Characterization of Sphingomonas Species Found as Predominant Members in the Culturable Bacterial Community of a Green Pigment-Containing Sclerotium Grain from Mt. Myoko (Japan) Volcanic Ash Soil

Microbes and Environments

Volumn 18, Issue 3, 2003, Pages 126-132

  Ohta, Hiroyuki ^a   Yagi, Michie ^a   Suzuki, Junko ^a,c   Fujitake, Nobuhide ^b   Watanabe, Makiko ^c  

^a IBARAKI UNIVERSITY   (Japan)

^b KOBE UNIVERSITY   (Japan)

^c TOKYO INSTITUTE OF TECHNOLOGY   (Japan)

Author keywords

green pigment; P type humic acid; sclerotium; Sphingomonas

Indexed keywords

EID: 11144347786     PISSN: 13426311     EISSN: 13474405     Source Type: Journal    
DOI: 10.1264/jsme2.18.126     Document Type: Article

References (35)

1. Alexander, M. 1977. Introduction to Soil Microbiology, 2nd ed. John Wiley and Sons, New York, USA.
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 faenia sp. nov., air-, dustborne and Antarctic, orange pigmented, psychrotolerant bacteria and emended description of the genus Sphingomonas. Int. J. Syst. Evol. Microbiol. 53: 1253–1260.
3. Cameron, D.W. and M.D. Sidell. 1978. 1,3,6,8,11,13-Hexa-chloro-4,10-dihydroxy-dinaphtho [2,1-b:1',2'-d] furan-5,9-dione. A polychloro quinone from green soils. Aust. J. Chem. 31: 1323–1333.
4. Daub, M.E. and M. Ehrenshaft. 2000. The photoactivated Cercospora toxin cercosporin: contributions to plant disease and fundamental biology. Ann. Rev. Phytopathol. 28: 461–490.
5. Fredrickson, J.K., D.L. Balkwill, G.R. Drake, M.F. Romine, D.B. Ringelberg and D.C. White. 1995. Aromatic-degrading Sphingomonas isolates from the deep subsurface. Appl. Environ. Microbiol. 61: 1917–1922.
6. Fujitake, N., T. Suzuki, M. Fukumoto and Y. Oji. 1998. Predomination of dimers over naturally occurring anthraquinones in soil. J. Nat. Prod. 61: 189–192.
7. Gibson, D.T., R.L. Roberts, M.C. Wells and V.M. Kobal. 1973. Oxidation of biphenyl by a Beijerinckia species. Biochem. Biophys. Res. Commun. 50: 211–219.
8. Hiraishi, A. 1992. Direct automated sequencing of 16S rDNA amplified by polymerase chain reaction from bacterial cultures without DNA purification. Lett. Appl. Microbiol. 15: 210–213.
9. Hiraishi, A., H. Kuraishi and K. Kawahara. 2000. Emendation of the description of Blastomonas natatoria (Sly 1985) Sly and Cahill 1997 as an aerobic photosynthetic bacterium and reclassification of Erythromonas ursincola Yurkov et al. 1997 as Blastomonas ursincola comb. nov. Int. J. Syst. Evol. Microbiol. 50: 1113–1118.
10. Kumada, K. and H.M. Hurst. 1967. Green humic acid and its possible origin as a fungal metabolite. Nature 214: 631–633.
11. Kumada, K., S. Ohta and Y. Ohsumi. 1966. A study on the humus composition of alpine grassland soils in Japanese Alps. J. Sci. Soil Manure, Japan 37: 289–291 (in Japanese).
12. Kumada, K. and O. Sato. 1965. Humus composition of podzols, studies on P type humic acid. II, J. Sci. Soil Manure, Japan 36: 373–378 (in Japanese).
13. Kumada, K., O. Sato, Y. Ohsumi and S. Ohta. 1967. Humus composition of mountain soils in Central Japan with special reference to the distribution of P type humic acid. Soil Sci. Plant Nutr. 13: 151–158.
14. Kusukawa, N., T. Uemori, K. Asada and I. Kato. 1990. Rapid and reliable protocol for direct sequencing of material amplified by the polymerase chain reaction. Biotechniques 9: 66–72.
15. Maniatis, T., E.F. Fritsch and J. Sambrook. 1982. Molecular cloning: a laboratory manual. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory.
16. Mitsui, H., K. Gorlach, H. Lee, R. Hattori and T. Hattori. 1997. Incubation time and media requirements of culturable bacteria from different phylogenetic groups. J. Microbiol. Methods. 30: 103–110.
17. Mueller, J.G., P.J. Chapman, B.O. Blattmann and P.H. Pritchard. 1990. Isolation and characterization of a fluoranthene-utilizing strain of Pseudomonas paucimobilis. Appl. Environ. Microbiol. 56: 1079–1086.
18. Ohta, H. and T. Hattori. 1980. Bacteria sensitive to nutrient broth medium in terrestrial environments. Soil Sci. Plant Nutr. 26: 99–107.
19. Ohta, H. and T. Hattori. 1983. Oligotrophic bacteria on organic debris and plant roots in a paddy field soil. Soil Biol. Biochem. 15: 1–8.
20. Pearson, W.R. and D.J. Lipman. 1988. Improved tools for biological sequence comparison. Proc. Natl. Acad. Sci. USA 85: 2444- 2448.
21. Saitou, N. and M. Nei. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406–425.
22. Sato, O. and K. Kumada. 1967. The chemical nature of the green fraction of P type humic acid. Soil Sci. Plant Nutr. 13: 121–122.
23. 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 analysis. Int. J. Syst. Evol. Microbiol. 51: 1405–1417.
24. Thompson, J.D., D.G. Higgins and T.J. Gibson. 1994. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weigh matrix choice. Nucleic Acids Res. 22: 4673- 4680.
25. Thomson, R.H. 1971. Distribution and Biogenesis, p. 1–38. In Naturally Occurring Quinones, 2nd ed. Academic Press, London.
26. Wang, G.C.Y. and Y. Wang. 1997. Frequency of formation of chimeric molecules as a consequence of PCR coamplification of 16S rRNA genes from mixed bacterial genomes. Appl. Environ. Microbiol. 63: 4645–4650.
27. Watanabe, M., N. Fujitake, H. Ohta and T. Yokoyama. 2001. Aluminum concentrations in sclerotia from a buried humic horizon of volcanic ash soils in Mt. Myko, Central Japan. Soil Sci. Plant Nutr. 47: 411–418.
28. Watanabe, M., T. Kado, H. Ohta and N. Fujitake. 2002. Distribution and development of sclerotium grains as influenced by aluminum status in volcanic ash soils. Soil Sci. Plant Nutr. 48: 569–575.
29. 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.
30. White, D.C., S.D. Sutton and D.B. Ringelberg. 1996. The genus Sphingomonas: physiology and ecology. Curr. Opinion Microbiol. 7: 301–306.
31. Yabuuchi, E., Y. Kosako, N. Fujiwara, T. Naka, I. Matsunaga, H. Ogura and K. Kobayashi. 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.
32. Yabuuchi, E., Y. Kosako, T. Naka, S. Suzuki and I. Yano. 1999. Proposal of Sphingomonas suberifaciens (van Bruggen, Jochimsen and Brown 1990) comb. nov., Sphingomonas natatoria (Sly 1985) comb. nov., Sphingomonas ursincloa (Yurkov et al. 1997) comb. nov., and emendation of the genus Sphingomonas. Microbiol. Immunol. 43: 339–349.
33. Yabuuchi, E., I. Yano, H. Oyaizu, Y. Hashimoto, T. Ezaki and H. Yamanoto. 1990. Proposals of Sphingomonas paucimobilis gen. nov. and comb. nov., Sphingomonas parapaucimobilis sp. nov., Sphingomonas yanoikuyae sp. nov., Sphingomonas adhesiva sp. nov., Sphingomonas capsulata comb. nov., and two genospecies of the genus Sphingomonas. Microbiol. Immunol. 34: 99–119.
34. Yagi, M., Y. Ikunaga, N. Fujitake, H. Ohta and M. Watanabe. 2000. Microbial flora of sclerotia grains in Tsubame soil from Mt. Myoko. Abstracts of the annual meeting, Japanese Society of Soil Science and Plant Nutrition 46: 35 (in Japanese).
35. Zylstra, G.J. and E. Kim. 1997. Aromatic hydrocarbon degra dation by Sphingomonas yanoikuyae B1. J. Ind. Microbiol. Biotechnol. 19: 408–414.