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Title: Complete genome sequence of Pseudomonas stutzeri strain RCH2 isolated from a Hexavalent Chromium [Cr(VI)] contaminated site

Abstract

Hexavalent Chromium [Cr(VI)] is a widespread contaminant found in soil, sediment, and ground water in several DOE sites, including Hanford 100 H area. In order to stimulate microbially mediated reduction of Cr(VI) at this site, a poly-lactate hydrogen release compound was injected into the chromium contaminated aquifer. The targeted enrichment of dominant nitrate-reducing bacteria post injection resulted in the isolation of Pseudomonas stutzeri strain RCH2. P. stutzeri strain RCH2 was isolated using acetate as the electron donor and is a complete denitrifier. Experiments with anaerobic washed cell suspension of strain RCH2 revealed it could reduce Cr(VI) and Fe(III). We sequenced the genome of strain RCH2 using a combination of Illumina and 454 sequencing technologies and contained a circular chromosome of 4.6 Mb and three plasmids. Furthermore, global genome comparisons of strain RCH2 with six other fully sequenced P. stutzeri strains revealed most genomic regions are conserved, however strain RCH2 has an additional 244 genes, some of which are involved in chemotaxis, Flp pilus biogenesis and pyruvate/2-oxogluturate complex formation.

Authors:
ORCiD logo [1];  [2];  [1];  [1];  [1];  [1];  [3];  [1];  [1];  [1];  [4]
  1. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  2. Univ. of Tennessee, Knoxville, TN (United States)
  3. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  4. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of Tennessee, Knoxville, TN (United States)
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1354676
Alternate Identifier(s):
OSTI ID: 1379726
Grant/Contract Number:  
AC05-00OR22725; AC02-05CH11231; AC02-05CH1123
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Standards in Genomic Sciences
Additional Journal Information:
Journal Volume: 12; Journal Issue: 1; Journal ID: ISSN 1944-3277
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES; pseudomonas; nitrate reduction; chromium; Hanford 100H

Citation Formats

Chakraborty, Romy, Woo, Hannah, Dehal, Paramvir, Walker, Robert, Zemla, Marcin, Auer, Manfred, Goodwin, Lynne A., Kazakov, Alexey, Novichkov, Pavel, Arkin, Adam P., and Hazen, Terry C. Complete genome sequence of Pseudomonas stutzeri strain RCH2 isolated from a Hexavalent Chromium [Cr(VI)] contaminated site. United States: N. p., 2017. Web. doi:10.1186/s40793-017-0233-7.
Chakraborty, Romy, Woo, Hannah, Dehal, Paramvir, Walker, Robert, Zemla, Marcin, Auer, Manfred, Goodwin, Lynne A., Kazakov, Alexey, Novichkov, Pavel, Arkin, Adam P., & Hazen, Terry C. Complete genome sequence of Pseudomonas stutzeri strain RCH2 isolated from a Hexavalent Chromium [Cr(VI)] contaminated site. United States. doi:10.1186/s40793-017-0233-7.
Chakraborty, Romy, Woo, Hannah, Dehal, Paramvir, Walker, Robert, Zemla, Marcin, Auer, Manfred, Goodwin, Lynne A., Kazakov, Alexey, Novichkov, Pavel, Arkin, Adam P., and Hazen, Terry C. Wed . "Complete genome sequence of Pseudomonas stutzeri strain RCH2 isolated from a Hexavalent Chromium [Cr(VI)] contaminated site". United States. doi:10.1186/s40793-017-0233-7. https://www.osti.gov/servlets/purl/1354676.
@article{osti_1354676,
title = {Complete genome sequence of Pseudomonas stutzeri strain RCH2 isolated from a Hexavalent Chromium [Cr(VI)] contaminated site},
author = {Chakraborty, Romy and Woo, Hannah and Dehal, Paramvir and Walker, Robert and Zemla, Marcin and Auer, Manfred and Goodwin, Lynne A. and Kazakov, Alexey and Novichkov, Pavel and Arkin, Adam P. and Hazen, Terry C.},
abstractNote = {Hexavalent Chromium [Cr(VI)] is a widespread contaminant found in soil, sediment, and ground water in several DOE sites, including Hanford 100 H area. In order to stimulate microbially mediated reduction of Cr(VI) at this site, a poly-lactate hydrogen release compound was injected into the chromium contaminated aquifer. The targeted enrichment of dominant nitrate-reducing bacteria post injection resulted in the isolation of Pseudomonas stutzeri strain RCH2. P. stutzeri strain RCH2 was isolated using acetate as the electron donor and is a complete denitrifier. Experiments with anaerobic washed cell suspension of strain RCH2 revealed it could reduce Cr(VI) and Fe(III). We sequenced the genome of strain RCH2 using a combination of Illumina and 454 sequencing technologies and contained a circular chromosome of 4.6 Mb and three plasmids. Furthermore, global genome comparisons of strain RCH2 with six other fully sequenced P. stutzeri strains revealed most genomic regions are conserved, however strain RCH2 has an additional 244 genes, some of which are involved in chemotaxis, Flp pilus biogenesis and pyruvate/2-oxogluturate complex formation.},
doi = {10.1186/s40793-017-0233-7},
journal = {Standards in Genomic Sciences},
number = 1,
volume = 12,
place = {United States},
year = {Wed Feb 08 00:00:00 EST 2017},
month = {Wed Feb 08 00:00:00 EST 2017}
}

Journal Article:
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