Abstract
BackgroundSphingobium spp. are efficient degraders of a wide range of chlorinated and aromatic hydrocarbons. In particular, strains which harbour the lin pathway genes mediating 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).ResultsEfficient HCH degraders phylogenetically clustered in a closely 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 except 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, these strains, although non-motile, but posses flagellar assembly genes. While strains HDIPO4 and IP26 contained the complete set of lin genes, DS20 was entirely devoid of lin genes (except linKLMN) whereas, 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 known for their different enantioselectivity.ConclusionThe bacteria isolated from HCH dumpsites provide a natural testing ground to study variations in the lin system and their effects on degradation efficacy. Further, the diversity in the lin gene sequences and copy number, their arrangement with respect to IS6100 and evidence for potential plasmid content elucidate possible evolutionary acquisition mechanisms for this pathway. This study further opens the horizon for selection of bacterial strains for inclusion in an HCH bioremediation consortium and suggests that HDIPO4, IP26 and B90A would be appropriate candidates for inclusion.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-1014) contains supplementary material, which is available to authorized users.
Highlights
Sphingobium spp. are efficient degraders of a wide range of chlorinated and aromatic hydrocarbons
The variation in genome size can be partially correlated to the presence of genomic islands; IP26 maintained the largest genome and the highest genomic island content, while LL03 had the least (Table 1)
Strains LL03 and DS20 were isolated from HCH dumpsites in the Czech Republic and India, respectively, and these strains had two different CRISPR/CAS systems, that may correspond to their different geographical locations
Summary
Sphingobium spp. are efficient degraders of a wide range of chlorinated and aromatic hydrocarbons. Strains which harbour the lin pathway genes mediating the degradation of hexachlorocyclohexane (HCH) isomers are of interest due to the widespread persistence of this contaminant. Purification of γ-HCH (10-12%) from the mixture leads to the formation of HCH muck (88-90% of the total HCH mixture) having mainly α (60-70%), β (5-12%), δ (6-10%), and ε (3-4%) isomers [5]. This has been generally discarded in the open by the side of industrial units creating a large number of HCH dumpsites between the 1960s to the 1980s around the world [6]. Sphingobium spp. are often enriched in HCH dumpsites and have been shown to acquire and maintain genes associated with HCH degradation [7,8,9,10]
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