Journal of Microbiology

The Microbiological Society of Korea (한국미생물학회)
권호 표지

Sphingopyxis granuli sp. nov., a $\beta$-Glucosidase-Producing Bacterium in the Family Sphingomonadaceae in $\alpha$-4 Subclass of the Proteobacteria

  • Kim Myung Kyum (Environmental and Molecular Microbiology Lab., Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST)) ;
  • Im Wan Taek (Environmental and Molecular Microbiology Lab., Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST)) ;
  • Ohta Hiroyuki (Department of Bioresource Science, Ibaraki University College of Agriculture) ;
  • Lee Myung Jin (Environmental and Molecular Microbiology Lab., Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), NeoPharm Co., Ltd) ;
  • Lee Sung Taik (Environmental and Molecular Microbiology Lab., Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST))
  • Published : 2005.04.01
Download PDF
⟨ Previous Next ⟩

Abstract

Strain Kw07$^T$, a Gram-negative, non-spore-forming, rod-shaped bacterium, was isolated from granules in an Up-flow Anaerobic Sludge Blanket (UASB) bioreactor used in the treatment of brewery waste­water. 16S rRNA gene sequence analysis revealed that strain Kw07T belongs to the a-4 subclass of the Proteobacteria, and the highest degree of sequence similarity was determined to be to Sphingopyxis macrogoltabida IFO 15033T (97.8%). Chemotaxonomic data revealed that strain Kw07T possesses a quinone system with the predominant compound Q-I0, the predominant fatty acid C,s:, OJ7c, and sphingolipids, aU of which corroborated our assignment ofthe strain to the Sphingopyxis genus. The results of DNA-DNA hybridization and physiological and biochemical tests clearly demonstrated that strain Kw07T represents a distinct species. Based on these data, Kw07T (= KCTC 12209T = NBRC 100800T) should be classified as the type strain for a novel Sphingopyxis species, for which the name Sphingopyxis granuli sp. novo has been proposed.

Keywords

References

  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. Kampfer. 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 https://doi.org/10.1099/ijs.0.02461-0
  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 https://doi.org/10.1007/BF00422247
  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 https://doi.org/10.1099/00207713-39-3-224
  7. Felsenstein, J. 1985. Confidence limit on phylogenies: an approach using the bootstrap. Evolution 39, 783-791 https://doi.org/10.2307/2408678
  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 https://doi.org/10.1099/ijs.0.02301-0
  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 https://doi.org/10.1016/0922-338X(91)90056-M
  10. Godoy, F., M. Vancanneyt, M. Martinez, A. Steinblichel, 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 https://doi.org/10.1099/ijs.0.02375-0
  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. Kampfer, P., R. Witzenberger, E.B.M. Denner, H.-J. Busse, and A. Neef. 2002. Sphingopyxis witflariensls sp. nov. isolated from activated sludge. Int. J. Syst. Evol. Microbiol. 52, 2029-2034 https://doi.org/10.1099/ijs.0.02217-0
  13. Kimura, M. 1983. The Neutral Theory of Molecular Evolution. Cambridge: Cambridge University Press, Cambridge, New York
  14. Kumar, S., K. Tamura, LB. Jakobsen, and M. Nei. 2001. MEGA2: Molecular Evolutionary Genetics Analysis software. Bioinformatics 17, 1244-1245 https://doi.org/10.1093/bioinformatics/17.12.1244
  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 https://doi.org/10.1099/ijs.0.02829-0
  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 https://doi.org/10.1099/00207713-39-2-159
  18. Rivas, R., A. Abril, M.E. Trujillo, and E. Velazquez. 2004. Sphingomonas phyllosphaerae sp. nov., from the phyllosphere of Acacia caven in Argentina. Int. J. Syst. Evol. Microbiol. 54, 2147-2150 https://doi.org/10.1099/ijs.0.63102-0
  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, $55^{\circ}C$, UASC reactor. Biotechnol. Bioeng. 49, 229-246 https://doi.org/10.1002/(SICI)1097-0290(19960205)49:3<229::AID-BIT1>3.0.CO;2-M
  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 https://doi.org/10.1016/0043-1354(93)90191-J
  23. Shin, Y.K., J.-S. Lee, C.O. Chun, H.-J. Kim. and Y.-H. Park. 1996. Isoprenoid quinine profiles of the Leclercia adecarboxylata KCTC $1036^T$ 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 highmolecular-mass polycyclic aromatic hydrocarbon-degrading bacterium isolated from estuarine sediment. Int. J. Evol. Syst. Microbiol. 54, 1483-1487 https://doi.org/10.1099/ijs.0.02945-0
  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 https://doi.org/10.1099/00207713-44-4-846
  26. Takeuchi, M., F. Kawai, Y. Shimada, and A. Yokota. 1993. Taxonomic study of polyethylene glycol-utilizing bacteria: emended description ofthe 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 https://doi.org/10.1016/S0723-2020(11)80473-X
  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 https://doi.org/10.1111/j.1574-6968.1984.tb01388.x
  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. Kampfer, and M.K. Mannisto. 2005. Novosphingobium lentum sp. nov., a psychrotolerant bacterium from a polychlorophenol bioremediation process. Int. J. Syst. Evol. Microbiol. 55, 583-588 https://doi.org/10.1099/ijs.0.63386-0
  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 https://doi.org/10.1099/ijs.0.02581-0
  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 https://doi.org/10.1099/ijs.0.01868-0
  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 https://doi.org/10.1099/ijs.0.63218-0