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Title: Genome analysis and physiological comparison of Alicycliphilus denitrificans strains BC and K601T

Abstract

The genomes of the Betaproteobacteria Alicycliphilus denitrificans strains BC and K601T have been sequenced to get insight into the physiology of the two strains. Strain BC degrades benzene with chlorate as electron acceptor. The cyclohexanol-degrading denitrifying strain K601T is not able to use chlorate as electron acceptor, while strain BC cannot degrade cyclohexanol. The 16S rRNA sequences of strains BC and K601T are identical and the fatty acid methyl ester patterns of the strains are similar. Basic Local Alignment Search Tool (BLAST) analysis of predicted open reading frames of both strains showed most hits with Acidovorax sp. JS42, a bacterium that degrades nitro-aromatics. The genomes include strain-specific plasmids (pAlide201 in strain K601T and pAlide01 and pAlide02 in strain BC). Key genes of chlorate reduction in strain BC were located on a 120 kb megaplasmid (pAlide01), which was absent in strain K601T. Genes involved in cyclohexanol degradation were only found in strain K601T. Benzene and toluene are degraded via oxygenase-mediated pathways in both strains. Genes involved in the meta-cleavage pathway of catechol are present in the genomes of both strains. Strain BC also contains all genes of the ortho-cleavage pathway. The large number of mono- and dioxygenase genes in the genomesmore » suggests that the two strains have a broader substrate range than known thus far.« less

Authors:
 [1];  [1];  [1];  [1];  [2];  [2];  [2];  [3];  [2];  [2];  [4];  [4];  [5];  [5];  [6];  [7];  [1];  [1];  [1];  [1] more »;  [1];  [1] « less
  1. Wageningen University and Research Centre, The Netherlands
  2. Los Alamos National Laboratory (LANL)
  3. U.S. Department of Energy, Joint Genome Institute
  4. ORNL
  5. Deltares, The Netherlands
  6. HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany
  7. CorpoGen, Bogota Colombia
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
Work for Others (WFO)
OSTI Identifier:
1087491
DOE Contract Number:  
DE-AC05-00OR22725
Resource Type:
Journal Article
Journal Name:
PLoS ONE
Additional Journal Information:
Journal Volume: 8; Journal Issue: 6; Journal ID: ISSN 1932--6203
Country of Publication:
United States
Language:
English

Citation Formats

Oosterkamp, Margreet J., Veuskens, Teun, Saia, Flavia Talarico, Weelink, Sander A.B., Goodwin, Lynne A., Daligault, Hajnalka E., Bruce, David, Detter, J. Chris, Tapia, Roxanne, Han, Cliff, Land, Miriam L, Hauser, Loren John, Langenhoff, A. M., Gerritse, Jan, Van Berkel, Willem J. H., Pieper, Dietmar, Junca, Howard, Smidt, Hauke, Schraa, Gosse, Davids, Mark, Schaap, Peter J, Plugge, Caroline M., and Stams, Alfons J. M. Genome analysis and physiological comparison of Alicycliphilus denitrificans strains BC and K601T. United States: N. p., 2013. Web. doi:10.1371/journal.pone.0066971.
Oosterkamp, Margreet J., Veuskens, Teun, Saia, Flavia Talarico, Weelink, Sander A.B., Goodwin, Lynne A., Daligault, Hajnalka E., Bruce, David, Detter, J. Chris, Tapia, Roxanne, Han, Cliff, Land, Miriam L, Hauser, Loren John, Langenhoff, A. M., Gerritse, Jan, Van Berkel, Willem J. H., Pieper, Dietmar, Junca, Howard, Smidt, Hauke, Schraa, Gosse, Davids, Mark, Schaap, Peter J, Plugge, Caroline M., & Stams, Alfons J. M. Genome analysis and physiological comparison of Alicycliphilus denitrificans strains BC and K601T. United States. https://doi.org/10.1371/journal.pone.0066971
Oosterkamp, Margreet J., Veuskens, Teun, Saia, Flavia Talarico, Weelink, Sander A.B., Goodwin, Lynne A., Daligault, Hajnalka E., Bruce, David, Detter, J. Chris, Tapia, Roxanne, Han, Cliff, Land, Miriam L, Hauser, Loren John, Langenhoff, A. M., Gerritse, Jan, Van Berkel, Willem J. H., Pieper, Dietmar, Junca, Howard, Smidt, Hauke, Schraa, Gosse, Davids, Mark, Schaap, Peter J, Plugge, Caroline M., and Stams, Alfons J. M. 2013. "Genome analysis and physiological comparison of Alicycliphilus denitrificans strains BC and K601T". United States. https://doi.org/10.1371/journal.pone.0066971.
@article{osti_1087491,
title = {Genome analysis and physiological comparison of Alicycliphilus denitrificans strains BC and K601T},
author = {Oosterkamp, Margreet J. and Veuskens, Teun and Saia, Flavia Talarico and Weelink, Sander A.B. and Goodwin, Lynne A. and Daligault, Hajnalka E. and Bruce, David and Detter, J. Chris and Tapia, Roxanne and Han, Cliff and Land, Miriam L and Hauser, Loren John and Langenhoff, A. M. and Gerritse, Jan and Van Berkel, Willem J. H. and Pieper, Dietmar and Junca, Howard and Smidt, Hauke and Schraa, Gosse and Davids, Mark and Schaap, Peter J and Plugge, Caroline M. and Stams, Alfons J. M.},
abstractNote = {The genomes of the Betaproteobacteria Alicycliphilus denitrificans strains BC and K601T have been sequenced to get insight into the physiology of the two strains. Strain BC degrades benzene with chlorate as electron acceptor. The cyclohexanol-degrading denitrifying strain K601T is not able to use chlorate as electron acceptor, while strain BC cannot degrade cyclohexanol. The 16S rRNA sequences of strains BC and K601T are identical and the fatty acid methyl ester patterns of the strains are similar. Basic Local Alignment Search Tool (BLAST) analysis of predicted open reading frames of both strains showed most hits with Acidovorax sp. JS42, a bacterium that degrades nitro-aromatics. The genomes include strain-specific plasmids (pAlide201 in strain K601T and pAlide01 and pAlide02 in strain BC). Key genes of chlorate reduction in strain BC were located on a 120 kb megaplasmid (pAlide01), which was absent in strain K601T. Genes involved in cyclohexanol degradation were only found in strain K601T. Benzene and toluene are degraded via oxygenase-mediated pathways in both strains. Genes involved in the meta-cleavage pathway of catechol are present in the genomes of both strains. Strain BC also contains all genes of the ortho-cleavage pathway. The large number of mono- and dioxygenase genes in the genomes suggests that the two strains have a broader substrate range than known thus far.},
doi = {10.1371/journal.pone.0066971},
url = {https://www.osti.gov/biblio/1087491}, journal = {PLoS ONE},
issn = {1932--6203},
number = 6,
volume = 8,
place = {United States},
year = {Tue Jan 01 00:00:00 EST 2013},
month = {Tue Jan 01 00:00:00 EST 2013}
}