Abundance and activity of vinyl chloride (VC)-oxidizing bacteria in a dilute groundwater VC plume biostimulated with oxygen and ethene

Mattes, Timothy E.; Jin, Yang; Livermore, Joshua A.; Pearl, Meredith; Liu, Xikun

doi:10.1007/s00253-015-6771-2

Cited by 26 publications

(34 citation statements)

References 49 publications

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“…Molecular oxygen and ethene were injected into the VC plume at the Carver site to promote VC oxidation, with apparent success (42). Reverse transcription-qPCR (RT-qPCR) evidence of VC oxidizer activity in Carver site groundwater has also been reported (38). Biostimulation of the VC plume with an oxygen-releasing compound was conducted at the Oceana site, where VC concentrations have been decreasing since 2004 (43).…”

Section: Methodsmentioning

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: Methodsmentioning

confidence: 99%

mentioning

confidence: 99%

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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“…RNA and protein biomarkers may serve as the key piece of evidence and may even inform quantitative forecasting of in situ rates of bioremediation. A range of studies have examined reductive dehalogenase (RDase) gene expression in a lab setting [ 13 , 14 , 15 , 16 , 17 , 18 , 19 , 20 , 21 , 22 ], and select studies have also successfully detected RDase gene transcripts [ 14 , 23 , 24 ] or VC-oxidizing enzyme transcripts [ 25 ] in soils and sediments. Based on these studies, a suite of potential biomarkers has been generated and includes RDases and other oxidoreductase targets such as the NiFe hydrogenase, Hup [ 26 ].…”

Section: Introductionmentioning

confidence: 99%

Biomarkers’ Responses to Reductive Dechlorination Rates and Oxygen Stress in Bioaugmentation Culture KB-1TM

et al. 2018

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Using mRNA transcript levels for key functional enzymes as proxies for the organohalide respiration (OHR) rate, is a promising approach for monitoring bioremediation populations in situ at chlorinated solvent-contaminated field sites. However, to date, no correlations have been empirically derived for chlorinated solvent respiring, Dehalococcoides mccartyi (DMC) containing, bioaugmentation cultures. In the current study, genome-wide transcriptome and proteome data were first used to confirm the most highly expressed OHR-related enzymes in the bioaugmentation culture, KB-1TM, including several reductive dehalogenases (RDases) and a Ni-Fe hydrogenase, Hup. Different KB-1™ DMC strains could be resolved at the RNA and protein level through differences in the sequence of a common RDase (DET1545-like homologs) and differences in expression of their vinyl chloride-respiring RDases. The dominant strain expresses VcrA, whereas the minor strain utilizes BvcA. We then used quantitative reverse-transcriptase PCR (qRT-PCR) as a targeted approach for quantifying transcript copies in the KB-1TM consortium operated under a range of TCE respiration rates in continuously-fed, pseudo-steady-state reactors. These candidate biomarkers from KB-1TM demonstrated a variety of trends in terms of transcript abundance as a function of respiration rate over the range: 7.7 × 10−12 to 5.9 × 10−10 microelectron equivalents per cell per hour (μeeq/cell∙h). Power law trends were observed between the respiration rate and transcript abundance for the main DMC RDase (VcrA) and the hydrogenase HupL (R2 = 0.83 and 0.88, respectively), but not transcripts for 16S rRNA or three other RDases examined: TceA, BvcA or the RDase DET1545 homologs in KB1TM. Overall, HupL transcripts appear to be the most robust activity biomarker across multiple DMC strains and in mixed communities including DMC co-cultures such as KB1TM. The addition of oxygen induced cell stress that caused respiration rates to decline immediately (>95% decline within one hour). Although transcript levels did decline, they did so more slowly than the respiration rate observed (transcript decay rates between 0.02 and 0.03 per hour). Data from strain-specific probes on the pangenome array strains suggest that a minor DMC strain in KB-1™ that harbors a bvcA homolog preferentially recovered following oxygen stress relative to the dominant, vcrA-containing strain.

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“…Molecular oxygen and ethene were injected into the VC plume at the Carver site to promote VC oxidation, with apparent success 159 . Reverse-transcription qPCR (RT-qPCR) evidence of VC-oxidizer activity at Carver site groundwater has also been reported 111 . Biostimulation of the VC plume with an oxygen releasing compound was conducted at the Oceana site, where VC concentrations have been decreasing since 2004 160 .…”

Section: Introductionmentioning

confidence: 93%

“…The EaCoMT gene (often designated as etnE) could be a useful biomarker for aerobic VC biodegradation in the field. Quantitative PCR (qPCR) assays for etnE have been developed 77,97,111 and applied 65,78,111,158 in an effort to understand VC biodegradation in microcosm studies as well as directly from environmental samples. James Fish of Alaska Department of Environmental Conservation; *Quantification of etnE genes at CARV, SOLD, and OCEA were published previously 77 and are provided here for reference and used in correlation analyses.…”

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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Abundance and activity of vinyl chloride (VC)-oxidizing bacteria in a dilute groundwater VC plume biostimulated with oxygen and ethene

Cited by 26 publications

References 49 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

Biomarkers’ Responses to Reductive Dechlorination Rates and Oxygen Stress in Bioaugmentation Culture KB-1TM

Aerobic vinyl chloride degradation at the microbial community level

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