited tomato varieties were found significantly different which growing in the same environment under the identical managements. It suggested that different soil microbes in rhizospheres exactly were recruited by different phenotypes tomato varieties related to fruit color formation.

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.

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.

Synthetic Biology Approaches to Hydrocarbon Biosensors: A Review

Monooxygenases are a class of enzymes that facilitate the bacterial degradation of alkanes and alkenes. The regulatory components associated with monooxygenases are nature's own hydrocarbon sensors, and once functionally characterised, these components can be used to create rapid, inexpensive and sensitive biosensors for use in applications such as bioremediation and metabolic engineering. Many bacterial monooxygenases have been identified, yet the regulation of only a few of these have been investigated in detail. A wealth of genetic and functional diversity of regulatory enzymes and promoter elements still remains unexplored and unexploited, both in published genome sequences and in yet-to-be-cultured bacteria. In this review we examine in detail the current state of research on monooxygenase gene regulation, and on the development of transcription-factor-based microbial biosensors for detection of alkanes and alkenes. A new framework for the systematic characterisation of the underlying genetic components and for further development of biosensors is presented, and we identify focus areas that should be targeted to enable progression of more biosensor candidates to commercialisation and deployment in industry and in the environment.

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.

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.

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.

Identification of the hcb Gene Operon Involved in Catalyzing Aerobic Hexachlorobenzene Dechlorination in Nocardioides sp. Strain PD653

Nocardioides sp. strain PD653 was the first identified aerobic bacterium capable of mineralizing hexachlorobenzene (HCB). In this study, strain PD653-B2, which was unexpectedly isolated from a subculture of strain PD653, was found to lack the ability to transform HCB or pentachloronitrobenzene into pentachlorophenol. Comparative genome analysis of the two strains revealed that genetic rearrangement had occurred in strain PD653-B2, with a genomic region present in strain PD653 being deleted. In silico analysis allowed three open reading frames within this region to be identified as candidate genes involved in HCB dechlorination. Assays using recombinant Escherichia coli cells revealed that an operon is responsible for both oxidative HCB dechlorination and pentachloronitrobenzene denitration. The metabolite pentachlorophenol was detected in the cultures produced in the E. coli assays. Significantly less HCB-degrading activity occurred in assays under oxygen-limited conditions ([O₂] < 0.5 mg liter^-1) than under aerobic assays, suggesting that monooxygenase is involved in the reaction. In this operon, hcbA1 was found to encode a monooxygenase involved in HCB dechlorination. This monooxygenase may form a complex with the flavin reductase encoded by hcbA3, increasing the HCB-degrading activity of PD653.IMPORTANCE The organochlorine fungicide HCB is widely distributed in the environment. Bioremediation can effectively remove HCB from contaminated sites, but HCB-degrading microorganisms have been isolated in few studies and the genes involved in HCB degradation have not been identified. In this study, possible genes involved in the initial step of the mineralization of HCB by Nocardioides sp. strain PD653 were identified. The results improve our understanding of the protein families involved in the dechlorination of HCB to give pentachlorophenol.

Identification and characterisation of isoprene-degrading bacteria in an estuarine environment

Approximately one‐third of volatile organic compounds (VOCs) emitted to the atmosphere consists of isoprene, originating from the terrestrial and marine biosphere, with a profound effect on atmospheric chemistry. However, isoprene provides an abundant and largely unexplored source of carbon and energy for microbes. The potential for isoprene degradation in marine and estuarine samples from the Colne Estuary, UK, was investigated using DNA‐Stable Isotope Probing (DNA‐SIP). Analysis at two timepoints showed the development of communities dominated by Actinobacteria including members of the genera Mycobacterium, Rhodococcus, Microbacterium and Gordonia. Representative isolates, capable of growth on isoprene as sole carbon and energy source, were obtained from marine and estuarine locations, and isoprene‐degrading strains of Gordonia and Mycobacterium were characterised physiologically and their genomes were sequenced. Genes predicted to be required for isoprene metabolism, including four‐component isoprene monooxygenases (IsoMO), were identified and compared with previously characterised examples. Transcriptional and activity assays of strains growing on isoprene or alternative carbon sources showed that growth on isoprene is an inducible trait requiring a specific IsoMO. This study is the first to identify active isoprene degraders in estuarine and marine environments using DNA‐SIP and to characterise marine isoprene‐degrading bacteria at the physiological and molecular level.

Microbial degradation of chloroethenes: a review

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

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

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

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

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

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.

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.

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.

Isolation of two novel marine ethylene-assimilating bacteria, Haliea species ETY-M and ETY-NAG, containing particulate methane monooxygenase-like genes

Two novel ethylene-assimilating bacteria, strains ETY-M and ETY-NAG, were isolated from seawater around Japan. The characteristics of both strains were investigated, and phylogenetic analyses of their 16S rRNA gene sequences showed that they belonged to the genus Haliea. In C1-4 gaseous hydrocarbons, both strains grew only on ethylene, but degraded ethane, propylene, and propane in addition to ethylene. Methane, n-butane, and i-butane were not utilized or degraded by either strain. Soluble methane monooxygenase-type genes, which are ubiquitous in alkene-assimilating bacteria for initial oxidation of alkenes, were not detected in these strains, although genes similar to particulate methane monooxygenases (pMMO)/ammonia monooxygenases (AMO) were observed. The phylogenetic tree of the deduced amino acid sequences formed a new clade near the monooxygenases of ethane-assimilating bacteria similar to other clades of pMMOs in type I, type II, and Verrucomicrobia methanotrophs and AMOs in alpha and beta proteobacteria.

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.

Untangling the multiple monooxygenases of Mycobacterium chubuense strain NBB4, a versatile hydrocarbon degrader

Mycobacterium strain NBB4 was isolated on ethene as part of a bioprospecting study searching for novel monooxygenase (MO) enzymes of interest to biocatalysis and bioremediation. Previous work indicated that strain NBB4 contained an unprecedented diversity of MO genes, and we hypothesized that each MO type would support growth on a distinct hydrocarbon substrate. Here, we attempted to untangle the relationships between MO types and hydrocarbon substrates. Strain NBB4 was shown to grow on C2 -C4 alkenes and C2 -C16 alkanes. Complete gene clusters encoding six different monooxygenases were recovered from a fosmid library, including homologues of ethene MO (etnABCD), propene MO (pmoABCD), propane MO (smoABCD), butane MO (smoXYB1C1Z), cytochrome P450 (CYP153; fdx-cyp-fdr) and alkB (alkB-rubA1-rubA2). Catabolic enzymes involved in ethene assimilation (EtnA, EtnC, EtnD, EtnE) and alkane assimilation (alcohol and aldehyde dehydrogenases) were identified by proteomics, and we showed for the first time that stress response proteins (catalase/peroxidase, chaperonins) were induced by growth on C2 -C5 alkanes and ethene. Surprisingly, none of the identified MO genes could be specifically associated with oxidation of small alkanes, and thus the nature of the gaseous alkane MO in NBB4 remains mysterious.

The membrane-associated monooxygenase in the butane-oxidizing Gram-positive bacterium Nocardioides sp. strain CF8 is a novel member of the AMO/PMO family

The Gram-positive bacterium Nocardioides sp. strain CF8 uses a membrane-associated monooxygenase (pBMO) to grow on butane. The nucleotide sequences of the genes encoding this novel monooxygenase were revealed through analysis of a de novo assembled draft genome sequence determined by high-throughput sequencing of the whole genome. The pBMO genes were in a similar arrangement to the genes for ammonia monooxygenase (AMO) from the ammonia-oxidizing bacteria and for particulate methane monooxygenase (pMMO) from the methane-oxidizing bacteria. The pBMO genes likely constitute an operon in the order bmoC, bmoA and bmoB. The nucleotide sequence was less than 50% similar to the genes for AMO and pMMO. The operon for pBMO was confirmed to be a single copy in the genome by Southern and computational analyses. In an incubation on butane the increase of transcriptional activity of the pBmoA gene was congruent with the increase of pBMO activity and suggested correspondence between gene expression and the utilization of butane. Phylogenetic comparison revealed distant but significant similarity of all three pBMO subunits to homologous members of the AMO/pMMO family and indicated that the pBMO represents a deeply branching third lineage of this group of particulate monooxygenases. No other bmoCAB-like genes were found to cluster with pBMO lineage in phylogenetic analysis by database searches including genomic and metagenomic sequence databases. pBMO is the first example of the AMO/pMMO-like monooxygenase from Gram-positive bacteria showing similarities to proteobacterial pMMO and AMO sequences.

Genome Sequence of the ethene- and vinyl chloride-oxidizing actinomycete Nocardioides sp. strain JS614

Nocardioides sp. strain JS614 grows on ethene and vinyl chloride (VC) as sole carbon and energy sources and is of interest for bioremediation and biocatalysis. Sequencing of the complete genome of JS614 provides insight into the genetic basis of alkene oxidation, supports ongoing research into the physiology and biochemistry of growth on ethene and VC, and provides biomarkers to facilitate detection of VC/ethene oxidizers in the environment. This is the first genome sequence from the genus Nocardioides and the first genome of a VC/ethene-oxidizing bacterium.

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.

Extending the alkene substrate range of vinyl chloride utilizing Nocardioides sp. strain JS614 with ethene oxide

Nocardioides sp. strain JS614 grows on the C(2) alkenes ethene (Eth), vinyl chloride, and vinyl fluoride as sole carbon sources. The presence of 400-800 microM ethene oxide (EtO) extended the growth substrate range to propene (C(3)) and butene (C(4)). Propene-dependent growth of JS614 was CO(2) dependent and was prevented by the carboxylase/reductase inhibitor 2-bromoethanesulfonic acid, sodium salt (BES), while growth on Eth was not CO(2) dependent or BES sensitive. Although unable to promote growth, both propene and propene oxide (PrO)-induced expression of the genes encoding the alpha subunit of alkene monooxygenase (etnC) and epoxyethane CoM transferase (etnE) to similar levels as did Eth and EtO. Propene was transformed by Eth-grown and propene-grown/EtO-induced JS614 to PrO at a rate 4.2 times faster than PrO was consumed. As a result PrO accumulated in growth medium to 900 microM during EtO-induced growth on propene. PrO (50-100 microM) exerted inhibitory effects on growth of JS614 on both acetate and Eth, and on EtO-induced growth on Eth. However, higher EtO concentrations (300-400 microM) overcame the negative effects of PrO on Eth-dependent growth.

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

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

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

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

High-level chromate resistance in Arthrobacter sp. strain FB24 requires previously uncharacterized accessory genes

Background

The genome of Arthrobacter sp. strain FB24 contains a chromate resistance determinant (CRD), consisting of a cluster of 8 genes located on a 10.6 kb fragment of a 96 kb plasmid. The CRD includes chrA, which encodes a putative chromate efflux protein, and three genes with amino acid similarities to the amino and carboxy termini of ChrB, a putative regulatory protein. There are also three novel genes that have not been previously associated with chromate resistance in other bacteria; they encode an oxidoreductase (most similar to malate:quinone oxidoreductase), a functionally unknown protein with a WD40 repeat domain and a lipoprotein. To delineate the contribution of the CRD genes to the FB24 chromate [Cr(VI)] response, we evaluated the growth of mutant strains bearing regions of the CRD and transcript expression levels in response to Cr(VI) challenge.

Results

A chromate-sensitive mutant (strain D11) was generated by curing FB24 of its 96-kb plasmid. Elemental analysis indicated that chromate-exposed cells of strain D11 accumulated three times more chromium than strain FB24. Introduction of the CRD into strain D11 conferred chromate resistance comparable to wild-type levels, whereas deletion of specific regions of the CRD led to decreased resistance. Using real-time reverse transcriptase PCR, we show that expression of each gene within the CRD is specifically induced in response to chromate but not by lead, hydrogen peroxide or arsenate. Higher levels of chrA expression were achieved when the chrB orthologs and the WD40 repeat domain genes were present, suggesting their possible regulatory roles.

Conclusion

Our findings indicate that chromate resistance in Arthrobacter sp. strain FB24 is due to chromate efflux through the ChrA transport protein. More importantly, new genes have been identified as having significant roles in chromate resistance. Collectively, the functional predictions of these additional genes suggest the involvement of a signal transduction system in the regulation of chromate efflux and warrants further study.

A molecular key for building hyphae aggregates: the role of the newly identified Streptomyces protein HyaS

Streptomycetes produce many metabolites with medical and biotechnological applications. During fermentations, their hyphae build aggregates, a process in which the newly identified protein HyaS plays an important role. The corresponding hyaS gene is present within all investigated Streptomyces species. Reporter fusions indicate that transcription of hyaS occurs within substrate hyphae of the Streptomyces lividans wild type (WT). The HyaS protein is dominantly associated with the substrate hyphae. The WT strain forms cylindrically shaped clumps of densely packed substrate hyphae, often fusing to higher aggregates (pellets), which remain stably associated during shaking. Investigations by electron microscopy suggest that HyaS induces tight fusion‐like contacts among substrate hyphae. In contrast, the pellets of the designed hyaS disruption mutant ΔH are irregular in shape, contain frequently outgrowing bunches of hyphae, and fuse less frequently. ΔH complemented with a plasmid carrying hyaS resembles the WT phenotype. Biochemical studies indicate that the C‐terminal region of HyaS has amine oxidase activity. Investigations of ΔH transformants, each carrying a specifically mutated gene, lead to the conclusion that the in situ oxidase activity correlates with the pellet‐inducing role of HyaS, and depends on the presence of certain histidine residues. Furthermore, the level of undecylprodigiosin, a red pigment with antibiotic activity, is influenced by the engineered hyaS subtype within a strain. These data present the first molecular basis for future manipulation of pellets, and concomitant production of secondary metabolites during biotechnological processes.

Getting a handle on the role of coenzyme M in alkene metabolism

Coenzyme M (2-mercaptoethanesulfonate; CoM) is one of several atypical cofactors discovered in methanogenic archaea which participate in the biological reduction of CO(2) to methane. Elegantly simple, CoM, so named for its role as a methyl carrier in all methanogenic archaea, is the smallest known organic cofactor. It was thought that this cofactor was used exclusively in methanogenesis until it was recently discovered that CoM is a key cofactor in the pathway of propylene metabolism in the gram-negative soil microorganism Xanthobacter autotrophicus Py2. A four-step pathway requiring CoM converts propylene and CO(2) to acetoacetate, which feeds into central metabolism. In this process, CoM is used to activate and convert highly electrophilic epoxypropane, formed from propylene epoxidation, into a nucleophilic species that undergoes carboxylation. The unique properties of CoM provide a chemical handle for orienting compounds for site-specific redox chemistry and stereospecific catalysis. The three-dimensional structures of several of the enzymes in the pathway of propylene metabolism in defined states have been determined, providing significant insights into both the enzyme mechanisms and the role of CoM in this pathway. These studies provide the structural basis for understanding the efficacy of CoM as a handle to direct organic substrate transformations at the active sites of enzymes.

The genome of Polaromonas sp. strain JS666: insights into the evolution of a hydrocarbon- and xenobiotic-degrading bacterium, and features of relevance to biotechnology

Polaromonas sp. strain JS666 can grow on cis-1,2-dichloroethene (cDCE) as a sole carbon and energy source and may be useful for bioremediation of chlorinated solvent-contaminated sites. Analysis of the genome sequence of JS666 (5.9 Mb) shows a bacterium well adapted to pollution that carries many genes likely to be involved in hydrocarbon and xenobiotic catabolism and metal resistance. Clusters of genes coding for haloalkane, haloalkanoate, n-alkane, alicyclic acid, cyclic alcohol, and aromatic catabolism were analyzed in detail, and growth on acetate, catechol, chloroacetate, cyclohexane carboxylate, cyclohexanol, ferulate, heptane, 3-hydroxybenzoate, hydroxyquinol, gentisate, octane, protocatechuate, and salicylate was confirmed experimentally. Strain JS666 also harbors diverse putative mobile genetic elements, including retrons, inteins, a miniature inverted-repeat transposable element, insertion sequence transposases from 14 families, eight genomic islands, a Mu family bacteriophage, and two large (338- and 360-kb) plasmids. Both plasmids are likely to be self-transferable and carry genes for alkane, alcohol, aromatic, and haloacid metabolism. Overall, the JS666 genome sequence provides insights into the evolution of pollutant-degrading bacteria and provides a toolbox of catabolic genes with utility for biotechnology.

Archaeoglobus infectus sp. nov., a novel thermophilic, chemolithoheterotrophic archaeon isolated from a deep-sea rock collected at Suiyo Seamount, Izu-Bonin Arc, western Pacific Ocean

A novel thermophilic, strictly anaerobic archaeon, designated strain Arc51T, was isolated from a rock sample collected from a deep-sea hydrothermal field in Suiyo Seamount, Izu-Bonin Arc, western Pacific Ocean. Cells of the isolate were irregular cocci with single flagella and exhibited blue-green fluorescence at 436 nm. The optimum temperature, pH and NaCl concentration for growth were 70 degrees C, pH 6.5 and 3 % (w/v), respectively. Strain Arc51T could grow on thiosulfate or sulfite as an electron acceptor in the presence of hydrogen. This strain required acetate as a carbon source for its growth, suggesting that the reductive acetyl CoA pathway for CO2 fixation was incomplete. In addition, coenzyme M (2-mercaptoethanesulfonic acid), which is a known methyl carrier in methanogenesis, was also a requirement for growth of the strain. Analysis of the 16S rRNA gene sequence revealed that the isolate was similar to members of the genus Archaeoglobus, with sequence similarities of 93.6-97.2 %; the closest relative was Archaeoglobus veneficus. Phylogenetic analyses of the dsrAB and apsA genes, encoding the alpha and beta subunits of dissimilatory sulfite reductase and the alpha subunit of adenosine-5'-phosphosulfate reductase, respectively, produced results similar to those inferred from comparisons based on the 16S rRNA gene sequence. On the basis of phenotypic and phylogenetic data, strain Arc51T represents a novel species of the genus Archaeoglobus, for which the name Archaeoglobus infectus sp. nov. is proposed. The type strain is Arc51T (=NBRC 100649T=DSM 18877T).