title: Characterization of Rhizobium naphthalenivorans sp. nov. with special emphasis on aromatic compound degradation and multilocus sequence analysis of housekeeping genes.
abstract: 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 μm in width and 1.2‒3.0 μm 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 (C18:1ω7c and/or C18:1ω6c), and significant proportions of C18:0 and C19:0 cyclo ω8cis 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 107585T = KCTC 23252T).
authors.affiliation: Department of Environmental and Life Sciences, Toyohashi University of Technology, Toyohashi 441􀈂8580, Japan.
authors.forename: Shinichi
authors.initials: S
authors.lastname: Kaiya
authors.forename: Owen
authors.initials: O
authors.lastname: Rubaba
authors.forename: Naoko
authors.initials: N
authors.lastname: Yoshida
authors.forename: Takeshi
authors.initials: T
authors.lastname: Yamada
authors.forename: Akira
authors.initials: A
authors.lastname: Hiraishi
mesh_terms: D000332:Aerobiosis; D001482:Base Composition; D001711:Biotransformation; D002244:Carbon / Q000378:metabolism; D016000:Cluster Analysis; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics*; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D021903:DNA, Ribosomal Spacer / Q000737:chemistry / Q000235:genetics; D005227:Fatty Acids / Q000032:analysis; D005407:Flagella / Q000502:physiology; D005798:Genes, Bacterial; D020043:Genes, Essential; D008124:Locomotion; D008969:Molecular Sequence Data; D058885:Multilocus Sequence Typing; D009281:Naphthalenes / Q000378:metabolism*; D009693:Nucleic Acid Hybridization; D010802:Phylogeny; D011809:Quinones / Q000032:analysis; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012231:Rhizobium / Q000145:classification* / Q000235:genetics / Q000378:metabolism* / Q000502:physiology; D017422:Sequence Analysis, DNA
chemical_list: D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D021903:DNA, Ribosomal Spacer; D005227:Fatty Acids; D009281:Naphthalenes; D011809:Quinones; D012336:RNA, Ribosomal, 16S; D002244:Carbon; C007229:decalin