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 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 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.

背景：鞘氨醇单胞菌属（Sphingobium spp.）是一类能够高效降解多种氯化烃与芳香烃的微生物。其中，携带介导六氯环己烷（hexachlorocyclohexane, HCH）异构体降解的lin通路基因的菌株尤为受到关注，因为这类污染物在环境中广泛且持久残留。本研究通过比较6株从HCH堆放场分离得到的新测序鞘氨醇单胞菌（菌株LL03、DS20、IP26、HDIPO4、P25及RL3）的草图基因组，与3株已有的鞘氨醇单胞菌基因组（S. indicum B90A、S. japonicum UT26S及Sphingobium sp. SYK6），解析了HCH选择压力下lin通路的演化与分化过程。
结果：高效降解HCH的菌株在系统发育上聚为一个紧密相关的类群，包含UT26S、B90A、HDIPO4与IP26；其中HDIPO4与IP26的平均核苷酸一致性（Average Nucleotide Identity, ANI）值大于98%，被归类为亚种。9株菌株的共有基因仅占总基因集的10%以内，但在除SYK6外的8株HCH相关菌株中，共有基因占比提升至近25%。研究发现与氮胁迫响应及双组分系统（two-component systems）相关的基因显著富集。尽管分离源中未检测到这些外源性化合物，这些菌株仍携带多种非HCH相关的外源性物质降解通路。此外，这些菌株虽无运动性，但拥有完整的鞭毛组装基因。其中，HDIPO4与IP26含有完整的lin基因集；DS20仅保留linKLMN基因，完全缺失其余lin通路基因；而LL03、P25及RL3则为lin通路缺陷菌株，仅携带不完整的lin代谢通路。进一步分析显示，HDIPO4中的linA基因是两个天然变异体linA1与linA2的杂交体，这两种变异体具有不同的对映选择性。
结论：从HCH堆放场分离得到的菌株为研究lin系统的变异及其对降解效能的影响提供了天然的实验模型。此外，lin基因序列与拷贝数的多样性、其与插入序列IS6100的排列方式，以及潜在质粒携带的证据，均阐明了该通路可能的进化获取机制。本研究为筛选可用于HCH生物修复（bioremediation）联合体的菌株拓展了方向，并表明HDIPO4、IP26及B90A可作为合适的候选菌株纳入该修复体系。