Sphingobium baderi sp. nov., isolated from a hexachlorocyclohexane dump site

Int J Syst Evol Microbiol. 2013 Feb;63(Pt 2):673-678. doi: 10.1099/ijs.0.039834-0. Epub 2012 Apr 27.

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)).

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Typing Techniques
  • Base Composition
  • Biodegradation, Environmental
  • Czech Republic
  • DNA, Bacterial / genetics
  • Fatty Acids / analysis
  • Hexachlorocyclohexane*
  • Molecular Sequence Data
  • Nucleic Acid Hybridization
  • Phylogeny*
  • RNA, Ribosomal, 16S / genetics
  • Sequence Analysis, DNA
  • Soil Microbiology*
  • Soil Pollutants
  • Spermidine / analysis
  • Sphingomonadaceae / classification*
  • Sphingomonadaceae / genetics
  • Sphingomonadaceae / metabolism
  • Ubiquinone / analogs & derivatives
  • Ubiquinone / analysis

Substances

  • DNA, Bacterial
  • Fatty Acids
  • RNA, Ribosomal, 16S
  • Soil Pollutants
  • Ubiquinone
  • Hexachlorocyclohexane
  • coenzyme Q10
  • Spermidine

Associated data

  • GENBANK/JN695620