Sphingomonas soli sp. nov., a β-glucosidase-producing bacterium in the family Sphingomonadaceae in the α-4 subgroup of the Proteobacteria

International Journal of Systematic and Evolutionary Microbiology

Volumn 56, Issue 4, 2006, Pages 703-707

  Yang, Deok Chun ^a   Im, Wan Taek ^b   Kim, Myung Kyum ^b   Ohta, Hiroyuki ^c   Lee, Sung Taik ^b  

^a Kyung Hee University   (South Korea)

^b Korea Advanced Institute of Science and Technology (KAIST)   (South Korea)

^c IBARAKI UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; BACTERIAL RNA; BETA GLUCOSIDASE; FATTY ACID; GLYCOSPHINGOLIPID; RNA 16S; UBIQUINONE;

ARTICLE; BACTERIAL STRAIN; BACTERIUM ISOLATION; CELL SHAPE; CHEMOTAXONOMY; CONTROLLED STUDY; DNA DNA HYBRIDIZATION; ENZYME SYNTHESIS; GINSENG; GRAM NEGATIVE BACTERIUM; LIPID ANALYSIS; NEW SPECIES; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEOBACTERIA; RNA SEQUENCE; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; SOIL; SOUTH KOREA; SPHINGOMONADACEAE; SPHINGOMONAS; SPHINGOMONAS ASACCHAROLYTICA; SPHINGOMONAS KOREENSIS; SPHINGOMONAS MALI; SPHINGOMONAS PRUNI; SPHINGOMONAS SOLI; STRAIN DIFFERENCE;

BETA-GLUCOSIDASE; MOLECULAR SEQUENCE DATA; NUCLEIC ACID HYBRIDIZATION; PHYLOGENY; RNA, RIBOSOMAL, 16S; SOIL MICROBIOLOGY; SPHINGOMONADACEAE; SPHINGOMONAS;

BACTERIA (MICROORGANISMS); NEGIBACTERIA; PANAX GINSENG; PROTEOBACTERIA; SPHINGOMONADACEAE; SPHINGOMONAS; SPHINGOMONAS ASACCHAROLYTICA; SPHINGOMONAS KOREENSIS; SPHINGOMONAS MALI; SPHINGOMONAS PRUNI;

EID: 33646187536     PISSN: 14665026     EISSN: None     Source Type: Journal    
DOI: 10.1099/ijs.0.63839-0     Document Type: Article

References (32)

1. Buck, J. D. (1982). Nonstaining (KOH) method for determination of Gram reactions of marine bacteria. Appl Environ Microbiol 44, 992-993.
2. Busse, H.-J., Denner, E. B. M., 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 Microbiol 53, 1253-1260.
3. Cappuccino, J. G. & Sherman, N. (2002). Microbiology. a Laboratory Manual, 6th edn. San Francisco: Pearson Education, Inc. and Benjamin Cummings.
4. Collins, M. D. & Jones, D. (1981). Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implications. Microbiol Rev 45, 316-354.
5. Ezaki, T., Hashimoto, Y. & 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 Bacteriol 39, 224-229.
6. Felsenstein, J. (1985). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783-791.
7. Fitch, W. M. (1972). Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20, 406-416.
8. Fujii, K., Satomi, M., Morita, N., Motomura, T., Tanaka, T. & Kikuchi, S. (2003). Novosphingobium tardaugens sp. nov., an oestradiol-degrading bacterium isolated from activated sludge of a sewage treatment plant in Tokyo. Int J Syst Evol Microbiol 53, 47-52.
9. Godoy, F., Vancanneyt M., Martínez, M., Steinbüchel, A., Swings, J. & Rehm, B. H. A. (2003). Sphingopyxis chilensis sp. nov., a chlorophenol-degrading bacterium that accumulates polyhydroxyalkanoate, and transfer of Sphingomonas alaskensis to Sphingopyxis alaskensis comb. nov. Int J Syst Evol Microbiol 53, 473-477.
10. Hall, T. A. (1999). BIOEDIT: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41, 95-98.
11. Kämpfer, P., Witzenberger, R., Denner, E. B. M., Busse, H.-J. & Neef, A. (2002). Sphingopyxis witflariensis sp. nov. isolated from activated sludge. Int J Syst Evol Microbiol 52, 2029-2034.
12. Kim, M. K., Im, W.-T., Ohta, H., Lee, M. & Lee, S.-T. (2005). Sphingopyxis granuli sp. nov., a β-glucosidase-producing bacterium in the family Sphingomonadaceae in α-4 subclass of the Proteobacteria. J Microbiol 43, 152-157.
13. Kimura, M. (1983). The Neutral Theory of Molecular Evolution. Cambridge: Cambridge University Press.
14. Kumar, S., Tamura, K. & Nei, M. (2004). MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5, 150-163.
15. 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 Microbiol 51, 1491-1498.
16. Li, Y., Kawamura, Y., Fujiwara, N., Naka, T., Liu, H., Huang, X., Kobayashi, K. & Ezaki, T. (2004). Sphingomonas yabuuchiae sp. nov. and Brevundimonas nasdae sp. nov., isolated from the Russian space laboratory Mir. Int J Syst Evol Microbiol 54, 819-825.
17. Mesbah, M., Premachandran, U. & Whitman, W. B. (1989). Precise measurement of the G + C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 39, 159-167.
18. MIDI (1999). Sherlock Microbial Identification System Operating Manual, version 3.0. Newark, DE: MIDI, Inc.
19. Rivas, R., Abril, A., Trujillo, M. E. & Velázquez, E. (2004). Sphingomonas phyllosphaerae sp. nov., from the phyllosphere of Acacia caven in Argentina. Int J Syst Evol Microbiol 54, 2147-2150.
20. Saitou, N. & Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406-425.
21. T. J Microbiol Biotechnol 6, 68-69.
22. Sohn, J. H., Kwon, K. K., Kang, J.-H., Jung, H.-B. & Kim, S.J. (2004). Novosphingobium pentaromativorans sp. nov., a high-molecular-mass polycyclic aromatic hydrocarbon-degrading bacterium isolated from estuarine sediment. Int J Syst Evol Microbiol 54, 1483-1487.
23. Stackebrandt, E. & Goebel, B. M. (1994). Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 44, 846-849.
24. 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 Bacteriol 45, 334-341.
25. 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 Microbiol 51, 1405-1417.
26. 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 Res 25, 4876-4882.
27. Tiirola, M. A., Busse, H.J., Kämpfer, P. & Männistö, M. K. (2005). Novosphingobium lentum sp. nov., a psychrotolerant bacterium from a polychlorophenol bioremediation process. Int J Syst Evol Microbiol 55, 583-588.
28. Ushiba, Y., Takahara, Y. & Ohta, H. (2003). Sphingobium amiense sp. nov., a novel nonylphenol-degrading bacterium isolated from a river sediment. Int J Syst Evol Microbiol 53, 2045-2048.
29. 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 Immunol 34, 99-119.
30. Yabuuchi, E., Kosako, Y., Fujiwara, N., Naka, T., Matsunaga, I., Ogura, H. & Kobayashi, K. (2002). Emendation of the genus Sphingomonas Yabuuchi et al. 1990 and junior objective synonymy of the species of three genera, Sphingobium, Novosphingobium and Sphingopyxis, in conjunction with Blastomonas ursincola. Int J Syst Evol Microbiol 52, 1485-1496.
31. Yoon, J.-H. & Oh, T.-K. (2005). Sphingopyxis flavimaris sp. nov., isolated from sea water of the Yellow Sea in Korea. Int J Syst Evol Microbiol 55, 369-373.
32. Yoon, J.-H., Lee, C.-H., Yeo, S.-H. & Oh, T.-K. (2005). Sphingopyxis baekryungensis sp. nov., an orange-pigmented bacterium isolated from sea water of the Yellow Sea in Korea. Int J Syst Evol Microbiol 55, 1223-1227.