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University of California-Berkeley: Dataset Details, ID=GSE9612

Superfund Research Program

Toxic Substances in the Environment

Center Director: Martyn T. Smith
Grant Number: P42ES004705
Funding Period: 1987-2027
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Title: Comparative Genomics of D. ethenogenes 195 and an Unsequenced Dehalococcoides-Containing Enrichment Culture

Accession Number: GSE9612

Link to Dataset:

Repository: Gene Expression Omnibus (GEO)

Data Type(s): Gene Expression

Experiment Type(s): Genome variation profiling by array

Organism(s): Dehalococcoides

Summary: Tetrachloroethene (PCE) and trichloroethene (TCE) are prevalent groundwater contaminants that can be completely reductively dehalogenated by Dehalococcoides organisms. A Dehalococcoides-containing microbial consortium (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 (strain 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 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 bioremediation of PCE and TCE in the environment. Keywords: comparative genomic hybridization

Publication(s) associated with this dataset:
  • West K, Johnson DR, Hu P, DeSantis TZ, Brodie EL, Lee PH, Feil H, Andersen GL, Zinder S, Alvarez-Cohen L. 2008. Comparative genomics of "Dehalococcoides ethenogenes" 195 and an enrichment culture containing unsequenced "Dehalococcoides" strains. Appl Environ Microbiol 74(11):3533-3540. doi:10.1128/AEM.01835-07 PMID:18359838 PMCID:PMC2423027
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