title: Hexachlorocyclohexane-degrading bacterial strains Sphingomonas paucimobilis B90A, UT26 and Sp+, having similar lin genes, represent three distinct species, Sphingobium indicum sp. nov., Sphingobium japonicum sp. nov. and Sphingobium francense sp. nov., and reclassification of [Sphingomonas] chungbukensis as Sphingobium chungbukense comb. nov.
abstract: Three strains of Sphingomonas paucimobilis, B90A, UT26 and Sp+, isolated from different geographical locations, were found to degrade hexachlorocyclohexane. Phylogenetic analysis based on 16S rRNA gene sequences indicated that these strains do not fall in a clade that includes the type strain, Sphingomonas paucimobilis ATCC 29837(T), but form a coherent cluster with [Sphingomonas] chungbukensis IMSNU 11152(T) followed by Sphingobium chlorophenolicum ATCC 33790(T). The three strains showed low DNA-DNA relatedness values with Sphingomonas paucimobilis ATCC 29837(T) (8-25%), [Sphingomonas] chungbukensis IMSNU 11152(T) (10-17%), Sphingobium chlorophenolicum ATCC 33790(T) (23-54%) and Sphingomonas xenophaga DSM 6383(T) (10-28%), indicating that they do not belong to any of these species. Although the three strains were found to be closely related to each other based on 16S rRNA gene sequence similarity (99.1-99.4%), DNA-DNA relatedness (19-59%) and pulsed-field gel electrophoresis (PFGE) patterns indicated that they possibly represent three novel species of the genus Sphingobium. The three strains could also be readily distinguished by biochemical tests. The three strains showed similar polar lipid profiles and contained sphingoglycolipids. The strains differed from each other in fatty acid composition but contained the predominant fatty acids characteristic of other Sphingobium species. A phylogenetic study based on 16S rRNA gene sequences showed that [Sphingomonas] chungbukensis IMSNU 11152(T) formed a cluster with members of the genus Sphingobium. Based on these results, it is proposed that strains B90A, UT26 and Sp+, previously known as Sphingomonas paucimobilis, are the type strains of Sphingobium indicum sp. nov. (=MTCC 6364(T)=CCM 7286(T)), Sphingobium japonicum sp. nov. (=MTCC 6362(T)=CCM 7287(T)) and Sphingobium francense sp. nov. (=MTCC 6363(T)=CCM 7288(T)), respectively. It is also proposed that [Sphingomonas] chungbukensis be transferred to Sphingobium chungbukense comb. nov.
authors.affiliation: Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi - 110007, India.
authors.forename: Rinku
authors.initials: R
authors.lastname: Pal
authors.affiliation: Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi - 110007, India.
authors.forename: Shashi
authors.initials: S
authors.lastname: Bala
authors.affiliation: Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi - 110007, India.
authors.forename: Mandeep
authors.initials: M
authors.lastname: Dadhwal
authors.affiliation: Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi - 110007, India.
authors.forename: Mukesh
authors.initials: M
authors.lastname: Kumar
authors.affiliation: Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi - 110007, India.
authors.forename: Gauri
authors.initials: G
authors.lastname: Dhingra
authors.affiliation: Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi - 110007, India.
authors.forename: Om
authors.initials: O
authors.lastname: Prakash
authors.affiliation: Center for Cellular and Molecular Biology, Hyderabad - 500007, India.
authors.forename: S R
authors.initials: SR
authors.lastname: Prabagaran
authors.affiliation: Center for Cellular and Molecular Biology, Hyderabad - 500007, India.
authors.forename: S
authors.initials: S
authors.lastname: Shivaji
authors.affiliation: Department of Genetics, University of Kaiserslautern, 67663 Kaiserslautern, Germany.
authors.forename: John
authors.initials: J
authors.lastname: Cullum
authors.affiliation: EPFL, ENAC-ISTE, Laboratory of Environmental Biotechnology, CH 1015 Lausanne, Switzerland.
authors.forename: Christof
authors.initials: C
authors.lastname: Holliger
authors.affiliation: Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi - 110007, India.
authors.forename: Rup
authors.initials: R
authors.lastname: Lal
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics* / Q000378:metabolism; D015373:Bacterial Typing Techniques; D001673:Biodegradation, Environmental; D004269:DNA, Bacterial / Q000032:analysis; D004275:DNA, Ribosomal / Q000032:analysis; D020459:Genes, rRNA; D001556:Hexachlorocyclohexane / Q000378:metabolism*; D008969:Molecular Sequence Data; D009693:Nucleic Acid Hybridization; D010641:Phenotype; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA; D042301:Sphingomonadaceae / Q000145:classification* / Q000201:enzymology / Q000235:genetics / Q000502:physiology; D020578:Sphingomonas / Q000145:classification* / Q000201:enzymology / Q000235:genetics / Q000502:physiology
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S; D001556:Hexachlorocyclohexane