Data from: Comparative genomic analysis of nine Sphingobium strains: insights into their evolution and Hexachlorocyclohexane (HCH) degradation pathways

Background: Sphingobium spp. are efficient degraders of a wide range of
chlorinated and aromatic hydrocarbons. In particular, strains which
harbour the lin pathway genes mediate the degradation of
hexachlorocyclohexane (HCH) isomers are of interest due to the widespread
persistence of this contaminant. Here we examined the evolution and
diversification of the lin pathway under the selective pressure of HCH, by
comparing the draft genomes of six newly-sequenced Sphingobium spp.
(strains LL03, DS20, IP26, HDIPO4, P25 and RL3) isolated from HCH
dumpsites, with three existing genomes (S. indicum B90A, S. japonicum
UT26S and Sphingobium sp. SYK6). Results: Efficient HCH degraders
taxonomically clustered in a closly related group comprising of UT26S,
B90A, HDIPO4 and IP26, where HDIPO4 and IP26 were classified as subspecies
with ANI value >98%. Less than 10% of the total gene content was
shared among all nine strains, but among the eight HCH-associated strains,
that is all but SYK6, the shared gene content jumped to nearly 25%. Genes
associated with nitrogen stress response and two-component systems were
found to be enriched. The strains also housed many xenobiotic degradation
pathways other than HCH, despite the absence of these xenobiotics from
isolation sources. Additionally, the strains, while non-motile, each
possessed flagellar assembly genes. While strains HDIPO4 and IP26
contained the complete set of lin genes, DS20 was entirely devoid of lin
genes (except linKLMN) and LL03, P25 and RL3 were identified as lin
deficient strains, as they housed incomplete lin pathways. Further, in
HDIPO4, linA was found as a hybrid of two natural variants i.e., linA1 and
linA2 having different enantioselectivity. Conclusion: The bacteria
isolated from HCH dumpsites provide a natural testing ground to study
variations in the lin system and their effects on degradation efficiacy.
Further, the diversity in the lin gene sequences and copy number, their
arrangement with respect to IS6100, and evidence for potential plasmid
content elucidates possible evolutionary acquisition mechanisms for this
pathway. This study further opens the horizon for selection of bacterial
for inclusion in an HCH bioremediation consortium, and suggests that
HDIPO4, IP26 and B90A would be appropriate candidates for inclusion.