Elucidating carbon uptake from vinyl chloride using stable isotope probing and Illumina sequencing

Paes, Fernanda; Liu, Xikun; Mattes, Timothy E.; Cupples, Alison M.

doi:10.1007/s00253-015-6606-1

Cited by 30 publications

(24 citation statements)

References 42 publications

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“…Although Nocardioides sp. JS614 is the sole isolated VC-and ethene-assimilating representative of the Nocardioides genus (21), a related Nocardioides strain was implicated as a dominant microbial community member of a VC-degrading enrichment culture likely using VC as a carbon and energy source (41). Taken together, these data suggest that Nocardioides sp.…”

Section: Discussionsupporting

confidence: 52%

“…Previously, our understanding of EaCoMT gene diversity was based on 16 sequences from VC-, ethene-, and propene-assimilating isolates and a few EaCoMT genes sequenced from VC and ethene enrichment cultures (41,60). T-RFLP analysis has now revealed 192 different EaCoMT T-RFs.…”

Section: Discussionmentioning

confidence: 99%

“…Quantitative PCR (qPCR) assays for etnE have been developed (36)(37)(38) and applied (38)(39)(40)(41) in an effort to understand VC biodegradation in microcosm studies as well as directly from environmental samples. However, because etnE sequences in ethene-and VC-assimilating bacteria are very similar, the EaCoMT gene qPCR assay cannot distinguish VC-assimilating bacteria from ethene-assimilating bacteria that fortuitously degrade VC.…”

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confidence: 99%

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

Liu

Mattes

2016

Appl Environ Microbiol

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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...

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Section: Discussionsupporting

confidence: 52%

Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

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

Liu

Mattes

2016

Appl Environ Microbiol

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“…Incubations for DNA-and RNA-SIP can be performed either in vitro using laboratory microcosms constructed from field-collected samples (e.g. [56,57,58,59]) or in situ using incubation directly in soil or sediment (e.g. [60,61]) and in situ microcosms in groundwater wells (e.g.…”

Section: Current Opinion In Biotechnologymentioning

confidence: 99%

Application of stable isotope tools for evaluating natural and stimulated biodegradation of organic pollutants in field studies

Fischer¹,

Manefield²,

Bombach³

2016

Current Opinion in Biotechnology

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“…In a previous study, we investigated the microorganisms able to uptake carbon from VC in a mixed culture capable of slower VC degradation (~120 µmol in 45 days) using SIP and also examined etnE abundance in the heavy SIP fractions 65 (Appendix II, first study). In the present study, the overall objective was to identify microorganisms associated with carbon uptake from VC in an enrichment culture (derived from different groundwater than the previous study) capable of more rapid VC degradation (~120 µmol in 7 days).…”

Section: Introductionmentioning

confidence: 99%

Aerobic vinyl chloride degradation at the microbial community level

Liu¹

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When came to the University of Iowa, I was on a non-thesis track. Later on, I developed interest in microbial research, and Dr. Mattes kindly allowed me to work voluntarily in his lab, which later on turned into a funded research role. Dr. Mattes has been an excellent advisor, who has provided enormous guidance on experiments and especially writing, for a non-native English speaker like me. Nonetheless, the best things I appreciated about Dr. Mattes are his rigorous scientific attitude and trust in me to explore the research questions I am interested with new technologies. I am grateful to be in such a small but nice lab group. Dr. Yang Oh Jin and Mengchen Lee handed me the initial labs skills for microbiology research. Carly and Tristan helped me constructed and monitored the enrichment cultures. Special thanks to my "secondary advisor", collaborator and close friend, Dr. Yi Liang, for supporting me not only in my research career, but also my personal life. I also would like to thank other previous and present members,

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Elucidating carbon uptake from vinyl chloride using stable isotope probing and Illumina sequencing

Cited by 30 publications

References 42 publications

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

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

Application of stable isotope tools for evaluating natural and stimulated biodegradation of organic pollutants in field studies

Aerobic vinyl chloride degradation at the microbial community level

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