National Laboratory Title Localized Plasticity in the Streamlined Genomes of Vinyl Chloride

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. Citation: McMurdie PJ, Behrens SF, Müller JA, Göke J, Ritalahti KM, et al. (2009) Localized Plasticity in the Streamlined Genomes of Vinyl Chloride Respiring Dehalococcoides. PLoS Genet 5(11): e1000714. doi:10.1371/journal.pgen.1000714 Academic Editor: Josep Casadesús, Universidad de Sevilla, Spain Received July 6, 2009; Accepted October 8, 2009; Published November 6, 2009 Copyright: 2009 McMurdie et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: This work was supported by the Strategic Environmental Research Defense Project (SERDP) to AMS and FL by grants ER-1588 and ER-1586, respectively. SH was partially funded by grant NSF-DMS-0241246, JAM was partially funded by grant MSU 52019621187, and PJM was partially funded by fellowship grant FP91671901 from the U.S. Environmental Protection Agency’s Science to Achieve Results (STAR) program. Genome sequencing and assembly was performed under the auspices of the U.S. Department of Energy’s Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * E-mail: spormann@stanford.edu