Pangenomic insights into Dehalobacter evolution and acquisition of functional genes for bioremediation

<i>Dehalobacter</i> is a genus of organohalide-respiring bacteria that is recognized for its fastidious growth using reductive dehalogenases (RDases). In the SC05 culture, however, a <i>Dehalobacter</i> population also mineralizes dichloromethane (DCM) produced by chloroform dechlorination using the <i>mec</i> cassette, just downstream of its active RDase. A closed genome of this DCM-mineralizing lineage has previously evaded assembly. Here, we present the genomes of two novel <i>Dehalobacter</i> strains, each of which was assembled from the metagenome of a distinct subculture from SC05. A pangenomic analysis of the <i>Dehalobacter</i> genus, including RDase synteny and phylogenomics, reveals at least five species of <i>Dehalobacter</i> based on average nucleotide identity, RDase and core gene synteny, as well as differential functional genes. An integration hotspot is also pinpointed in the <i>Dehalobacter</i> genome, in which many recombinase islands have accumulated. This nested recombinase island encodes the active RDase and <i>mec</i> cassette in both SC05 <i>Dehalobacter</i> genomes, indicating the transfer of key functional genes between species of <i>Dehalobacter</i>. Horizontal gene transfer between these two novel <i>Dehalobacter</i> strains has implications for the evolutionary history within the SC05 subcultures and of the <i>Dehalobacter</i> genus as a whole, especially regarding adaptation to anthropogenic chemicals.