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
2020-09-24
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
  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 Fletcher M., Floodgate G. D. Orlando, FL: Academic Press;
    [Google Scholar]
  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., Sphingomonascapsulata 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

Supplementary material 1

PDF

Most cited this month Most Cited RSS feed

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