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

Abstract

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 lawmore » 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.« less

Authors:
 [1];  [1];  [1];  [1];  [1];  [1]
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  1. Cornell Univ., Ithaca, NY (United States)
Publication Date:
Research Org.:
Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER); National Science Foundation (NSF); U.S. Department of Defense (DOD)
OSTI Identifier:
1628466
Grant/Contract Number:  
AC06-76RL01830; CBET-0731169; W911NF-07-1-024
Resource Type:
Accepted Manuscript
Journal Name:
Microorganisms
Additional Journal Information:
Journal Volume: 6; Journal Issue: 1; Journal ID: ISSN 2076-2607
Publisher:
MDPI
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Microbiology; organohalide respiration; Dehalococcoides; trichloroethene; biomarkers; Geobacter; proteomics

Citation Formats

Heavner, Gretchen, Mansfeldt, Cresten, Debs, Garrett, Hellerstedt, Sage, Rowe, Annette, and Richardson, Ruth. Biomarkers’ Responses to Reductive Dechlorination Rates and Oxygen Stress in Bioaugmentation Culture KB-1TM. United States: N. p., 2018. Web. doi:10.3390/microorganisms6010013.
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Heavner, Gretchen, Mansfeldt, Cresten, Debs, Garrett, Hellerstedt, Sage, Rowe, Annette, & Richardson, Ruth. Biomarkers’ Responses to Reductive Dechlorination Rates and Oxygen Stress in Bioaugmentation Culture KB-1TM. United States. https://doi.org/10.3390/microorganisms6010013
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Heavner, Gretchen, Mansfeldt, Cresten, Debs, Garrett, Hellerstedt, Sage, Rowe, Annette, and Richardson, Ruth. Thu . "Biomarkers’ Responses to Reductive Dechlorination Rates and Oxygen Stress in Bioaugmentation Culture KB-1TM". United States. https://doi.org/10.3390/microorganisms6010013. https://www.osti.gov/servlets/purl/1628466.
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@article{osti_1628466,
title = {Biomarkers’ Responses to Reductive Dechlorination Rates and Oxygen Stress in Bioaugmentation Culture KB-1TM},
author = {Heavner, Gretchen and Mansfeldt, Cresten and Debs, Garrett and Hellerstedt, Sage and Rowe, Annette and Richardson, Ruth},
abstractNote = {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.},
doi = {10.3390/microorganisms6010013},
journal = {Microorganisms},
number = 1,
volume = 6,
place = {United States},
year = {Thu Feb 08 00:00:00 EST 2018},
month = {Thu Feb 08 00:00:00 EST 2018}
}
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https://doi.org/10.3390/microorganisms6010013
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  • DOI: 10.1021/acs.est.6b05050

Dehalococcoides ethenogenes Strain 195 Reductively Dechlorinates Diverse Chlorinated Aromatic Pollutants
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  • Environmental Science & Technology, Vol. 38, Issue 7
  • DOI: 10.1021/es034989b

Comparative Evaluation of Chloroethene Dechlorination to Ethene by Dehalococcoides -like Microorganisms
journal, September 2004

  • Cupples, Alison M.; Spormann, Alfred M.; McCarty, Perry L.
  • Environmental Science & Technology, Vol. 38, Issue 18
  • DOI: 10.1021/es049965z

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
  • DOI: 10.1021/es071455s

Relating Chloroethene Respiration Rates in Dehalococcoides to Protein and mRNA Biomarkers
journal, August 2012

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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.
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  • DOI: 10.1021/es702912t

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
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Sustained Aerobic Oxidation of Vinyl Chloride at Low Oxygen Concentrations
journal, February 2010

  • Gossett, James M.
  • Environmental Science & Technology, Vol. 44, Issue 4
  • DOI: 10.1021/es9033974

Statistical Analysis of Membrane Proteome Expression Changes in Saccharomyces c erevisiae
journal, September 2006

  • Zybailov, Boris; Mosley, Amber L.; Sardiu, Mihaela E.
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Spectral Probabilities and Generating Functions of Tandem Mass Spectra: A Strike against Decoy Databases
journal, August 2008

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  • Journal of Proteome Research, Vol. 7, Issue 8
  • DOI: 10.1021/pr8001244

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
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Detoxification of vinyl chloride to ethene coupled to growth of an anaerobic bacterium
journal, July 2003

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  • Nature, Vol. 424, Issue 6944
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Phosphate dysregulation via the XPR1–KIDINS220 protein complex is a therapeutic vulnerability in ovarian cancer
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Experimental validation of novel and conventional approaches to quantitative real-time PCR data analysis
journal, July 2003

Isolation and characterization of Dehalococcoides sp. strain FL2, a trichloroethene (TCE)- and 1,2-dichloroethene-respiring anaerobe
journal, September 2005

Absolute quantification of Dehalococcoides proteins: enzyme bioindicators of chlorinated ethene dehalorespiration
journal, October 2009

Microbial composition of chlorinated ethene-degrading cultures dominated by Dehalococcoides: Quantitative PCR of dechlorinating cultures
journal, December 2006

Isolation of a Bacterium That Reductively Dechlorinates Tetrachloroethene to Ethene
journal, June 1997

Expression of Reductive Dehalogenase Genes in Dehalococcoides ethenogenes Strain 195 Growing on Tetrachloroethene, Trichloroethene, or 2,3-Dichlorophenol
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Identity and Substrate Specificity of Reductive Dehalogenases Expressed in Dehalococcoides-Containing Enrichment Cultures Maintained on Different Chlorinated Ethenes
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Monitoring Abundance and Expression of "Dehalococcoides" Species Chloroethene-Reductive Dehalogenases in a Tetrachloroethene-Dechlorinating Flow Column
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Quantifying Genes and Transcripts To Assess the In Situ Physiology of "Dehalococcoides" spp. in a Trichloroethene-Contaminated Groundwater Site
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Reductive Dechlorination of Chlorinated Ethenes and 1,2-Dichloroethane by “Dehalococcoides ethenogenes” 195
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Molecular Analysis of Dehalococcoides 16S Ribosomal DNA from Chloroethene-Contaminated Sites throughout North America and Europe
journal, February 2002

Molecular Identification of the Catabolic Vinyl Chloride Reductase from Dehalococcoides sp. Strain VS and Its Environmental Distribution
journal, August 2004

Characterization of a Highly Enriched Dehalococcoides-Containing Culture That Grows on Vinyl Chloride and Trichloroethene
journal, September 2004

Multiple Reductive-Dehalogenase-Homologous Genes Are Simultaneously Transcribed during Dechlorination by Dehalococcoides-Containing Cultures
journal, December 2005

An Internal Reference Technique for Accurately Quantifying Specific mRNAs by Real-Time PCR with Application to the tceA Reductive Dehalogenase Gene
journal, July 2005

Quantitative PCR Confirms Purity of Strain GT, a Novel Trichloroethene-to-Ethene-Respiring Dehalococcoides Isolate
journal, March 2006

Comparative metagenomics of three Dehalococcoides-containing enrichment cultures: the role of the non-dechlorinating community
journal, January 2012

Microbial Community Response of an Organohalide Respiring Enrichment Culture to Permanganate Oxidation
journal, August 2015

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    Detection of Organohalide-Respiring Enzyme Biomarkers at a Bioaugmented TCE-Contaminated Field Site
    journal, June 2019

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    journal, July 2019

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