Lessons from the genomes of lindane‐degrading sphingomonads

Abstract

Summary Bacterial strains capable of degrading man‐made xenobiotic compounds are good materials to study bacterial evolution towards new metabolic functions. Lindane (γ‐hexachlorocyclohexane, γ‐HCH, or γ‐BHC) is an especially good target compound for the purpose, because it is relatively recalcitrant but can be degraded by a limited range of bacterial strains. A comparison of the complete genome sequences of lindane‐degrading sphingomonad strains clearly demonstrated that (i) lindane‐degrading strains emerged from a number of different ancestral hosts that have recruited lin genes encoding enzymes that are able to channel lindane to central metabolites, (ii) in sphingomonads lin genes have been acquired by horizontal gene transfer mediated by different plasmids and in which IS6100 plays a role in recruitment and distribution of genes, and (iii) IS6100 plays a role in dynamic genome rearrangements providing genetic diversity to different strains and ability to evolve to other states. Lindane‐degrading bacteria whose genomes change so easily and quickly are also fascinating starting materials for tracing the bacterial evolution process experimentally in a relatively short time period. As the origin of the specific lin genes remains a mystery, such genes will be useful probes for exploring the cryptic ‘gene pool’ available to bacteria.

Isolation and genomic characterization of the ibuprofen‐degrading bacterium Sphingomonas strain MPO218

“…This IS 6100 element is an 880 bp replicative IS that apparently has no preference of target specificity (Mahillon and Chandler, 1998). This element has been shown to play an essential role in the evolution of lindane‐degrading Sphingomonas by recruiting and rearranging the lin genes (Nagata et al ., 2019). Interestingly, in addition to the DNA rearrangements that can occur during the transposition process, homologous recombination between two copies of IS 6100 appears to occur, suggesting that IS 6100 may thus contribute to dynamic genome rearrangement in lindane degraders (Nagata et al ., 2019).…”

“…This element has been shown to play an essential role in the evolution of lindane‐degrading Sphingomonas by recruiting and rearranging the lin genes (Nagata et al ., 2019). Interestingly, in addition to the DNA rearrangements that can occur during the transposition process, homologous recombination between two copies of IS 6100 appears to occur, suggesting that IS 6100 may thus contribute to dynamic genome rearrangement in lindane degraders (Nagata et al ., 2019). On the other hand, it is also important to note that IS 6100 is involved in the loss of lin genes and, therefore, may contribute to adaptation to other conditions in which these genes are no longer necessary (Nagata et al ., 2011).…”

Novosphingobium silvae sp. nov., isolated from subtropical forest soil

“…As members of the well-known sphingomonads group, Novosphingobium spp. are also characterized by the outstanding degradation capacity of polycyclic aromatic compounds [2–5], such as Novosphingobium aromaticivorans , Novosphingobium pentaromativorans and Novosphingobium taihuense [6–8]. Until December 2019, 49 species of the genus had been validly published [9], including the recently described Novosphingobium meiothermophilum [10].…”

“…Furthermore, strain FGD1 T lacked lin genes responsible for bioremediation of hexachlorocyclohexane also evidenced by the KEGG map. However, biodegradation of hexachlorocyclohexane in the genus Novosphingobium had been frequently described, especially from soils contaminated by hexachlorocyclohexane [3, 31]. As a consequence of the relatively low number of genes for aromatic compounds biodegradation, the novel strain might be inferior in biodegradation of aromatic compounds.…”

Identification of two fnr genes and characterisation of their role in the anaerobic switch in Sphingopyxis granuli strain TFA

“…Ubiquity is reflected in that they are found in most of the environments, although they play a particularly important role in nutrient cycling in marine environments 4 due to its excellent adaptation to oligotrophic environments 5 . Their metabolic versatility includes the ability of many of them to degrade different recalcitrant molecules such as polycyclic aromatic hydrocarbons 6 or xenobiotic compounds such as lindane 7 , frequently harbouring this biodegradative capacity in plasmids 8 .…”