Localized Plasticity in the Streamlined Genomes of Vinyl Chloride Respiring <em>Dehalococcoides</em>

Abstract

<div><p>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, <em>Dehalococcoides</em> sp. strains VS and BAV1. Notably, the respective VC reductase encoding genes, <em>vcrAB</em> and <em>bvcAB</em>, 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 <em>Dehalococcoides</em> 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 <em>Dehalococcoides</em> genomes, an elevated number of repeated elements including insertion sequences (IS), as well as 91 of 96 <em>rdhAB</em>, genes that putatively encode terminal reductases in organohalide respiration. Only three core <em>rdhA</em> orthologous groups were identified, and only one of these groups is supported by synteny. The low number of core <em>rdhAB</em>, contrasted with the high <em>rdhAB</em> 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 <em>Dehalococccoides</em>. 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.</p></div>