Abstract
Vinyl chloride (VC) is a human carcinogen and widespread priority pollutant. Here we report the first, to our knowledge, complete genome sequences of microorganisms able to respire VC, Dehalococcoides sp. strains VS and BAV1. Notably, the respective VC reductase encoding genes, vcrAB and bvcAB, were found embedded in distinct genomic islands (GEIs) with different predicted integration sites, suggesting that these genes were acquired horizontally and independently by distinct mechanisms. A comparative analysis that included two previously sequenced Dehalococcoides genomes revealed a contextually conserved core that is interrupted by two high plasticity regions (HPRs) near the Ori. These HPRs contain the majority of GEIs and strain-specific genes identified in the four Dehalococcoides genomes, an elevated number of repeated elements including insertion sequences (IS), as well as 91 of 96 rdhAB, genes that putatively encode terminal reductases in organohalide respiration. Only three core rdhA orthologous groups were identified, and only one of these groups is supported by synteny. The low number of core rdhAB, contrasted with the high rdhAB numbers per genome (up to 36 in strain VS), as well as their colocalization with GEIs and other signatures for horizontal transfer, suggests that niche adaptation via organohalide respiration is a fundamental ecological strategy in Dehalococccoides. This adaptation has been exacted through multiple mechanisms of recombination that are mainly confined within HPRs of an otherwise remarkably stable, syntenic, streamlined genome among the smallest of any free-living microorganism.
Highlights
Vinyl chloride (VC) – a proven human carcinogen [1] – and other chloroethenes, such as trichloroethene (TCE) and tetrachloroethene (PCE), are among the most frequently detected groundwater contaminants in the United States of America and other industrialized countries [2]
We show that the integration site for the vcr-genomic islands (GEIs) is not unique to this GEI nor to strain VS, but instead appears to be an integration site associated with many other strainspecific rdhA in strains VS, 195, and CBDB1
Concluding Remarks We describe the emergence of a genomic structure in which rdhA and associated genes, as well as other strain-specific genes are concentrated predominantly within two high plasticity regions (HPRs) near the Ori
Summary
Vinyl chloride (VC) – a proven human carcinogen [1] – and other chloroethenes, such as trichloroethene (TCE) and tetrachloroethene (PCE), are among the most frequently detected groundwater contaminants in the United States of America and other industrialized countries [2]. Two Dhc genome sequences of isolates that cannot respire VC revealed many full-length non-identical reductive dehalogenase homologous genes (rdhAB) per genome; 17 in D. ethenogenes strain 195 [9] and 32 in Dhc strain CBDB1 [10]. These genome sequences revealed a bias in the location of rdhAB and associated genes toward the origin of replication (Ori) and the leading strand [9,10]. Culture-based studies have shown that strains 195 and CBDB1 contribute to dechlorination of a variety of priority pollutants including polychlorinated ethenes [13], benzenes [14], phenols [15], dibenzo-p-dioxins [16], dibenzofurans, biphenyls, Author Summary
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