Polyphasic assignment of an aromatic-degrading Pseudomonas sp., strain DJ77, in the genus Sphingomonas as Sphingomonas chungbukensis sp. nov.

Abstract

Pseudomonas sp. strain DJ77, which was described as an aromatic-degrading bacterium, was investigated to clarify its taxonomic position. Phylogenetic analysis based on 16S rDNA sequences indicated that the strain belonged to the genus Sphingomonas and formed a monophyletic clade with the type strains of Sphingomonas chlorophenolica, Sphingomonas herbicidovorans and Sphingomonas yanoikuyae with sequence similarity values of 981, 961 and 956 %, respectively. Genomic relatedness based on DNA-DNA hybridization of strain DJ77 to these strains is 7-14 %. Strain DJ77 contained ubiquinone 10 as the main respiratory quinone, and the GMC content of DNA was 63 mol %. The organism contained octadecenoic acid (67 %) as major cellular fatty acid. Strain DJ77 can be readily differentiated from representative members of the genus Sphingomonas using a battery of biochemical tests. On the basis of polyphasic evidence, it is proposed that strain DJ77, previously known as Pseudomonas sp., be reclassified in the genus Sphingomonas as Sphingomonas chungbukensis sp. nov. The type strain is strain DJ77 T (l KCTC 2955 T l IMSNU 11152 T ).Keywords : Sphingomonas chungbukensis sp. nov., polyphasic classification, 16S rDNA sequencing, DNA-DNA hybridization INTRODUCTIONStrain DJ77 T , which degrades biphenyl and phenanthrenes, was isolated from contaminated sediment of an industrial complex near Taejon, Republic of Korea, and subsequently identified as Pseudomonas sp. on the basis of the limited number of morphological and physiologic properties (Kim et al., 1986). Recently, Kim (1999) this strain (Jung et al., 1996 ; Kim et al., 1997a, b ;Shin et al., 1997 ;Hwang et al., 1999 ;Kim et al., 1999). A comparative study showed that the genes and gene orders for aromatic hydrocarbon degradation of strain DJ77 T were strikingly similar to the corresponding genes of Sphingomonas species, such as Sphingomonas paucimobilis EPA505, Sphingomonas yanoikuyae B1, ' Sphingomonas agrestis ' HV3 and Sphingomonas aromaticivorans F199 (Mueller et al., 1990 ;Kim, 1996 ;Yrja$ la$ et al., 1997 ;Romine et al., 1999). The members of the genus Sphingomonas have been reported to degrade various aromatic hydrocarbons (Wittich et al., 1992 ;Ka et al., 1994 ; Fredrickson et al., 1995 ;Khan et al., 1996). In this study, we applied a polyphasic approach to identify strain DJ77 T . On the basis of chemotaxonomic, physiological and molecular systematic evidence, we propose that Pseudomonas sp. strain DJ77 T be reclassified in the genus Sphingomonas as Sphingomonas chungbukensis sp. nov. Sphingomonas chungbukensis sp. nov. METHODSBacterial strains and cultures. Strain DJ77 T , S. chlorophenolica DSM 7098 T , S. herbicidovorans DSM 11019 T and S. yanoikuyae KCTC 2818 T were grown on Trypticase soy agar (TSA ; BBL) at 28 mC. Morphology. The morphological properties were examined after growth on TSA at 28 mC for 2 d by light microscopy and scanning electron microscopy (JEOL model JSM-6400). Determination of physiological characteristics. The oxidation of 95 different ca...

Psychroserpens mesophilus sp. nov., a mesophilic marine bacterium belonging to the family Flavobacteriaceae isolated from a young biofilm

“…The DNA G+C content of strain KOPRI 13649 T , as determined using the thermal denaturation method of Kim et al (2000), was 29?8 mol%, a value similar to that of P. burtonensis. The major respiratory quinone was determined to be menaquinone according to the reversed-phase TLC method described by Kim et al (2000) and was confirmed to be MK-6 following the HPLC method of Collins (1985).…”

“…The major respiratory quinone was determined to be menaquinone according to the reversed-phase TLC method described by Kim et al (2000) and was confirmed to be MK-6 following the HPLC method of Collins (1985).…”

Sphingobium olei sp. nov., isolated from oil-contaminated soil

“…nov. IMMIB HF-1 T ; 2, S. amiense YT T ; 3, S. cloacae JCM 10874 T ; 4, S. yanoikuyae JCM 7371 T ; 5, S. chlorophenolicum DSM 8671; 6, S. herbicidovorans DSM 11019 T ; 7, S. chungbukense KCTC 2955 T ; 8, S. indicum B90A T ; 9, S. japonicum UT26 T ; 10, S. francense Sp+ T ; 11, S. xenophagum BN6 T ; 12, S. aromaticiconvertens DSM 12677 T . Data are from the following sources: strain 1, this study; strains 2-6, Ushiba et al (2003); strain 7, Kim et al (2000); strains 8-10, Pal et al (2005); strain 11, Stolz et al (2000) and strain 12, Wittich et al (2007). +, Positive; 2, negative; ND, no data available.…”

Sphingobium aromaticiconvertens sp. nov., a xenobiotic-compound-degrading bacterium from polluted river sediment

“…Table 1. Cellular fatty acid composition of strain RW16 T , Sphingobium species and Sphingomonas cloacae Strains: 1, Sphingobium amiense JCM 11777 T (data from Ushiba et al, 2003); 2, Sphingobium chlorophenolicum ATCC 33790 T (data from this study); 3, Sphingobium chungbukense DJ77 T (Kim et al, 2000); 4, Sphingomonas cloacae JCM 10874 T (Fujii et al, 2001); 5, Sphingobium francense CCM 7288 T (Pal et al, 2005); 6, Sphingobium herbicidovorans DSM 11019 T (this study); 7, Sphingobium indicum CCM 7286 T (Pal et al, 2005); 8, Sphingobium japonicum CCM 7287 T (Pal et al, 2005); 9, strain RW16 T ; 10, Sphingobium xenophagum DSM 6383 T ; 11, Sphingobium yanoikuyae IFO 15102 T (data in columns 9-11 from this study). Values shown are percentages of total fatty acids.…”