Characterization of Rhizobium naphthalenivorans sp nov with special emphasis on aromatic compound degradation and multilocus sequence analysis of housekeeping genes

Three strains of aerobic chemoorganotrophic naphthalene-degrading bacteria (designated TSY03b(T), TSY04, and TSW01) isolated from sediment of a polychlorinated-dioxin-transforming microcosm were characterized. These strains had Gram-negative-stained, rod-shaped cells measuring 0.6-0.9 mu m in width and 1.2-3.0 mu m in length and were motile by means of peritrichous flagella. Naphthalene was utilized as the sole carbon and energy source, and the transcription of a putative aromatic-ring hydroxylating gene was inducible by naphthalene. The major component of cellular fatty acids was summed feature 8 (C-18:1 omega 7c and/or C-18:1 omega 6c), and significant proportions of C-18:0 and C-19:0 cyclo omega 8cis were also found. The major respiratory quinone was ubiquinone-10. The G+C content of the DNA was 60.3-60.9 mol%. Phylogenetic analyses by studying sequence information on the housekeeping atpD, dnaK, glnII, gyrB, and recA genes as well as on 16S rRNA genes and the 16S-23S rDNA internal transcribed spacer region revealed that the strains grouped with members of the genus Rhizobium, with Rhizobium selenitireducens as their closest relative but formed a distinct lineage at the species level. This was confirmed by genomic DNA-DNA hybridization studies. These phenotypic, genotypic, and phylogenetic data strongly suggest that our isolates should be classified under a novel species of the genus Rhizobium. Thus, we propose the name Rhizobium naphthalenivorans sp.nov. to accommodate the novel isolates. The type strain is TSY03b(T) (= NBRC 107585(T) = KCTC 23252(T)).