Detection of Organohalide-Respiring Enzyme Biomarkers at a Bioaugmented TCE-Contaminated Field Site
Abstract
RNA-based biomarkers have been successfully detected at field sites undergoing in situ bioremediation, but the detection of expressed enzymes is a more direct way to prove activity for a particular biocatalytic process of interest since they provide evidence of potential in situ activity rather than simply confirming presence and abundance of genes in a given population by measurement of DNA copies using qPCR. Here we successfully applied shotgun proteomics to field samples from a trichloroethene (TCE)-contaminated industrial site in southern Ontario, Canada that had been bioaugmented with the commercially available KB-1TM microbial culture. The KB-1TM culture contains multiple strains of Dehalococcoides mccartyi (D. mccartyi) as well as an organohalide respiring Geobacter species. The relative abundances of specific enzymatic proteins were subsequently compared to corresponding qPCR-derived levels of DNA and RNA biomarkers in the same samples. Samples were obtained from two wells with high hydraulic connectivity to the KB-1TM-bioaugemented enhanced in situ bioremediation system, and two control wells that showed evidence of low levels of native organohalide respiring bacteria (OHRB), Dehalococcoides and Geobacter. Enzymes involved in organohalide respiration were detected in the metaproteomes of all four field samples, as were chaperonins of D. mccartyi, chemotaxis proteins, and ATPases. The most highlymore »
- Authors:
-
- Cornell Univ., Ithaca, NY (United States). School of Civil and Environmental Engineering
- Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Biological Sciences Division
- Univ. of Toronto, ON (Canada). Dept. of Chemical Engineering and Applied Chemistry
- Publication Date:
- Research Org.:
- Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
- Sponsoring Org.:
- USDOE
- OSTI Identifier:
- 1567199
- Report Number(s):
- PNNL-SA-147432
Journal ID: ISSN 1664-302X
- Grant/Contract Number:
- AC05-76RL01830
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Frontiers in Microbiology
- Additional Journal Information:
- Journal Volume: 10; Journal ID: ISSN 1664-302X
- Publisher:
- Frontiers Research Foundation
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; reductive dehalogenase, organohalide respiration, Dehalococcoides, Trichloroethene, biomarkers, Geobacter, proteomics, KB-1
Citation Formats
Heavner, Gretchen L., Mansfeldt, Cresten B., Wilkins, Michael J., Nicora, Carrie D., Debs, Garrett E., Edwards, Elizabeth A., and Richardson, Ruth E. Detection of Organohalide-Respiring Enzyme Biomarkers at a Bioaugmented TCE-Contaminated Field Site. United States: N. p., 2019.
Web. doi:10.3389/fmicb.2019.01433.
Heavner, Gretchen L., Mansfeldt, Cresten B., Wilkins, Michael J., Nicora, Carrie D., Debs, Garrett E., Edwards, Elizabeth A., & Richardson, Ruth E. Detection of Organohalide-Respiring Enzyme Biomarkers at a Bioaugmented TCE-Contaminated Field Site. United States. doi:https://doi.org/10.3389/fmicb.2019.01433
Heavner, Gretchen L., Mansfeldt, Cresten B., Wilkins, Michael J., Nicora, Carrie D., Debs, Garrett E., Edwards, Elizabeth A., and Richardson, Ruth E. Thu .
"Detection of Organohalide-Respiring Enzyme Biomarkers at a Bioaugmented TCE-Contaminated Field Site". United States. doi:https://doi.org/10.3389/fmicb.2019.01433. https://www.osti.gov/servlets/purl/1567199.
@article{osti_1567199,
title = {Detection of Organohalide-Respiring Enzyme Biomarkers at a Bioaugmented TCE-Contaminated Field Site},
author = {Heavner, Gretchen L. and Mansfeldt, Cresten B. and Wilkins, Michael J. and Nicora, Carrie D. and Debs, Garrett E. and Edwards, Elizabeth A. and Richardson, Ruth E.},
abstractNote = {RNA-based biomarkers have been successfully detected at field sites undergoing in situ bioremediation, but the detection of expressed enzymes is a more direct way to prove activity for a particular biocatalytic process of interest since they provide evidence of potential in situ activity rather than simply confirming presence and abundance of genes in a given population by measurement of DNA copies using qPCR. Here we successfully applied shotgun proteomics to field samples from a trichloroethene (TCE)-contaminated industrial site in southern Ontario, Canada that had been bioaugmented with the commercially available KB-1TM microbial culture. The KB-1TM culture contains multiple strains of Dehalococcoides mccartyi (D. mccartyi) as well as an organohalide respiring Geobacter species. The relative abundances of specific enzymatic proteins were subsequently compared to corresponding qPCR-derived levels of DNA and RNA biomarkers in the same samples. Samples were obtained from two wells with high hydraulic connectivity to the KB-1TM-bioaugemented enhanced in situ bioremediation system, and two control wells that showed evidence of low levels of native organohalide respiring bacteria (OHRB), Dehalococcoides and Geobacter. Enzymes involved in organohalide respiration were detected in the metaproteomes of all four field samples, as were chaperonins of D. mccartyi, chemotaxis proteins, and ATPases. The most highly expressed RDase in the bioaugmentation culture (VcrA) was the most highly detected enzyme overall in the bioaugmented groundwater samples. In one background groundwater well, we found high expression of the Geobacter pceA RDase. The DNA and RNA biomarkers detected using qPCR-based assays were a set of orthologs of Dehalococcoides reductive dehalogenases (VcrA, TceA, BvcA, dehalogenase “DET1545”), and the Ni-Fe uptake hydrogenase, HupL. Within a sample, RNA levels for key enzymes correlated with relative protein abundance. These results indicate that laboratory observations of TCE-bioremediation biomarker protein expression are recapitulated in field environmental systems and that both RNA and protein biomarker monitoring hold promise for activity monitoring of in situ populations of OHRB.},
doi = {10.3389/fmicb.2019.01433},
journal = {Frontiers in Microbiology},
number = ,
volume = 10,
place = {United States},
year = {2019},
month = {6}
}
Web of Science
Figures / Tables:

Works referenced in this record:
Overview of organohalide-respiring bacteria and a proposal for a classification system for reductive dehalogenases
journal, April 2013
- Hug, Laura A.; Maphosa, Farai; Leys, David
- Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 368, Issue 1616
Temporal Expression of Respiratory Genes in an Enrichment Culture Containing Dehalococcoides ethenogenes
journal, August 2006
- Rahm, B. G.; Morris, R. M.; Richardson, R. E.
- Applied and Environmental Microbiology, Vol. 72, Issue 8
The little bacteria that can - diversity, genomics and ecophysiology of ‘Dehalococcoides’ spp. in contaminated environments: Ecophysiology of ‘Dehalococcoides’ spp.
journal, September 2009
- Taş, Neslihan; Van Eekert, Miriam H. A.; De Vos, Willem M.
- Microbial Biotechnology, Vol. 3, Issue 4
Biomarkers’ Responses to Reductive Dechlorination Rates and Oxygen Stress in Bioaugmentation Culture KB-1TM
journal, February 2018
- Heavner, Gretchen; Mansfeldt, Cresten; Debs, Garrett
- Microorganisms, Vol. 6, Issue 1
Genomic, transcriptomic and proteomic analyses of Dehalobacter UNSWDHB in response to chloroform
journal, August 2016
- Jugder, Bat-Erdene; Ertan, Haluk; Wong, Yie Kuan
- Environmental Microbiology Reports, Vol. 8, Issue 5
Monitoring Abundance and Expression of "Dehalococcoides" Species Chloroethene-Reductive Dehalogenases in a Tetrachloroethene-Dechlorinating Flow Column
journal, August 2008
- Behrens, S.; Azizian, M. F.; McMurdie, P. J.
- Applied and Environmental Microbiology, Vol. 74, Issue 18
Metabolism of trichloroethylene.
journal, May 2000
- Lash, L. H.; Fisher, J. W.; Lipscomb, J. C.
- Environmental Health Perspectives, Vol. 108, Issue suppl 2
Organic cofactors in the metabolism of Dehalococcoides mccartyi strains
journal, April 2013
- Schipp, Christian J.; Marco-Urrea, Ernest; Kublik, Anja
- Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 368, Issue 1616
Identity and Substrate Specificity of Reductive Dehalogenases Expressed in Dehalococcoides-Containing Enrichment Cultures Maintained on Different Chlorinated Ethenes
journal, May 2015
- Liang, Xiaoming; Molenda, Olivia; Tang, Shuiquan
- Applied and Environmental Microbiology, Vol. 81, Issue 14
The Hydrogenase Chip: a tiling oligonucleotide DNA microarray technique for characterizing hydrogen-producing and -consuming microbes in microbial communities
journal, October 2011
- Marshall, Ian PG; Berggren, Dusty RV; Azizian, Mohammad F.
- The ISME Journal, Vol. 6, Issue 4
An Internal Reference Technique for Accurately Quantifying Specific mRNAs by Real-Time PCR with Application to the tceA Reductive Dehalogenase Gene
journal, July 2005
- Johnson, D. R.; Lee, P. K. H.; Holmes, V. F.
- Applied and Environmental Microbiology, Vol. 71, Issue 7
Correlation of Respiratory Gene Expression Levels and Pseudo-Steady-State PCE Respiration Rates in Dehalococcoides ethenogenes
journal, January 2008
- Rahm, Brian G.; Richardson, Ruth E.
- Environmental Science & Technology, Vol. 42, Issue 2
Proteome profile and proteogenomics of the organohalide-respiring bacterium Dehalococcoides mccartyi strain CBDB1 grown on hexachlorobenzene as electron acceptor
journal, February 2014
- Schiffmann, Christian L.; Jehmlich, Nico; Otto, Wolfgang
- Journal of Proteomics, Vol. 98
Cleaning up with genomics: applying molecular biology to bioremediation
journal, October 2003
- Lovley, Derek R.
- Nature Reviews Microbiology, Vol. 1, Issue 1
Molecular Identification of the Catabolic Vinyl Chloride Reductase from Dehalococcoides sp. Strain VS and Its Environmental Distribution
journal, August 2004
- Muller, J. A.; Rosner, B. M.; von Abendroth, G.
- Applied and Environmental Microbiology, Vol. 70, Issue 8
Absolute quantification of Dehalococcoides proteins: enzyme bioindicators of chlorinated ethene dehalorespiration
journal, October 2009
- Werner, Jeffrey J.; Ptak, A. Celeste; Rahm, Brian G.
- Environmental Microbiology, Vol. 11, Issue 10
Design and Verification of a Pangenome Microarray Oligonucleotide Probe Set for Dehalococcoides spp.
journal, June 2011
- Hug, Laura A.; Salehi, Maryam; Nuin, Paulo
- Applied and Environmental Microbiology, Vol. 77, Issue 15
An integrative overview of genomic, transcriptomic and proteomic analyses in organohalide respiration research
journal, January 2018
- Türkowsky, Dominique; Jehmlich, Nico; Diekert, Gabriele
- FEMS Microbiology Ecology, Vol. 94, Issue 3
Molecular Analysis of Dehalococcoides 16S Ribosomal DNA from Chloroethene-Contaminated Sites throughout North America and Europe
journal, February 2002
- Hendrickson, E. R.; Payne, J. A.; Young, R. M.
- Applied and Environmental Microbiology, Vol. 68, Issue 2
Relating Chloroethene Respiration Rates in Dehalococcoides to Protein and mRNA Biomarkers
journal, August 2012
- Rowe, Annette R.; Heavner, Gretchen L.; Mansfeldt, Cresten B.
- Environmental Science & Technology, Vol. 46, Issue 17
Comparative Proteomics of Dehalococcoides spp. Reveals Strain-Specific Peptides Associated with Activity
journal, November 2006
- Morris, R. M.; Fung, J. M.; Rahm, B. G.
- Applied and Environmental Microbiology, Vol. 73, Issue 1
Concurrent Ethene Generation and Growth of Dehalococcoides Containing Vinyl Chloride Reductive Dehalogenase Genes During an Enhanced Reductive Dechlorination Field Demonstration
journal, December 2008
- Scheutz, Charlotte; Durant, Neal d.; Dennis, Philip
- Environmental Science & Technology, Vol. 42, Issue 24
Identification of a Chlorobenzene Reductive Dehalogenase in Dehalococcoides sp. Strain CBDB1
journal, October 2007
- Adrian, L.; Rahnenfuhrer, J.; Gobom, J.
- Applied and Environmental Microbiology, Vol. 73, Issue 23
Transcriptional Expression of the tceA Gene in a Dehalococcoides-Containing Microbial Enrichment
journal, November 2005
- Johnson, D. R.; Lee, P. K. H.; Holmes, V. F.
- Applied and Environmental Microbiology, Vol. 71, Issue 11
Growth of a Dehalococcoides-Like Microorganism on Vinyl Chloride and cis-Dichloroethene as Electron Acceptors as Determined by Competetive PCR
journal, July 2003
- Cupples, A. M.; Spormann, A. M.; McCarty, P. L.
- Applied and Environmental Microbiology, Vol. 69, Issue 7
Dehalococcoides mccartyi gen. nov., sp. nov., obligately organohalide-respiring anaerobic bacteria relevant to halogen cycling and bioremediation, belong to a novel bacterial class, Dehalococcoidia classis nov., order Dehalococcoidales ord. nov. and family Dehalococcoidaceae fam. nov., within the phylum Chloroflexi
journal, April 2012
- Loffler, F. E.; Yan, J.; Ritalahti, K. M.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 63, Issue Pt 2
Growth and Yields of Dechlorinators, Acetogens, and Methanogens during Reductive Dechlorination of Chlorinated Ethenes and Dihaloelimination of 1,2-Dichloroethane
journal, April 2007
- Duhamel, Melanie; Edwards, Elizabeth A.
- Environmental Science & Technology, Vol. 41, Issue 7
Quantifying Genes and Transcripts To Assess the In Situ Physiology of "Dehalococcoides" spp. in a Trichloroethene-Contaminated Groundwater Site
journal, March 2008
- Lee, P. K. H.; Macbeth, T. W.; Sorenson, K. S.
- Applied and Environmental Microbiology, Vol. 74, Issue 9
Expression of Reductive Dehalogenase Genes in Dehalococcoides ethenogenes Strain 195 Growing on Tetrachloroethene, Trichloroethene, or 2,3-Dichlorophenol
journal, May 2007
- Fung, J. M.; Morris, R. M.; Adrian, L.
- Applied and Environmental Microbiology, Vol. 73, Issue 14
Multiple Reductive-Dehalogenase-Homologous Genes Are Simultaneously Transcribed during Dechlorination by Dehalococcoides-Containing Cultures
journal, December 2005
- Waller, A. S.; Krajmalnik-Brown, R.; Loffler, F. E.
- Applied and Environmental Microbiology, Vol. 71, Issue 12
Development of a biomarker for Geobacter activity and strain composition; Proteogenomic analysis of the citrate synthase protein during bioremediation of U(VI): Geobacter citrate synthase biomarker
journal, December 2010
- Wilkins, Michael J.; Callister, Stephen J.; Miletto, Marzia
- Microbial Biotechnology, Vol. 4, Issue 1
Dehalococcoides mccartyi Strain DCMB5 Respires a Broad Spectrum of Chlorinated Aromatic Compounds
journal, November 2014
- Pöritz, Marlén; Schiffmann, Christian L.; Hause, Gerd
- Applied and Environmental Microbiology, Vol. 81, Issue 2
Universal sample preparation method for proteome analysis
journal, April 2009
- Wiśniewski, Jacek R.; Zougman, Alexandre; Nagaraj, Nagarjuna
- Nature Methods, Vol. 6, Issue 5
Transcription and mass-spectroscopic proteomic studies of electron transport oxidoreductases in Dehalococcoides ethenogenes
journal, September 2006
- Morris, R. M.; Sowell, S.; Barofsky, D.
- Environmental Microbiology, Vol. 8, Issue 9
Statistical Analysis of Membrane Proteome Expression Changes in Saccharomyces c erevisiae
journal, September 2006
- Zybailov, Boris; Mosley, Amber L.; Sardiu, Mihaela E.
- Journal of Proteome Research, Vol. 5, Issue 9
Large-scale analysis of the yeast proteome by multidimensional protein identification technology
journal, March 2001
- Washburn, Michael P.; Wolters, Dirk; Yates, John R.
- Nature Biotechnology, Vol. 19, Issue 3
Functional Characterization of Reductive Dehalogenases by Using Blue Native Polyacrylamide Gel Electrophoresis
journal, November 2012
- Tang, Shuiquan; Chan, Winnie W. M.; Fletcher, Kelly E.
- Applied and Environmental Microbiology, Vol. 79, Issue 3
Proteogenomic Monitoring of Geobacter Physiology during Stimulated Uranium Bioremediation
journal, August 2009
- Wilkins, M. J.; VerBerkmoes, N. C.; Williams, K. H.
- Applied and Environmental Microbiology, Vol. 75, Issue 20
Quantitative real-time RT-PCR data analysis: current concepts and the novel “gene expression’s C T difference” formula
journal, September 2006
- Schefe, Jan H.; Lehmann, Kerstin E.; Buschmann, Ivo R.
- Journal of Molecular Medicine, Vol. 84, Issue 11
Comparative metagenomics of three Dehalococcoides-containing enrichment cultures: the role of the non-dechlorinating community
journal, January 2012
- Hug, Laura A.; Beiko, Robert G.; Rowe, Annette R.
- BMC Genomics, Vol. 13, Issue 1
Relationship between Dehalococcoides DNA in ground water and rates of reductive dechlorination at field scale
journal, September 2006
- Lu, Xiaoxia; Wilson, John T.; Kampbell, Donald H.
- Water Research, Vol. 40, Issue 16
Bioremediation of Chlorinated Ethenes in Fractured Bedrock and Associated Changes in Dechlorinating and Nondechlorinating Microbial Populations
journal, May 2014
- Pérez-de-Mora, Alfredo; Zila, Anna; McMaster, Michaye L.
- Environmental Science & Technology, Vol. 48, Issue 10
Spectral Probabilities and Generating Functions of Tandem Mass Spectra: A Strike against Decoy Databases
journal, August 2008
- Kim, Sangtae; Gupta, Nitin; Pevzner, Pavel A.
- Journal of Proteome Research, Vol. 7, Issue 8
Experimental validation of novel and conventional approaches to quantitative real-time PCR data analysis
journal, July 2003
- Peirson, S. N.
- Nucleic Acids Research, Vol. 31, Issue 14
Dehalococcoides ’ Gene Transcripts As Quantitative Bioindicators of Tetrachloroethene, Trichloroethene, and cis -1,2-Dichloroethene Dehalorespiration Rates
journal, July 2008
- Rahm, Brian G.; Richardson, Ruth E.
- Environmental Science & Technology, Vol. 42, Issue 14
Localized Plasticity in the Streamlined Genomes of Vinyl Chloride Respiring Dehalococcoides
journal, November 2009
- McMurdie, Paul J.; Behrens, Sebastian F.; Müller, Jochen A.
- PLoS Genetics, Vol. 5, Issue 11
Monitoring Biodegradation of Ethene and Bioremediation of Chlorinated Ethenes at a Contaminated Site Using Compound-Specific Isotope Analysis (CSIA)
journal, January 2012
- Mundle, Scott O. C.; Johnson, Tiffany; Lacrampe-Couloume, Georges
- Environmental Science & Technology, Vol. 46, Issue 3
Isolation and Characterization of "Dehalococcoides" sp. Strain MB, Which Dechlorinates Tetrachloroethene to trans-1,2-Dichloroethene
journal, July 2009
- Cheng, D.; He, J.
- Applied and Environmental Microbiology, Vol. 75, Issue 18
Growth of a Dehalococcoides-Like Microorganism on Vinyl Chloride and cis-Dichloroethene as Electron Acceptors as Determined by Competitive PCR
journal, February 2003
- Cupples, A. M.; Spormann, A. M.; McCarty, P. L.
- Applied and Environmental Microbiology, Vol. 69, Issue 2
Works referencing / citing this record:
Quantitative real-time RT-PCR data analysis: current concepts and the novel “gene expression’s C T difference” formula
journal, September 2006
- Schefe, Jan H.; Lehmann, Kerstin E.; Buschmann, Ivo R.
- Journal of Molecular Medicine, Vol. 84, Issue 11
Proteome profile and proteogenomics of the organohalide-respiring bacterium Dehalococcoides mccartyi strain CBDB1 grown on hexachlorobenzene as electron acceptor
journal, February 2014
- Schiffmann, Christian L.; Jehmlich, Nico; Otto, Wolfgang
- Journal of Proteomics, Vol. 98
Relationship between Dehalococcoides DNA in ground water and rates of reductive dechlorination at field scale
journal, September 2006
- Lu, Xiaoxia; Wilson, John T.; Kampbell, Donald H.
- Water Research, Vol. 40, Issue 16
Growth and Yields of Dechlorinators, Acetogens, and Methanogens during Reductive Dechlorination of Chlorinated Ethenes and Dihaloelimination of 1,2-Dichloroethane
journal, April 2007
- Duhamel, Melanie; Edwards, Elizabeth A.
- Environmental Science & Technology, Vol. 41, Issue 7
Correlation of Respiratory Gene Expression Levels and Pseudo-Steady-State PCE Respiration Rates in Dehalococcoides ethenogenes
journal, January 2008
- Rahm, Brian G.; Richardson, Ruth E.
- Environmental Science & Technology, Vol. 42, Issue 2
Monitoring Biodegradation of Ethene and Bioremediation of Chlorinated Ethenes at a Contaminated Site Using Compound-Specific Isotope Analysis (CSIA)
journal, January 2012
- Mundle, Scott O. C.; Johnson, Tiffany; Lacrampe-Couloume, Georges
- Environmental Science & Technology, Vol. 46, Issue 3
Relating Chloroethene Respiration Rates in Dehalococcoides to Protein and mRNA Biomarkers
journal, August 2012
- Rowe, Annette R.; Heavner, Gretchen L.; Mansfeldt, Cresten B.
- Environmental Science & Technology, Vol. 46, Issue 17
Bioremediation of Chlorinated Ethenes in Fractured Bedrock and Associated Changes in Dechlorinating and Nondechlorinating Microbial Populations
journal, May 2014
- Pérez-de-Mora, Alfredo; Zila, Anna; McMaster, Michaye L.
- Environmental Science & Technology, Vol. 48, Issue 10
Dehalococcoides ’ Gene Transcripts As Quantitative Bioindicators of Tetrachloroethene, Trichloroethene, and cis -1,2-Dichloroethene Dehalorespiration Rates
journal, July 2008
- Rahm, Brian G.; Richardson, Ruth E.
- Environmental Science & Technology, Vol. 42, Issue 14
Concurrent Ethene Generation and Growth of Dehalococcoides Containing Vinyl Chloride Reductive Dehalogenase Genes During an Enhanced Reductive Dechlorination Field Demonstration
journal, December 2008
- Scheutz, Charlotte; Durant, Neal d.; Dennis, Philip
- Environmental Science & Technology, Vol. 42, Issue 24
Statistical Analysis of Membrane Proteome Expression Changes in Saccharomyces c erevisiae
journal, September 2006
- Zybailov, Boris; Mosley, Amber L.; Sardiu, Mihaela E.
- Journal of Proteome Research, Vol. 5, Issue 9
Spectral Probabilities and Generating Functions of Tandem Mass Spectra: A Strike against Decoy Databases
journal, August 2008
- Kim, Sangtae; Gupta, Nitin; Pevzner, Pavel A.
- Journal of Proteome Research, Vol. 7, Issue 8
Large-scale analysis of the yeast proteome by multidimensional protein identification technology
journal, March 2001
- Washburn, Michael P.; Wolters, Dirk; Yates, John R.
- Nature Biotechnology, Vol. 19, Issue 3
The Hydrogenase Chip: a tiling oligonucleotide DNA microarray technique for characterizing hydrogen-producing and -consuming microbes in microbial communities
journal, October 2011
- Marshall, Ian PG; Berggren, Dusty RV; Azizian, Mohammad F.
- The ISME Journal, Vol. 6, Issue 4
Universal sample preparation method for proteome analysis
journal, April 2009
- Wiśniewski, Jacek R.; Zougman, Alexandre; Nagaraj, Nagarjuna
- Nature Methods, Vol. 6, Issue 5
Cleaning up with genomics: applying molecular biology to bioremediation
journal, October 2003
- Lovley, Derek R.
- Nature Reviews Microbiology, Vol. 1, Issue 1
An integrative overview of genomic, transcriptomic and proteomic analyses in organohalide respiration research
journal, January 2018
- Türkowsky, Dominique; Jehmlich, Nico; Diekert, Gabriele
- FEMS Microbiology Ecology, Vol. 94, Issue 3
Experimental validation of novel and conventional approaches to quantitative real-time PCR data analysis
journal, July 2003
- Peirson, S. N.
- Nucleic Acids Research, Vol. 31, Issue 14
Organic cofactors in the metabolism of Dehalococcoides mccartyi strains
journal, April 2013
- Schipp, Christian J.; Marco-Urrea, Ernest; Kublik, Anja
- Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 368, Issue 1616
Overview of organohalide-respiring bacteria and a proposal for a classification system for reductive dehalogenases
journal, April 2013
- Hug, Laura A.; Maphosa, Farai; Leys, David
- Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 368, Issue 1616
Dehalococcoides mccartyi gen. nov., sp. nov., obligately organohalide-respiring anaerobic bacteria relevant to halogen cycling and bioremediation, belong to a novel bacterial class, Dehalococcoidia classis nov., order Dehalococcoidales ord. nov. and family Dehalococcoidaceae fam. nov., within the phylum Chloroflexi
journal, April 2012
- Loffler, F. E.; Yan, J.; Ritalahti, K. M.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 63, Issue Pt 2
Genomic, transcriptomic and proteomic analyses of Dehalobacter UNSWDHB in response to chloroform
journal, August 2016
- Jugder, Bat-Erdene; Ertan, Haluk; Wong, Yie Kuan
- Environmental Microbiology Reports, Vol. 8, Issue 5
Transcription and mass-spectroscopic proteomic studies of electron transport oxidoreductases in Dehalococcoides ethenogenes
journal, September 2006
- Morris, R. M.; Sowell, S.; Barofsky, D.
- Environmental Microbiology, Vol. 8, Issue 9
Absolute quantification of Dehalococcoides proteins: enzyme bioindicators of chlorinated ethene dehalorespiration
journal, October 2009
- Werner, Jeffrey J.; Ptak, A. Celeste; Rahm, Brian G.
- Environmental Microbiology, Vol. 11, Issue 10
The little bacteria that can - diversity, genomics and ecophysiology of ‘Dehalococcoides’ spp. in contaminated environments: Ecophysiology of ‘Dehalococcoides’ spp.
journal, September 2009
- Taş, Neslihan; Van Eekert, Miriam H. A.; De Vos, Willem M.
- Microbial Biotechnology, Vol. 3, Issue 4
Development of a biomarker for Geobacter activity and strain composition; Proteogenomic analysis of the citrate synthase protein during bioremediation of U(VI): Geobacter citrate synthase biomarker
journal, December 2010
- Wilkins, Michael J.; Callister, Stephen J.; Miletto, Marzia
- Microbial Biotechnology, Vol. 4, Issue 1
Design and Verification of a Pangenome Microarray Oligonucleotide Probe Set for Dehalococcoides spp.
journal, June 2011
- Hug, Laura A.; Salehi, Maryam; Nuin, Paulo
- Applied and Environmental Microbiology, Vol. 77, Issue 15
Expression of Reductive Dehalogenase Genes in Dehalococcoides ethenogenes Strain 195 Growing on Tetrachloroethene, Trichloroethene, or 2,3-Dichlorophenol
journal, May 2007
- Fung, J. M.; Morris, R. M.; Adrian, L.
- Applied and Environmental Microbiology, Vol. 73, Issue 14
Identity and Substrate Specificity of Reductive Dehalogenases Expressed in Dehalococcoides-Containing Enrichment Cultures Maintained on Different Chlorinated Ethenes
journal, May 2015
- Liang, Xiaoming; Molenda, Olivia; Tang, Shuiquan
- Applied and Environmental Microbiology, Vol. 81, Issue 14
Isolation and Characterization of "Dehalococcoides" sp. Strain MB, Which Dechlorinates Tetrachloroethene to trans-1,2-Dichloroethene
journal, July 2009
- Cheng, D.; He, J.
- Applied and Environmental Microbiology, Vol. 75, Issue 18
Temporal Expression of Respiratory Genes in an Enrichment Culture Containing Dehalococcoides ethenogenes
journal, August 2006
- Rahm, B. G.; Morris, R. M.; Richardson, R. E.
- Applied and Environmental Microbiology, Vol. 72, Issue 8
Monitoring Abundance and Expression of "Dehalococcoides" Species Chloroethene-Reductive Dehalogenases in a Tetrachloroethene-Dechlorinating Flow Column
journal, August 2008
- Behrens, S.; Azizian, M. F.; McMurdie, P. J.
- Applied and Environmental Microbiology, Vol. 74, Issue 18
Proteogenomic Monitoring of Geobacter Physiology during Stimulated Uranium Bioremediation
journal, August 2009
- Wilkins, M. J.; VerBerkmoes, N. C.; Williams, K. H.
- Applied and Environmental Microbiology, Vol. 75, Issue 20
Identification of a Chlorobenzene Reductive Dehalogenase in Dehalococcoides sp. Strain CBDB1
journal, October 2007
- Adrian, L.; Rahnenfuhrer, J.; Gobom, J.
- Applied and Environmental Microbiology, Vol. 73, Issue 23
Functional Characterization of Reductive Dehalogenases by Using Blue Native Polyacrylamide Gel Electrophoresis
journal, November 2012
- Tang, Shuiquan; Chan, Winnie W. M.; Fletcher, Kelly E.
- Applied and Environmental Microbiology, Vol. 79, Issue 3
Comparative Proteomics of Dehalococcoides spp. Reveals Strain-Specific Peptides Associated with Activity
journal, November 2006
- Morris, R. M.; Fung, J. M.; Rahm, B. G.
- Applied and Environmental Microbiology, Vol. 73, Issue 1
Quantifying Genes and Transcripts To Assess the In Situ Physiology of "Dehalococcoides" spp. in a Trichloroethene-Contaminated Groundwater Site
journal, March 2008
- Lee, P. K. H.; Macbeth, T. W.; Sorenson, K. S.
- Applied and Environmental Microbiology, Vol. 74, Issue 9
Dehalococcoides mccartyi Strain DCMB5 Respires a Broad Spectrum of Chlorinated Aromatic Compounds
journal, November 2014
- Pöritz, Marlén; Schiffmann, Christian L.; Hause, Gerd
- Applied and Environmental Microbiology, Vol. 81, Issue 2
Molecular Analysis of Dehalococcoides 16S Ribosomal DNA from Chloroethene-Contaminated Sites throughout North America and Europe
journal, February 2002
- Hendrickson, E. R.; Payne, J. A.; Young, R. M.
- Applied and Environmental Microbiology, Vol. 68, Issue 2
Growth of a Dehalococcoides-Like Microorganism on Vinyl Chloride and cis-Dichloroethene as Electron Acceptors as Determined by Competetive PCR
journal, July 2003
- Cupples, A. M.; Spormann, A. M.; McCarty, P. L.
- Applied and Environmental Microbiology, Vol. 69, Issue 7
Molecular Identification of the Catabolic Vinyl Chloride Reductase from Dehalococcoides sp. Strain VS and Its Environmental Distribution
journal, August 2004
- Muller, J. A.; Rosner, B. M.; von Abendroth, G.
- Applied and Environmental Microbiology, Vol. 70, Issue 8
Transcriptional Expression of the tceA Gene in a Dehalococcoides-Containing Microbial Enrichment
journal, November 2005
- Johnson, D. R.; Lee, P. K. H.; Holmes, V. F.
- Applied and Environmental Microbiology, Vol. 71, Issue 11
Multiple Reductive-Dehalogenase-Homologous Genes Are Simultaneously Transcribed during Dechlorination by Dehalococcoides-Containing Cultures
journal, December 2005
- Waller, A. S.; Krajmalnik-Brown, R.; Loffler, F. E.
- Applied and Environmental Microbiology, Vol. 71, Issue 12
An Internal Reference Technique for Accurately Quantifying Specific mRNAs by Real-Time PCR with Application to the tceA Reductive Dehalogenase Gene
journal, July 2005
- Johnson, D. R.; Lee, P. K. H.; Holmes, V. F.
- Applied and Environmental Microbiology, Vol. 71, Issue 7
Comparative metagenomics of three Dehalococcoides-containing enrichment cultures: the role of the non-dechlorinating community
journal, January 2012
- Hug, Laura A.; Beiko, Robert G.; Rowe, Annette R.
- BMC Genomics, Vol. 13, Issue 1
Metabolism of trichloroethylene.
journal, May 2000
- Lash, L. H.; Fisher, J. W.; Lipscomb, J. C.
- Environmental Health Perspectives, Vol. 108, Issue suppl 2
Localized Plasticity in the Streamlined Genomes of Vinyl Chloride Respiring Dehalococcoides
journal, November 2009
- McMurdie, Paul J.; Behrens, Sebastian F.; Müller, Jochen A.
- PLoS Genetics, Vol. 5, Issue 11
Biomarkers’ Responses to Reductive Dechlorination Rates and Oxygen Stress in Bioaugmentation Culture KB-1TM
journal, February 2018
- Heavner, Gretchen; Mansfeldt, Cresten; Debs, Garrett
- Microorganisms, Vol. 6, Issue 1
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