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

Abstract

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. IMPORTANCEThe 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. Short-chain alkenes (e.g., ethene, propene, and butenes) are common hydrocarbons in the environment, primarily encountered as fossil fuel components or products of living organisms or generated by the chemical industry (1). For instance, ethene is generated by both plants (2) and bacteria (3).Chlorinated alkenes (e.g., vinyl chloride [VC]) are also naturally occurring, albeit at very low levels (4). VC is produced industrially as a monomer for polyvinyl chloride plastics. However, most environmental VC is generated by incomplete anaerobic dechlorination of the widely used solvents tetrachloroethene (PCE) and trichloroethene (TCE) in groundwater, where ethene can also be generated as a complete dechlorination product (1). PCE, TCE, and VC are common groundwater contaminants (5), and sites contaminated with chloroethenes are widely distributed across the United States (6) and elsewhere (1, 7). VC is of particular concern as a known human carcinogen (8).In aerobic bacteria that utilize short...

Aerobic vinyl chloride degradation at the microbial community level

“…Samples were presented as from the center of the plume (left, 85R) to the edge (right, 11M). The abundance of etnE gene in Well 4M and 13M has been reported previously 98 .…”

“…Although VC has not been detected at the Wendell Ave. site, qPCR data (this study and 98 ) revealed that both etnC and etnE present (10 3~1 0 6 genes/L of groundwater)…”

“…Aerobic VC-assimilating bacteria are thought to be widely distributed in the environment, especially at chlorinated ethene contaminated sites 10,98 . In this study, ethene and VC-assimilating Nocardioides strains were significantly enriched after the groundwater was amended with ethene.…”

“…became more abundant during ethene and VC enrichment and was proved to be assimilating ethene and VC, we went back to investigate its presence in the original groundwater sample. etnE1 and etnE 98 . Taken together, the evidence showed that bacteria similar to Nocardioides sp.…”

“…The T-RFLP of functional gene etnE was based on the PCR using degenerate primer set COM F1L and COM R2E. This primer set has been used in amplifying etnE gene from pure and enrichment cultures and environmental samples 11,77,[96][97][98] . In this study, we discovered that this primer sets tends to amplify more etnE1 than etnE sequences ( means their ratio in JS614 should be 1:1.…”