Grape pomace compost harbors organohalide-respiring Dehalogenimonas species with novel reductive dehalogenase genes
Abstract
Here, organohalide-respiring bacteria play key roles in the natural chlorine cycle; however, most of the current knowledge is based on cultures from contaminated environments. We demonstrate that grape pomace compost without prior exposure to chlorinated solvents harbors a Dehalogenimonas (Dhgm) species capable of using chlorinated ethenes, including the human carcinogen and common groundwater pollutant vinyl chloride (VC) as electron acceptors. Grape pomace microcosms and derived solid-free enrichment cultures were able to dechlorinate trichloroethene (TCE) to less chlorinated daughter products including ethene. 16S rRNA gene amplicon and qPCR analyses revealed the predominance of Dhgm sequences, but no Dehalococcoides mccartyi (Dhc) biomarker genes were detected. The enumeration of Dhgm 16S rRNA genes demonstrated VC-dependent growth, and 6.55 ± 0.64 x 108 cells were produced per µmole of chloride released. Metagenome sequencing enabled the assembly of a Dhgm draft genome, and 52 putative reductive dehalogenase (RDase) genes were identified. Proteomic workflows identified a putative VC RDase with 49% and 56.1% amino acid similarity to the known VC RDases VcrA and BvcA, respectively. A survey of 1,173 groundwater samples collected from 111 chlorinated solvent-contaminated sites revealed that Dhgm 16S rRNA genes were frequently detected and outnumbered Dhc in 65% of the samples. Dhgm maymore »
- Authors:
-
[5];
[5];
[1]
- Univ. of Tennessee, Knoxville, TN (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
- Univ. of Tennessee, Knoxville, TN (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Chinese Academy of Sciences, Liaoning (China)
- Univ. of Tennessee, Knoxville, TN (United States)
- Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
- Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Univ. of Tennessee, Knoxville, TN (United States)
- Microbial Insights, Knoxville, TN (United States)
- Publication Date:
- Research Org.:
- Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
- Sponsoring Org.:
- USDOE
- OSTI Identifier:
- 1408046
- Grant/Contract Number:
- AC05-00OR22725
- Resource Type:
- Accepted Manuscript
- Journal Name:
- The ISME Journal
- Additional Journal Information:
- Journal Volume: 11; Journal ID: ISSN 1751-7362
- Publisher:
- Nature Publishing Group
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES; 54 ENVIRONMENTAL SCIENCES
Citation Formats
Yang, Yi, Higgins, Steven A., Yan, Jun, Şimşir, Burcu, Chourey, Karuna, Iyer, Ramsunder M., Hettich, Robert L., Baldwin, Brett, Ogles, Dora M., and Loffler, Frank E. Grape pomace compost harbors organohalide-respiring Dehalogenimonas species with novel reductive dehalogenase genes. United States: N. p., 2017.
Web. doi:10.1038/ismej.2017.127.
Yang, Yi, Higgins, Steven A., Yan, Jun, Şimşir, Burcu, Chourey, Karuna, Iyer, Ramsunder M., Hettich, Robert L., Baldwin, Brett, Ogles, Dora M., & Loffler, Frank E. Grape pomace compost harbors organohalide-respiring Dehalogenimonas species with novel reductive dehalogenase genes. United States. https://doi.org/10.1038/ismej.2017.127
Yang, Yi, Higgins, Steven A., Yan, Jun, Şimşir, Burcu, Chourey, Karuna, Iyer, Ramsunder M., Hettich, Robert L., Baldwin, Brett, Ogles, Dora M., and Loffler, Frank E. Tue .
"Grape pomace compost harbors organohalide-respiring Dehalogenimonas species with novel reductive dehalogenase genes". United States. https://doi.org/10.1038/ismej.2017.127. https://www.osti.gov/servlets/purl/1408046.
@article{osti_1408046,
title = {Grape pomace compost harbors organohalide-respiring Dehalogenimonas species with novel reductive dehalogenase genes},
author = {Yang, Yi and Higgins, Steven A. and Yan, Jun and Şimşir, Burcu and Chourey, Karuna and Iyer, Ramsunder M. and Hettich, Robert L. and Baldwin, Brett and Ogles, Dora M. and Loffler, Frank E.},
abstractNote = {Here, organohalide-respiring bacteria play key roles in the natural chlorine cycle; however, most of the current knowledge is based on cultures from contaminated environments. We demonstrate that grape pomace compost without prior exposure to chlorinated solvents harbors a Dehalogenimonas (Dhgm) species capable of using chlorinated ethenes, including the human carcinogen and common groundwater pollutant vinyl chloride (VC) as electron acceptors. Grape pomace microcosms and derived solid-free enrichment cultures were able to dechlorinate trichloroethene (TCE) to less chlorinated daughter products including ethene. 16S rRNA gene amplicon and qPCR analyses revealed the predominance of Dhgm sequences, but no Dehalococcoides mccartyi (Dhc) biomarker genes were detected. The enumeration of Dhgm 16S rRNA genes demonstrated VC-dependent growth, and 6.55 ± 0.64 x 108 cells were produced per µmole of chloride released. Metagenome sequencing enabled the assembly of a Dhgm draft genome, and 52 putative reductive dehalogenase (RDase) genes were identified. Proteomic workflows identified a putative VC RDase with 49% and 56.1% amino acid similarity to the known VC RDases VcrA and BvcA, respectively. A survey of 1,173 groundwater samples collected from 111 chlorinated solvent-contaminated sites revealed that Dhgm 16S rRNA genes were frequently detected and outnumbered Dhc in 65% of the samples. Dhgm may be more relevant contributors to chlorinated solvent reductive dechlorination in contaminated aquifers than is currently recognized, and non-polluted environments are a source of strictly organohalide-respiring bacteria with novel RDase genes.},
doi = {10.1038/ismej.2017.127},
journal = {The ISME Journal},
number = ,
volume = 11,
place = {United States},
year = {Tue Aug 15 00:00:00 EDT 2017},
month = {Tue Aug 15 00:00:00 EDT 2017}
}
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Works referencing / citing this record:
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