A novel bacterium (strain K4T) belonging to the genus Sphingomonas was isolated from tidal flat sediment in Korea. Its morphology, physiology, biochemical features and 16S rRNA gene sequence were characterized. Colonies of this strain are yellow in colour and the cells are rod-shaped, exhibiting negative Gram staining. The strain grows at 0–5 % (w/v) NaCl and 20–35 °C, with optimal growth occurring at 0 % (w/v) NaCl and 30 °C. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain K4T is associated with the genus Sphingomonas. Within the phylogenetic tree, this novel strain shares a branching point with Sphingomonas asaccharolytica Y-345T, with which it shares 97.3 % 16S rRNA gene sequence similarity. The polyamine pattern predominantly contains the Sphingomonas-specific triamine sym-homospermidine. Combined analysis of 16S rRNA gene sequences, DNA–DNA relatedness, physiological and biochemical test results identified genotypic and phenotypic differences between strain K4T and other Sphingomonas species. On the basis of these differentiating features, it is concluded that strain K4T (=KCTC 22050T=DSM 19475T) represents a novel species of the genus Sphingomonas, for which the name Sphingomonas aestuarii sp. nov. is proposed.
Baker, G. C., Smith, J. J. & Cowan, D. A.(2003). Review and re-analysis of domain-specific 16S primers. J Microbiol Methods55, 541–555.[CrossRef][Google Scholar]
Buck, J. D.(1982). Nonstaining (KOH) method for determination of gram reactions of marine bacteria. Appl Environ Microbiol44, 992–993.
[Google Scholar]
Busse, H.-J. & Auling, G.(1988). Polyamine pattern as a chemotaxonomic marker within the Proteobacteria. Syst Appl Microbiol11, 1–8.[CrossRef][Google Scholar]
Busse, H.-J., Kämpfer, P. & Denner, E. B.(1999). Chemotaxonomic characterisation of Sphingomonas. J Ind Microbiol Biotechnol23, 242–251.[CrossRef][Google Scholar]
Busse, H.-J., Denner, E. B., Buczolits, S., Salkinoja-Salonen, M., Bennasar, A. & Kämpfer, P.(2003).Sphingomonas aurantiaca sp. nov., Sphingomonas aerolata sp. nov. and Sphingomonas faeni sp. nov., air- and dustborne and Antarctic, orange-pigmented, psychrotolerant bacteria, and emended description of the genus Sphingomonas. Int J Syst Evol Microbiol53, 1253–1260.[CrossRef][Google Scholar]
Busse, H.-J., Hauser, E. & Kämpfer, P.(2005). Description of two novel species, Sphingomonas abaci sp. nov. and Sphingomonas panni sp. nov. Int J Syst Evol Microbiol55, 2565–2569.[CrossRef][Google Scholar]
Denner, E. B. M.(1999). Reclassification of Pseudomonas echinoides Neumann 1962, 343AL, in the genus Sphingomonas as Sphingomonas echinoides comb. nov. Int J Syst Bacteriol49, 1103–1109.[CrossRef][Google Scholar]
Ezaki, T., Hashimoto, H. & Yabuuchi, E.(1989). Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Bacteriol39, 224–229.[CrossRef][Google Scholar]
Felsenstein, J.(1981). Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol17, 368–376.[CrossRef][Google Scholar]
Kimura, M.(1980). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol16, 111–120.[CrossRef][Google Scholar]
Kumar, S., Tamura, K. & Nei, M.(2004).mega3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform5, 150–163.[CrossRef][Google Scholar]
Lee, J. S., Shin, Y. K., Yoon, J. H., Takeuchi, M., Pyun, Y. R. & Park, Y. H.(2001).Sphingomonas aquatilis sp. nov., Sphingomonas koreensis sp. nov., and Sphingomonas taejonensis sp. nov., yellow-pigmented bacteria isolated from natural mineral water. Int J Syst Evol Microbiol51, 1491–1498.
[Google Scholar]
Ohta, H., Hattori, R., Ushiba, Y., Mitsui, H., Ito, M., Watanabe, H., Tonosaki, A. & Hattori, T.(2004).Sphingomonas oligophenolica sp. nov., a halo- and organo-sensitive oligotrophic bacterium from paddy soil that degrades phenolic acids at low concentrations. Int J Syst Evol Microbiol54, 2185–2190.[CrossRef][Google Scholar]
Reddy, G. S. & Garcia-Pichel, F.(2007).Sphingomonas mucosissima sp. nov. and Sphingomonas desiccabilis sp. nov., from biological soil crusts in the Colorado Plateau, USA. Int J Syst Evol Microbiol57, 1028–1034.[CrossRef][Google Scholar]
Roh, S. W., Sung, Y., Nam, Y. D., Chang, H. W., Kim, K. H., Yoon, J. H., Jeon, C. O., Oh, H. M. & Bae, J. W.(2008).Arthrobacter soli sp. nov., a novel bacterium isolated from wastewater reservoir sediment. J Microbiol46, 40–44.[CrossRef][Google Scholar]
Saitou, N. & Nei, M.(1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol4, 406–425.
[Google Scholar]
Sasser, M.(1990).Identification of bacteria by gas chromatography of cellular fatty acids: MIDI Technical Note 101. Newark, DE: MIDI.
Schaeffer, A. B. & Fulton, M. D.(1933). A simplified method of staining endospores. Science77, 194[CrossRef][Google Scholar]
Smibert, R. M. & Krieg, N. R.(1994). Phenotypic characterization. In Methods for General and Molecular Bacteriology, pp. 607–654. Edited by P. Gerhardt, R. G. E. Murray, W. A. Wood & N. R. Krieg. Washington, DC: American Society for Microbiology.
Stolz, A., Busse, H.-J. & Kämpfer, P.(2007).Pseudomonas knackmussii sp. nov. Int J Syst Evol Microbiol57, 572–576.[CrossRef][Google Scholar]
Swofford, D. L.(2003).paup: Phylogenetic analysis using parsimony, version 4. Sunderland, MA: Sinauer Associates.
Takeuchi, M., Kawai, F., Shimada, Y. & Yokota, A.(1993). Taxonomic study of polyethylene glycol-utilizing bacteria: emended description of the genus Sphingomonas and new descriptions of Sphingomonas macrogoltabidus sp. nov., Sphingomonas sanguis sp. nov. and Sphingomonas terrae sp. nov. Syst Appl Microbiol16, 227–238.[CrossRef][Google Scholar]
Takeuchi, M., Sakane, T., Yanagi, M., Yamasato, K., Hamana, K. & Yokota, A.(1995). Taxonomic study of bacteria isolated from plants: proposal of Sphingomonas rosa sp. nov., Sphingomonas pruni sp. nov., Sphingomonas asaccharolytica sp. nov., and Sphingomonas mali sp. nov. Int J Syst Bacteriol45, 334–341.[CrossRef][Google Scholar]
Takeuchi, M., Hamana, K. & Hiraishi, A.(2001). Proposal of the genus Sphingomonas sensu stricto and three new genera, Sphingobium, Novosphingobium and Sphingopyxis, on the basis of phylogenetic and chemotaxonomic analyses. Int J Syst Evol Microbiol51, 1405–1417.
[Google Scholar]
Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F. & Higgins, D. G.(1997). The clustal_x windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res25, 4876–4882.[CrossRef][Google Scholar]
Tindall, B. J.(1990). Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett66, 199–202.[CrossRef][Google Scholar]
Wayne, L. G., Brenner, D. J., Colwell, R. R., Grimont, P. A. D., Kandler, O., Krichevsky, M. I., Moore, L. H., Moore, W. E. C., Murray, R. G. E. & other authors(1987). International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol37, 463–464.[CrossRef][Google Scholar]
Xie, C. H. & Yokota, A.(2006).Sphingomonas azotifigens sp. nov., a nitrogen-fixing bacterium isolated from the roots of Oryza sativa. Int J Syst Evol Microbiol56, 889–893.[CrossRef][Google Scholar]
Yabuuchi, E., Yano, I., Oyaizu, H., Hashimoto, Y., Ezaki, T. & Yamamoto, H.(1990). Proposals of Sphingomonas paucimobilis gen. nov. and comb. nov., Sphingomonas parapaucimobilis sp. nov., Sphingomonas yanoikuyae sp. nov., Sphingomonas adhaesiva sp. nov., Sphingomonas capsulata comb. nov., and two genospecies of the genus Sphingomonas. Microbiol Immunol34, 99–119.[CrossRef][Google Scholar]
Yang, D. C., Im, W. T., Kim, M. K., Ohta, H. & Lee, S. T.(2006).Sphingomonas soli sp. nov., a β-glucosidase-producing bacterium in the family Sphingomonadaceae in the α-4 subgroup of the Proteobacteria. Int J Syst Evol Microbiol56, 703–707.[CrossRef][Google Scholar]
Yoon, J. H., Lee, M. H., Kang, S. J., Lee, S. Y. & Oh, T. K.(2006).Sphingomonas dokdonensis sp. nov., isolated from soil. Int J Syst Evol Microbiol56, 2165–2169.[CrossRef][Google Scholar]