1887

Abstract

The taxonomic position of a halo- and organo-sensitive, oligotrophic soil bacterium, strain S213, was investigated. Cells were Gram-negative, non-motile, strictly aerobic, yellow-pigmented rods of short to medium length on diluted nutrient broth. When 0·1–0·4 % (w/v) NaCl was added to diluted media composed of peptone and meat extract, growth was inhibited with increasing NaCl concentration and the cells became long aberrant forms. When 6 mM CaCl was added, the cells grew quite normally and aberrant cells were no longer found at 0·1–0·5 % (w/v) NaCl. Chemotaxonomically, strain S213 contains chemical markers that indicate its assignment to the : the presence of ubiquinone Q-10 as the predominant respiratory quinone, C and C as major fatty acids, C 2-OH as the major 2-hydroxy fatty acid and sphingoglycolipids. 16S rRNA gene sequence analysis indicated that strain S213 belongs to the genus , exhibiting high sequence similarity to the 16S rRNA gene sequences of IFO 15500 (98·3 %), IFO 15498 (98·0 %), IFO 15499 (97·9 %) and DSM 1805 (97·8 %). The results of DNA–DNA hybridization experiments and its phenotypic characteristics clearly distinguished the strain from its nearest neighbours and demonstrate that strain S213 represents a novel species, for which the name sp. nov. is proposed. The type strain is S213 (=JCM 12082=CIP 107926).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.02959-0
2004-11-01
2019-12-13
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/54/6/ijs542185.html?itemId=/content/journal/ijsem/10.1099/ijs.0.02959-0&mimeType=html&fmt=ahah

References

  1. 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]
  2. Conn, H. J. ( 1914; ). Culture media for use in the plate method of counting soil bacteria. N Y Agric Exp Stn Tech Bull 38, 3–34.
    [Google Scholar]
  3. 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]
  4. 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.[CrossRef]
    [Google Scholar]
  5. Hattori, T. ( 1976; ). Plate count of bacteria in soil on a diluted nutrient broth as a culture medium. Rep Inst Agric Res Tohoku Univ 27, 23–30.
    [Google Scholar]
  6. Hattori, R. & Hattori, T. ( 1980; ). Sensitivity to salts and organic compounds of soil bacteria isolated on diluted media. J Gen Appl Microbiol 26, 1–14.[CrossRef]
    [Google Scholar]
  7. Hirai, Y., Haque, M., Yoshida, T., Yokota, K., Yasuda, T. & Oguma, K. ( 1995; ). Unique cholesteryl glucosides in Helicobacter pylori: composition and structural analysis. J Bacteriol 177, 5327–5333.
    [Google Scholar]
  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.[CrossRef]
    [Google Scholar]
  9. Kimura, M. ( 1980; ). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16, 111–120.[CrossRef]
    [Google Scholar]
  10. Komagata, K. & Suzuki, K. ( 1987; ). Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 19, 161–208.
    [Google Scholar]
  11. Lee, J.-S., Kook, S. Y., 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]
  12. Marmur, J. & Doty, P. ( 1962; ). Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature. J Mol Biol 5, 109–118.[CrossRef]
    [Google Scholar]
  13. Mitsui, H., Gorlach, K., Klee, H., Hattori, R. & Hattori, T. ( 1997a; ). Incubation time and media requirements of culturable bacteria from different phylogenetic groups. J Microbiol Methods 30, 103–110.[CrossRef]
    [Google Scholar]
  14. Mitsui, H., Hattori, R., Watanabe, H., Tonosaki, A. & Hattori, T. ( 1997b; ). Na+-induced structural change of a soil bacterium, S34, and Ca2+ requirement for preserving its original structure. J Bacteriol 179, 3350–3353.
    [Google Scholar]
  15. Ohta, H. ( 1982; ). Biology of soil oligotrophic bacteria. PhD thesis, Tohoku University (in Japanese).
  16. Ohta, H. ( 2001; ). Kinetic analysis of ferulic acid degradation by oligotrophic Sphingomonas sp. S213 during growth in batch and continuous cultures. Microb Environ 16, 9–17.[CrossRef]
    [Google Scholar]
  17. Ohta, H. & Hattori, T. ( 1980; ). Bacteria sensitive to nutrient broth medium in terrestrial environments. Soil Sci Plant Nutr 26, 99–107.[CrossRef]
    [Google Scholar]
  18. Ohta, H. & Hattori, T. ( 1983a; ). Oligotrophic bacteria on organic debris and plant roots in a paddy field soil. Soil Biol Biochem 15, 1–8.[CrossRef]
    [Google Scholar]
  19. Ohta, H. & Hattori, T. ( 1983b; ). Agromonas oligotrophica gen. nov., sp. nov., a nitrogen-fixing oligotrophic bacterium. Antonie Van Leeuwenhoek 49, 429–446.
    [Google Scholar]
  20. Pearson, W. & Lipman, D. ( 1988; ). Improved tools for biological sequence comparison. Proc Natl Acad Sci U S A 85, 2444–2448.[CrossRef]
    [Google Scholar]
  21. Saito, H. & Miura, K. ( 1963; ). Preparation of transforming deoxyribonucleic acid by phenol treatment. Biochim Biophys Acta 72, 619–629.[CrossRef]
    [Google Scholar]
  22. Saitou, N. & Nei, M. ( 1987; ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–425.
    [Google Scholar]
  23. Shindo, H. & Kuwatsuka, S. ( 1977; ). Behavior of phenolic substances in the decaying process of plants. VI. Changes in quality and quantity of phenolic substances in the decaying process of rice straw in a soil. Soil Sci Plant Nutr 23, 319–332.[CrossRef]
    [Google Scholar]
  24. Suwa, Y. & Hattori, T. ( 1984; ). Effects of nutrient concentration on the growth of soil bacteria. Soil Sci Plant Nutr 30, 397–403.[CrossRef]
    [Google Scholar]
  25. 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.[CrossRef]
    [Google Scholar]
  26. 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]
  27. 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]
  28. Whang, K. & Hattori, T. ( 1988; ). Oligotrophic bacteria from rendzina forest soil. Antonie Van Leeuwenhoek 54, 19–36.[CrossRef]
    [Google Scholar]
  29. Williams, S. T. ( 1985; ). Oligotrophy in soil: fact or fiction? In Bacteria in their Natural Environments, pp. 81–110. Edited by M. Fletcher & G. D. Floodgate. Orlando, FL: Academic Press.
  30. 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]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.02959-0
Loading
/content/journal/ijsem/10.1099/ijs.0.02959-0
Loading

Data & Media loading...

Supplements

vol. , part 6, pp. 2185–2190

Micrographs of the fine structures of strain S213 are available to download. [PDF](6.83MB)



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