1887

Abstract

A yellow-pigmented, Gram-negative, motile, strictly aerobic, pleomorphic bacterium (strain TDMA-16) was isolated from a freshwater sample collected at Misasa (Tottori, Japan). Strain TDMA-16 was slightly tolerant to gamma-ray irradiation and produced carotenoids, including zeaxanthin, nostoxanthin and an unknown carotenoid, effectively [1.7 mg (g dry cells)]. The DNA G+C content of strain TDMA-16 was 63.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences placed strain TDMA-16 in a distinct lineage in the family ; sequence data showed that strain TDMA-16 was most closely related to IFO 15500 (95.1 %), JSS7 (95.0 %), IFO 15498 (94.9 %), DSM 14444 (94.9 %) and IFO 15499 (94.5 %). The major fatty acids of strain TDMA-16 were C 6 (34.5 %) and C 7 (29.3 %). The presence of Q-10 as the main ubiquinone, the -specific sphingoglycolipid in the polar lipid profile and 2-hydroxy fatty acids, plus the absence of 3-hydroxy fatty acids, supported identification of this strain as a member of the genus . Phylogenetic distinctiveness and unique phenotypic characteristics differentiated strain TDMA-16 from closely related species. The results of polyphasic taxonomic analyses suggest that strain TDMA-16 represents a novel species, for which the name sp. nov. is proposed. The type strain is strain TDMA-16 (=NBRC 102120=DSM 18422=CCUG 53607).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.64828-0
2007-07-01
2019-10-18
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/57/7/1435.html?itemId=/content/journal/ijsem/10.1099/ijs.0.64828-0&mimeType=html&fmt=ahah

References

  1. Barrow, G. I. & Feltham, R. K. A. ( 1993; ). Cowan and Steel's Manual for the Identification of Medical Bacteria, 3rd edn. Cambridge: Cambridge University Press.
  2. Brosius, J., Palmer, M. L., Kennedy, P. J. & Noller, H. F. ( 1978; ). Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli. Proc Natl Acad Sci U S A 75, 4801–4805.[CrossRef]
    [Google Scholar]
  3. Buonaurio, R., Stravato, V. M., Kosako, Y., Fujiwara, N., Naka, T., Kobayashi, K., Cappelli, C. & Yabuuchi, E. ( 2002; ). Sphingomonas melonis sp. nov., a novel pathogen that causes brown spots on yellow Spanish melon fruits. Int J Syst Evol Microbiol 52, 2081–2087.[CrossRef]
    [Google Scholar]
  4. Busse, H. J., Kämpfer, P. & Denner, E. B. ( 1999; ). Chemotaxonomic characterisation of Sphingomonas. J Ind Microbiol Biotechnol 23, 242–251.[CrossRef]
    [Google Scholar]
  5. 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.[CrossRef]
    [Google Scholar]
  6. 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 Microbiol 55, 2565–2569.[CrossRef]
    [Google Scholar]
  7. Collins, M. D. ( 1994; ). Isoprenoid quinones. In Chemical Methods in Prokaryotic Systematics, pp. 265–310. Edited by M. Goodfellow & A. G. O'Donnell. Chichester: Wiley.
  8. Collins, M. D. & Jones, D. ( 1981; ). Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication. Microbiol Rev 45, 316–354.
    [Google Scholar]
  9. Denner, E. B. M., Kämpfer, P., Busse, H. J. & Moore, E. R. B. ( 1999; ). Reclassification of Pseudomonas echinoides Heumann 1962, 343AL, in the genus Sphingomonas as Sphingomonas echinoides comb. nov. Int J Syst Bacteriol 49, 1103–1109.[CrossRef]
    [Google Scholar]
  10. Ederer, M. M., Crawford, R. L., Herwig, R. P. & Orser, C. S. ( 1997; ). PCP degradation is mediated by closely related strains of the genus Sphingomonas. Mol Ecol 6, 39–49.[CrossRef]
    [Google Scholar]
  11. Felsenstein, J. ( 1993; ). phylip (phylogeny inference package), version 3.5c. Department of Genome Sciences, University of Washington, Seattle, USA.
  12. Jenkins, C. L., Andrewes, A. G., McQuade, T. J. & Starr, M. P. ( 1979; ). The pigment of Pseudomonas paucimobilis is a carotenoid (nostoxanthin), rather than a brominated aryl-polyene (xanthomonadin). Curr Microbiol 3, 1–4.[CrossRef]
    [Google Scholar]
  13. Kametani, K. & Matsumura, T. ( 1983; ). Determination of 238U, 234U, 226Ra and 228Ra in spring waters of Sanin district. Radioisotopes 32, 18–21 (in Japanese).[CrossRef]
    [Google Scholar]
  14. Kämpfer, P., Denner, E. B. M., Meyer, S., Moore, E. R. B. & Busse, H. J. ( 1997; ). Classification of ‘Pseudomonas azotocolligans’ Anderson 1955, 132, in the genus Sphingomonas as Sphingomonas trueperi sp. nov. Int J Syst Bacteriol 47, 577–583.[CrossRef]
    [Google Scholar]
  15. Kawahara, K., Seydel, U., Matsuura, M., Danbara, H., Rietschel, E. T. & Zahringer, U. ( 1991; ). Chemical structure of glycosphingolipids isolated from Sphingomonas paucimobilis. FEBS Lett 292, 107–110.[CrossRef]
    [Google Scholar]
  16. Kosako, Y., Yabuuchi, E., Naka, T., Fujiwara, N. & Kobayashi, K. ( 2000; ). Proposal of Sphingomonadaceae fam. nov., consisting of Sphingomonas Yabuuchi et al. 1990 , Erythrobacter Shiba and Shimidu 1982, Erythromicrobium Yurkov et al. 1994, Porphyrobacter Fuerst et al. 1993, Zymomonas Kluyver and van Niel 1936, and Sandaracinobacter Yurkov et al. 1997, with the type genus Sphingomonas Yabuuchi et al. 1990 . Microbiol Immunol 44, 563–575.[CrossRef]
    [Google Scholar]
  17. 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.
    [Google Scholar]
  18. Mesbah, M. & Whitman, W. B. ( 1989; ). Measurement of deoxyguanosine/thymidine ratios in complex mixtures by high-performance liquid chromatography for determination of the mole percentage guanine+cytosine of DNA. J Chromatogr 479, 297–306.[CrossRef]
    [Google Scholar]
  19. Nelis, H. J. & De Leenheer, A. P. ( 1989; ). Profiling and quantitation of bacterial carotenoids by liquid chromatography and photodiode array detection. Appl Environ Microbiol 55, 3065–3071.
    [Google Scholar]
  20. Norris, J. R., Ribbons, D. W. & Varma, A. K. (editors) ( 1985; ). Methods in Microbiology, vol. 18. London: Academic Press.
  21. Perrière, G. & Gouy, M. ( 1996; ). WWW-query: an on-line retrieval system for biological sequence banks. Biochimie 78, 364–369.[CrossRef]
    [Google Scholar]
  22. Rowe, N. J., Tunstall, J., Galbraith, L. & Wilkinson, S. G. ( 2000; ). Lipid composition and taxonomy of [Pseudomonas] echinoides: transfer to the genus Sphingomonas. Microbiology 146, 3007–3012.
    [Google Scholar]
  23. Saitou, N. & Nei, M. ( 1987; ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–425.
    [Google Scholar]
  24. Silva, C., Cabral, J. M. & van Keulen, F. ( 2004; ). Isolation of a beta-carotene over-producing soil bacterium, Sphingomonas sp. Biotechnol Lett 26, 257–262.[CrossRef]
    [Google Scholar]
  25. 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.
  26. Takeuchi, M. & Hiraishi, A. ( 2001; ). Taxonomic significance of 2-hydroxy fatty acid profiles of the species in the genus Sphingomonas and related taxa. IFO Res Commun 20, 72–82.
    [Google Scholar]
  27. 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.
    [Google Scholar]
  28. Thompson, J. D., Higgins, D. G. & Gibson, T. J. ( 1994; ). clustal_w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22, 4673–4680.[CrossRef]
    [Google Scholar]
  29. Tindall, B. J. ( 1990; ). Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 66, 199–202.[CrossRef]
    [Google Scholar]
  30. White, D. C., Sutton, S. D. & Ringelberg, D. B. ( 1996; ). The genus Sphingomonas: physiology and ecology. Curr Opin Biotechnol 7, 301–306.[CrossRef]
    [Google Scholar]
  31. Yabuuchi, E. & Kosako, Y. ( 2005; ). Family Sphingomonadaceae Kosako, Yabuuchi, Naka, Fijiwara and Kobayashi 2000b, 1953VP. In Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 2, part C, pp. 230–233. Edited by D. J. Brenner, N. R. Kreig, J. T. Staley & G. M. Garrity. New York: Springer.
  32. 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.[CrossRef]
    [Google Scholar]
  33. 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.[CrossRef]
    [Google Scholar]
  34. 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 Microbiol 56, 703–707.[CrossRef]
    [Google Scholar]
  35. 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 Microbiol 56, 2165–2169.[CrossRef]
    [Google Scholar]
  36. Zablotowicz, R. M., Leung, K. T., Alber, T., Cassidy, M. B., Trevors, J. T., Lee, H., Veldhuis, L. & Hall, J. C. ( 1999; ). Degradation of 2,4-dinitrophenol and selected nitroaromatic compounds by Sphingomonas sp. UG30. Can J Microbiol 45, 840–848.[CrossRef]
    [Google Scholar]
  37. Zipper, C., Nickel, K., Angst, W. & Kohler, H. P. ( 1996; ). Complete microbial degradation of both enantiomers of the chiral herbicide mecoprop [(RS)-2-(4-chloro-2-methylphenoxy)propionic acid] in an enantioselective manner by Sphingomonas herbicidovorans sp. nov. Appl Environ Microbiol 62, 4318–4322.
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.64828-0
Loading
/content/journal/ijsem/10.1099/ijs.0.64828-0
Loading

Data & Media loading...

Supplements

vol. , part 7, pp. 1435 - 1441

Scanning electron micrographs of cells of strain TDMA-16 . [PDF](480 KB)



PDF

Most Cited This Month

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error