Sphingopyxis granuli sp. nov., a β-glucosidase-producing bacterium in the family Sphingomonadaceae in α-4 subclass of the Proteobacteria

Journal of Microbiology

Volumn 43, Issue 2, 2005, Pages 152-157

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

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

^b IBARAKI UNIVERSITY   (Japan)

^c NeoPharm Co Ltd   (South Korea)

Author keywords

proteobacteria; Sphingomonadaceae; Sphingopyxis granuli

Indexed keywords

BETA GLUCOSIDASE; FATTY ACID; QUINONE DERIVATIVE; RIBOSOME RNA; SPHINGOLIPID; UBIDECARENONE;

ARTICLE; BACTERIAL STRAIN; BACTERIUM ISOLATION; BIOREACTOR; BIOSYNTHESIS; CHEMOTAXONOMY; CLASSIFICATION; CONTROLLED STUDY; DNA BASE COMPOSITION; DNA HYBRIDIZATION; ENZYMOLOGY; GENE SEQUENCE; GENETICS; GRAM NEGATIVE BACTERIUM; INDUSTRIAL WASTE; NONHUMAN; NUCLEIC ACID HYBRIDIZATION; PHYLOGENY; PROTEOBACTERIA; SEQUENCE HOMOLOGY; SLUDGE; SPHINGOMONADACEAE; SPHINGOPYXIS GRANULI; WASTE WATER;

BASE COMPOSITION; BETA-GLUCOSIDASE; NUCLEIC ACID HYBRIDIZATION; PHYLOGENY; SPHINGOMONADACEAE;

ALPHAPROTEOBACTERIA; BACTERIA (MICROORGANISMS); NEGIBACTERIA; PROTEOBACTERIA; SPHINGOMONADACEAE; SPHINGOPYXIS; SPHINGOPYXIS MACROGOLTABIDA;

EID: 19344364985     PISSN: 12258873     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (36)

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., E.B.M. Denner, S. Buczolits, M. Salkinoja-Salonen, A. Bennasar, and P. Kämpfer. 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. and N. Sherman. 2002. Microbiology: a laboratory manual, 6th ed. Pearson Education, Inc., California.
4. Collins, M.D. and D. Jones. 1981. Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implications. Microbiol. Rev. 45, 316-354.
5. de Zeeuw, W.J. and G. Lettinga. 1980. Use of anaerobic digestion for wastewater treatment. Antonie van Leeuwenhoek. 46, 110-112.
6. Ezaki, T., Y. Hashimoto, and E. Yabuuchi. 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.
7. Felsenstein, J. 1985. Confidence limit on phylogenies: an approach using the bootstrap. Evolution 39, 783-791.
8. Fujii, K., M. Satomi, N. Morita, T. Motomura, T. Tanaka, and S. Kikuchi. 2003. Novosphingobium tardaugens sp. nov., and oestradiol-degrading bacterium isolated from activated sludge of a sewage treatment plant in Tokyo. Int. J. Syst. Evol. Microbiol. 53, 47-52.
9. Fukuzaki, S., Y.J. Chang, N. Nishio, and S. Nagai. 1991. Characteristics of granular methanogenic sludges grown on lactate in a UASB reactor. J. Ferm. Bioeng. 72, 465-472.
10. Godoy, F., M. Vancanneyt, M. Martinez, A. Steinbüchel, J. Swings, and B.H.A. Rehm. 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.
11. 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.
12. Kämpfer, P., R. Witzenberger, E.B.M. Denner, H.-J. Busse, and A. Neef. 2002. Sphingopyxis witflariensis sp. nov. isolated from activated sludge. Int. J. Syst. Evol. Microbiol. 52, 2029-2034.
13. Kimura, M. 1983. The Neutral Theory of Molecular Evolution. Cambridge: Cambridge University Press, Cambridge, New York.
14. Kumar, S., K. Tamura, I.B. Jakobsen, and M. Nei. 2001. MEGA2: Molecular Evolutionary Genetics Analysis software. Bioinformatics 17, 1244-1245.
15. Li, Y., Y. Kawamura, N. Fujiwara, T. Naka, H. Liu, X. Huang, K. Kobayashi, and T. Ezaki. 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.
16. MacLeod, F.A., S.R. Guiot, and J.W. Costerton. 1990. Layered structure of biological aggregates produced in an upflow sludge bed and filter reactor. Appl. Environ. Microbiol. 56, 1598-1607.
17. Mesbah, M., U. Premachandran, and W.B. Whitman. 1989. Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int. J. Syst. Bacteriol. 39, 159-167.
18. Rivas, R., A. Abril, M.E. Trujillo, and E. Velázquez. 2004. Sphingomonas phyllosphaerae sp. nov., from the phyllosphere of Acacia caven in Argentina. Int. J. Syst. Evol. Microbiol. 54, 2147-2150.
19. Saitou, N. and M. Nei. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Bio. Evol. 4, 406-425.
20. Sasser, M. 1990. Identification of bacteria by gas chromatography of cellular fatty acids. MIDI Technical Note 101. Newark, DE: MIDI Inc.
21. Schmidt, J.E. and B.K. Ahring. 1996. Acetate and hydrogen metabolism in intact and disintegrated granules from an acetate-fed, 55°C, UASC reactor. Biotechnol. Bioeng. 49, 229-246.
22. Shen, C.F., N. Kosaric, and R. Blaszczyk. 1993. The effect of selected heavy metals (Ni, Co and Fe) on anaerobic granules and their extracellular polymeric substance (EPS). Water Res. 27, 25-33.
23. T. J. Micorobiol. Biotechnol. 6, 68-69.
24. Sohn, J.H., K.K. Kwon, J.-H. Kang, H.-B. Jung, and S.-J. Kim. 2004. Novosphingobium pentaromativorans sp. nov., a high-molecular-mass polycyclic aromatic hydrocarbon-degrading bacterium isolated from estuarine sediment. Int. J. Evol. Syst. Microbiol. 54, 1483-1487.
25. Stackebrandt, E. and B.M. Goebel. 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.
26. Takeuchi, M., F. Kawai, Y. Shimada, and A. Yokota. 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. Microbiol. 16, 227-238.
27. Takeuchi, M., K. Hamana, and A. Hiraishi. 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.
28. Tamaoka, J. and K. Komagata. 1984. Determination of DNA base composition by reversed phase high-performance liquid chromatography. FEMS Microbiol. Lett. 25, 125-128.
29. Thompson, J.D., T.J. Gibson, F. Plewniak, F. Jeanmougin, and D.G. Higgins. 1997. The Clustal_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 24, 4876-4882.
30. Tiirola, M.A., H.-J. Busse, P. Kämpfer, and M.K. Männistö. 2005. Novosphingobium lentum sp. nov., a psychrotolerant bacterium from a polychlorophenol bioremediation process. Int. J. Syst. Evol. Microbiol. 55, 583-588.
31. Ushiba, Y., Y. Takahara, and H. Ohta. 2003. Sphingobium amiense sp. nov., a novel nonylphenol-degrading bacterium isolated from a river sediment. Int. J. Syst. Evol. Microbiol. 53, 2045-2048.
32. Vancanneyt, M., F. Schut, C. Snauwaert, J. Goris, J. Swings, and J.C. Gottschal. 2001. Sphingomonas alaskensis sp. nov., a dominant bacterium from a marine oligotrophic environment. Int. J. Syst. Evol. Microbiol. 51, 73-79.
33. Weisburg, W.G., S.M. Barns, D.A. Pelletier, and D.J. Lane. 1991. 16S ribosomal DNA amplification for phylogenetic study. J. Bacteriol 173, 697-703.
34. Yabuuchi, E., I. Yano, H. Oyaizu, Y. Hashimoto, T. Ezaki, and H. Yamamoto. 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.
35. Yabuuchi, E., Y. Kosako, N. Fujiwara, T. Naka, I. Matsunaga, H. Ogura, and K. Kobayashi. 2002. Emendation of the genus Sphingomonas Yabuuuchi 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.
36. Yoon, J.-H. and T.-K. Oh. 2005. Sphingopyxis flavimaris sp. nov., isolated from sea water of the Yellow Sea in Korea. Int. J. Syst. Evol. Microbiol. 55, 369-373.