Sphingobium naphthae sp. nov., with the ability to degrade aliphatic hydrocarbons, isolated from oil-contaminated soil

Abstract

A light yellow-coloured, Gram-stain-negative, non-motile and rod-shaped bacterium, designated strain K-3-6T, capable of degrading aliphatic hydrocarbons was isolated from oil-contaminated soil of Biratnagar, Morang, Nepal. It was able to grow at 15-45 °C, at pH 5.0-9.5 and with 0-6 % (w/v) NaCl. Based on 16S rRNA gene sequence analysis, strain K-3-6T belongs to the genus Sphingobium and is closely related to Sphingobium olei IMMIB HF-1T (98.4 % similarity), Sphingobium abikonense NBRC 16140T (98.3 %), Sphingobium rhizovicinum CC-FH12-1T (97.9 %), Sphingobium lactosutens DS20T (97.9 %), Sphingobium amiense NBRC 102518T (97.2 %), Sphingobium phenoxybenzoativorans SC_3T (97.2 %) and Sphingobium fontiphilum Chen16-4T (97.0 %). The predominant respiratory quinone was ubiquinone-10 and the major polyamine was spermidine. The polar lipid profile revealed the presence of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, phosphatidyldimethylethanolamine, sphingoglycolipid and phosphatidylmonomethylethanolamine. The predominant fatty acids of strain K-3-6T were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C14 : 0, C16 : 0 and C14 : 0 2-OH. The genomic DNA G+C content was 65.6 mol%. Levels of DNA-DNA relatedness between strain K-3-6T and S. olei IMMIB HF-1T, S. abikonense NBRC 16140T, S. lactosutens DS20T, S. rhizovicinum CC-FH12-1T, S. amiense NBRC 102518T and S. fontiphilum Chen16-4T were 34.0, 33.3, 28.7, 26.3, 29.0 and 22.3 %, respectively. The morphological, physiological, chemotaxonomic and phylogenetic analyses clearly distinguished this strain from its closest phylogenetic neighbours. Thus, strain K-3-6T represents a novel species of the genus Sphingobium, for which the name Sphingobium naphthae sp. nov. is proposed. The type strain is K-3-6T (=KEMB 9005-449T=KACC 19001T=JCM 31713T).