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Applied and Environmental Microbiology, June 2008, p. 3533-3540, Vol. 74, No. 11
0099-2240/08/$08.00+0     doi:10.1128/AEM.01835-07
Copyright © 2008, American Society for Microbiology. All Rights Reserved.

Comparative Genomics of "Dehalococcoides ethenogenes" 195 and an Enrichment Culture Containing Unsequenced "Dehalococcoides" Strains {triangledown} ,{dagger}

Kimberlee A. West,1 David R. Johnson,1 Ping Hu,2 Todd Z. DeSantis,2 Eoin L. Brodie,2 Patrick K. H. Lee,1 Helene Feil,1 Gary L. Andersen,2 Stephen H. Zinder,3 and Lisa Alvarez-Cohen1,2*

Department of Civil and Environmental Engineering, University of California, Berkeley, California 94720-1170,1 Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720,2 Department of Microbiology, Cornell University, Ithaca, New York 148533

Received 7 August 2007/ Accepted 10 March 2008

Tetrachloroethene (PCE) and trichloroethene (TCE) are prevalent groundwater contaminants that can be completely reductively dehalogenated by some "Dehalococcoides" organisms. A Dehalococcoides-organism-containing microbial consortium (referred to as ANAS) with the ability to degrade TCE to ethene, an innocuous end product, was previously enriched from contaminated soil. A whole-genome photolithographic microarray was developed based on the genome of "Dehalococcoides ethenogenes" 195. This microarray contains probes designed to hybridize to >99% of the predicted protein-coding sequences in the strain 195 genome. DNA from ANAS was hybridized to the microarray to characterize the genomic content of the ANAS enrichment. The microarray results revealed that the genes associated with central metabolism, including an apparently incomplete carbon fixation pathway, cobalamin-salvaging system, nitrogen fixation pathway, and five hydrogenase complexes, are present in both strain 195 and ANAS. Although the gene encoding the TCE reductase, tceA, was detected, 13 of the 19 reductive dehalogenase genes present in strain 195 were not detected in ANAS. Additionally, 88% of the genes in predicted integrated genetic elements in strain 195 were not detected in ANAS, consistent with these elements being genetically mobile. Sections of the tryptophan operon and an operon encoding an ABC transporter in strain 195 were also not detected in ANAS. These insights into the diversity of Dehalococcoides genomes will improve our understanding of the physiology and evolution of these bacteria, which is essential in developing effective strategies for the bioremediation of PCE and TCE in the environment.

* Corresponding author. Mailing address: 760 Davis Hall, Department of Civil and Environmental Engineering, University of California, Berkeley, CA 94720-1710. Phone: (510) 643-8739. Fax: (510) 642-7483. E-mail: alvarez{at}ce.berkeley.edu

{triangledown} Published ahead of print on 21 March 2008.

{dagger} Supplemental material for this article may be found at http://aem.asm.org/.

Applied and Environmental Microbiology, June 2008, p. 3533-3540, Vol. 74, No. 11
0099-2240/08/$08.00+0     doi:10.1128/AEM.01835-07
Copyright © 2008, American Society for Microbiology. All Rights Reserved.



This article has been cited by other articles:

  • Cheng, D., He, J. (2009). Isolation and Characterization of "Dehalococcoides" sp. Strain MB, Which Dechlorinates Tetrachloroethene to trans-1,2-Dichloroethene. Appl. Environ. Microbiol. 75: 5910-5918 [Abstract] [Full Text]  
  • Tang, Y. J., Yi, S., Zhuang, W.-Q., Zinder, S. H., Keasling, J. D., Alvarez-Cohen, L. (2009). Investigation of Carbon Metabolism in "Dehalococcoides ethenogenes" Strain 195 by Use of Isotopomer and Transcriptomic Analyses. J. Bacteriol. 191: 5224-5231 [Abstract] [Full Text]  
  • Tas, N., van Eekert, M. H. A., Schraa, G., Zhou, J., de Vos, W. M., Smidt, H. (2009). Tracking Functional Guilds: "Dehalococcoides" spp. in European River Basins Contaminated with Hexachlorobenzene. Appl. Environ. Microbiol. 75: 4696-4704 [Abstract] [Full Text]  
  • Johnson, D. R., Brodie, E. L., Hubbard, A. E., Andersen, G. L., Zinder, S. H., Alvarez-Cohen, L. (2008). Temporal Transcriptomic Microarray Analysis of "Dehalococcoides ethenogenes" Strain 195 during the Transition into Stationary Phase. Appl. Environ. Microbiol. 74: 2864-2872 [Abstract] [Full Text]  


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