title: Sphingobium baderi sp. nov., isolated from a hexachlorocyclohexane dump site.
abstract: A Gram-stain-negative, rod-shaped and white-coloured bacterial strain, designated LL03(T), was isolated from hexachlorocyclohexane-contaminated soil at Spolana Neratovice, Czech Republic, where lindane was formerly produced. Strain LL03(T) was found to be a degrader of α-, γ- and δ-isomers of hexachlorocyclohexane, although no significant degradation activity was observed for the β-isomer. A neighbour-joining tree based on 16S rRNA gene sequences showed that strain LL03(T) occupied a distinct phylogenetic position in the Sphingobium cluster, showing the highest similarity with Sphingobium wenxiniae JZ-1(T) (99.2 %). The DNA G+C content of strain LL03(T) was 67.0 mol%. DNA-DNA relatedness values of strain LL03(T) with its close phylogenetic neighbours were below the threshold level of 70 %, supporting its identification as a representative of a novel species of the genus Sphingobium. The predominant respiratory quinone was ubiquinone Q-10. The polar lipid profile of strain LL03(T) also corresponded to those reported for other Sphingobium species (phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, phosphatidylmonomethylethanolamine and sphingoglycolipid), supporting its identification as a member of the genus Sphingobium. Spermidine was identified as the major polyamine. The predominant fatty acids were 16 : 0, summed feature 3 (16 : 1ω7c and/or 16 : 1ω6c), summed feature 8 (18 : 1ω7c and/or 18 : 1ω6c) and 14 : 0 2-OH. The polar lipid pattern, the presence of spermidine and ubiquinone Q-10, the predominance of the cellular fatty acids C(18 : 1)ω7c, C(16 : 0) and C(14 : 0) 2-OH and the G+C content of the genomic DNA supported the affiliation of the strain to the genus Sphingobium. The results obtained after DNA-DNA hybridization, biochemical and physiological tests clearly distinguished it from closely related species of the genus Sphingobium. Therefore, strain LL03(T) represents a novel species of the genus Sphingobium for which the name Sphingobium baderi LL03(T) sp. nov. is proposed; the type strain is LL03(T) ( = CCM 7981(T) = DSM 25433(T)).
authors.affiliation: Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi-110007, India.
authors.forename: Jasvinder
authors.initials: J
authors.lastname: Kaur
authors.affiliation: International Clinical Research Centre, St Anne's University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic.
authors.forename: Hana
authors.initials: H
authors.lastname: Moskalikova
authors.affiliation: Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi-110007, India.
authors.forename: Neha
authors.initials: N
authors.lastname: Niharika
authors.affiliation: Department of Histology and Embryology, Faculty of Medicine, Masaryk University, 625 00 Brno, Czech Republic.
authors.forename: Miroslava
authors.initials: M
authors.lastname: Sedlackova
authors.affiliation: Department of Histology and Embryology, Faculty of Medicine, Masaryk University, 625 00 Brno, Czech Republic.|International Clinical Research Centre, St Anne's University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic.
authors.forename: Ales
authors.initials: A
authors.lastname: Hampl
authors.affiliation: Loschmidt Laboratories and Research Centre for Toxic Compounds in the Environment, Faculty of Science, Masaryk University, 628 00 Brno, Czech Republic.|International Clinical Research Centre, St Anne's University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic.
authors.forename: Jiri
authors.initials: J
authors.lastname: Damborsky
authors.affiliation: Loschmidt Laboratories and Research Centre for Toxic Compounds in the Environment, Faculty of Science, Masaryk University, 628 00 Brno, Czech Republic.
authors.forename: Zbynek
authors.initials: Z
authors.lastname: Prokop
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: D015373:Bacterial Typing Techniques; D001482:Base Composition; D001673:Biodegradation, Environmental; D018153:Czech Republic; D004269:DNA, Bacterial / Q000235:genetics; D005227:Fatty Acids / Q000032:analysis; D001556:Hexachlorocyclohexane; D008969:Molecular Sequence Data; D009693:Nucleic Acid Hybridization; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA; D012988:Soil Microbiology; D012989:Soil Pollutants; D013095:Spermidine / Q000032:analysis; D042301:Sphingomonadaceae / Q000145:classification* / Q000235:genetics / Q000378:metabolism; D014451:Ubiquinone / Q000031:analogs & derivatives / Q000032:analysis
chemical_list: D004269:DNA, Bacterial; D005227:Fatty Acids; D012336:RNA, Ribosomal, 16S; D012989:Soil Pollutants; D014451:Ubiquinone; D001556:Hexachlorocyclohexane; C024989:coenzyme Q10; D013095:Spermidine