16S rDNA phylogeny and distribution of lin genes in novel hexachlorocyclohexane‐degrading Sphingomonas strains

Abstract

Hexachlorocyclohexane (HCH) is a highly recalcitrant pesticide that persists in soils. Three novel HCHdegrading strains (DS2, DS2-2 and DS3-1) were isolated after enrichment from HCH-contaminated soil from Germany. These strains efficiently degraded the a a a a -, g g g g -and d d d d -isomers of HCH, while strain DS3-1 also degraded b b b b -HCH. Based on 16S rDNA analysis, strain DS3-1 was closely related to Sphingomonas taejonensis , while strains DS2 and DS2-2 were closely related to Sphingomonas flava and seven HCHdegrading strains recently isolated from HCH-contaminated Spanish soil. Hence, geographic origin of the strains was not reflected in their phylogenetic affiliation. Subsequently, lin genes involved in HCH degradation, virtually identical to those from Sphingomonas paucimobilis strains UT26 from Japan and B90A from India, were identified in strains DS3-1, DS2, DS2-2 and five of the strains from Spain. The conserved lin gene sequences and structural organization, as well as the close association with IS 6100 , suggest a shared lin gene origin and recent horizontal gene transfer among phylogenetically diverged Sphingomonas strains in remote geographic locations. The loss of the ability to degrade g g g g -HCH was associated with the deletion of the linA gene, probably due to recombination involving IS 6100 elements, of which several copies are located in the lin cluster region.

Pseudomonas sp. to Sphingobium indicum: a journey of microbial degradation and bioremediation of Hexachlorocyclohexane

“…All these strains have been reported to contain similar linA, linB, linC, linD, linE, linR and linF genes for HCH degradation (Table 6). All the lin genes in these strains were also associated with IS6100 as already reported in S. indicum B90A, S. francense Sp+ and S. japonicum UT26 [8,27] (Table 7). Loss of lin genes is also associated with loss of IS6100.…”

“…Some Gram-positive HCH degrading bacteria like Bacillus circulans and Bacillus brevis have also been reported in literature that degrade all the HCH isomers including β-HCH [42]. Recently, several new HCH degrading bacterial strains have been isolated from dumpsites of Germany and Spain and all of them belong to the family Sphingomonadaceae [26,27]. The list of HCH degrading strains is increasing and new bacterial species that degrade HCH isomers are being added up (Table 4).…”

“…These studies indicated that the pathway for degradation of β-and δ-HCH is perhaps different from γ-and α-HCH. In addition, these studies raised several questions concerning the evolution of sphingomonads especially from high dose point contaminated sites [26,27]. Although, γ-and perhaps α-HCH seem to be completely mineralized by sphingomonads, it is not known whether they are used by these organisms as sources of carbon and energy [44].…”

“…These sites serve as reservoirs from where HCH residues are spreading to far off regions due to leaching and aerial transport. Such HCH dumpsites are present all over the world and have been reported from Rio de Janeiro (Brazil) [23] , Pontevedra (Spain) [24,25] , Bilbao (Spain) [26], Chemnitz (Germany) [27], North Carolina (US) [http://www.earthfax.com/WhiteRot/PCP.htm] and Bitterfi eld (Germany) [28], Lucknow (India) [29]. These reports are just a small proportion of dumpsites brought to public notice.…”

Localization of HCH catabolic genes (lin genes) in Sphingobium indicum B90A

“…Furthermore, S. indicum B90A was reported to contain several copies of an insertion sequence, IS6100 (originally isolated from a Gram-positive bacterium, Mycobacterium fortuitum FCI) 16 , which were found to be associated with most of the lin genes in this strain 15 . Recently, several HCH-degrading sphingomonads have been isolated from the HCH contaminated soils from different geographical locations [17][18][19][20][21][22] . These strains were found to contain lin genes highly similar to UT26 and B90A 14,[17][18][19] .…”