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Isolation of two new D ehalococcoides mccartyi strains with dissimilar dechlorination functions and their characterization by comparative genomics via microarray analysis
Author(s) -
Lee Patrick K. H.,
Cheng Dan,
West Kimberlee A.,
AlvarezCohen Lisa,
He Jianzhong
Publication year - 2013
Publication title -
environmental microbiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.954
H-Index - 188
eISSN - 1462-2920
pISSN - 1462-2912
DOI - 10.1111/1462-2920.12099
Subject(s) - strain (injury) , biology , genome , gene , 16s ribosomal rna , comparative genomics , bacteria , functional genomics , microarray , genomics , whole genome sequencing , reductive dechlorination , vinyl chloride , microbiology and biotechnology , genetics , biodegradation , chemistry , gene expression , anatomy , ecology , organic chemistry , copolymer , polymer
Summary Microbial reductive dechlorination of trichloroethene ( TCE ) in groundwater often results in the accumulation of dichloroethenes ( DCE s). D ehalococcoides mccartyi ( D hc ) are the only known bacteria capable of dechlorination beyond DCE to non‐toxic ethene. In this study, two newly isolated D hc strains (11a and 11a5) with dissimilar functional abilities are described. Strain 11a reductively dechlorinates TCE , 1,1‐ DCE , cis ‐ DCE , trans ‐ DCE , and vinyl chloride ( VC ) to ethene, while strain 11a5 dechlorinates TCE and all three DCE isomers only to VC . Each of these dechlorination reactions are coupled to growth by these strains. The VC dechlorination rate of strain 11a occurs at a rate of 258 nmol per min per mg of protein, about two times faster than previously reported stains. Strain 11a possesses the vcrA gene while strain 11a5 contains the tceA gene. Strains 11a and 11a5 share 100% 16 S rRNA gene sequence identity with previously sequenced D hc strains BAV1 and CBDB1 , placing it within the P inellas subgroup, and 85.4% and 89.5% of all genes present in the CBDB1 and BAV1 genomes were detected in strains 11a and 11a5, respectively, using a custom‐designed microarray targeting four sequenced D hc strains. Genes that were not detected in strains 11a and 11a5 are mostly within the high plasticity regions or integrated elements of the sequenced strains. This study reports the functional description and comparative genomics of two additional D hc isolates and provides evidence that the observed functional incongruence between the activity and core genome phylogenies of D hc strains is likely driven by the horizontal transfer of key reductive dehalogenase‐encoding genes.