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The genomes of two closely related  Dehalobacter  strains (strain CF and strain DCA) were assembled from the metagenome of an anaerobic enrichment culture that reductively dechlorinates chloroform (CF), 1,1,1-trichloroethane (1,1,1-TCA) and 1,1-dichloroethane (1,1-DCA). The 3.1 Mbp genomes of strain CF (that dechlorinates CF and 1,1,1-TCA) and strain DCA (that dechlorinates 1,1-DCA) each contain 17 putative reductive dehalogenase homologous ( rdh ) genes. These two genomes were systematically compared to three other available organohalide-respiring  Dehalobacter  genomes ( Dehalobacter restrictus  strain PER-K23,  Dehalobacter  sp. strain E1 and  Dehalobacter  sp. strain UNSWDHB), and to the genomes of  Dehalococcoides mccartyi  strain 195 and  Desulfitobacterium hafniense  strain Y51. This analysis compared 42 different metabolic and physiological categories. The genomes of strains CF and DCA share 90% overall average nucleotide identity and >99.8% identity over a 2.9 Mbp alignment that excludes large insertions, indicating that these genomes differentiated from a close common ancestor. This differentiation was likely driven by selection pressures around two orthologous reductive dehalogenase genes,  cfrA  and  dcrA , that code for the enzymes that reduce CF or 1,1,1-TCA and 1,1-DCA. The many reductive dehalogenase genes found in the five  Dehalobacter  genomes cluster into two small conserved regions and were often associated with Crp/Fnr transcriptional regulators. Specialization is on-going on a strain-specific basis, as some strains but not others have lost essential genes in the Wood-Ljungdahl (strain E1) and corrinoid biosynthesis pathways (strains E1 and PER-K23). The gene encoding phosphoserine phosphatase, which catalyzes the last step of serine biosynthesis, is missing from all five  Dehalobacter  genomes, yet  D. restrictus  can grow without serine, suggesting an alternative or unrecognized biosynthesis route exists. In contrast to  D. mccartyi , a complete heme biosynthesis pathway is present in the five  Dehalobacter  genomes. This pathway corresponds to a newly described alternative heme biosynthesis route first identified in Archaea. This analysis of organohalide-respiring  Firmicutes  and  Chloroflexi  reveals profound evolutionary differences despite very similar niche-specific metabolism and function.

frontiers in microbiology

Sister Dehalobacter Genomes Reveal Specialization in Organohalide Respiration and Recent Strain Differentiation Likely Driven by Chlorinated Substrates