Journal Article

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

Oldach, Phoebe, Verma, Helianthous, Gilbert, Jack A, Kumar, Roshan, Sangwan, Naseer, Khurana, Jitendra P, Lal, Rup

2014

Overview

Background Sphingobium 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). Results Efficient 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. Conclusion The 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 IS 6100 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.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,Springer
• Subject: Amino Acid Sequence / Analysis / Animal Genetics and Genomics / Aromatic hydrocarbons / Base Composition / BASIC BIOLOGICAL SCIENCES / Biomedical and Life Sciences / Bioremediation / Chlorinated hydrocarbons / Chromosome Mapping / Cluster Analysis / Colleges & universities / Comparative and evolutionary genomics / Comparative Genomic Hybridization / Computational Biology / Contaminants / Evolution, Molecular / Flagella - genetics / Gene Expression Profiling / Genes / Genes, Bacterial / Genetic aspects / Genome Size / Genome, Bacterial / Genomes / Genomics / Hexachlorocyclohexane / Hexachlorocyclohexane (HCH) / Hexachlorocyclohexane - chemistry / Hexachlorocyclohexane - metabolism / Laboratories / Life Sciences / lin genes / Metabolic Networks and Pathways / Microarrays / Microbial Genetics and Genomics / Molecular biology / Molecular Sequence Data / Nitrogen - metabolism / Phylogeny / Physiological aspects / Plant Genetics and Genomics / Plasmids - genetics / Polycyclic aromatic hydrocarbons / Proteomics / Research Article / Scholarships & fellowships / Selection, Genetic / Sequence Alignment / Sphingobium / Sphingomonadaceae - genetics / Sphingomonadaceae - metabolism / Values / Xenobiotic compounds / Xenobiotics