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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.

Localized Plasticity in the Streamlined Genomes of Vinyl Chloride Respiring Dehalococcoides