1887

Abstract

A Gram-staining-negative, aerobic, non-motile, rod-shaped and yellow-pigmented bacterium, designated strain THG-DN6.20, was isolated from a lotus pond near Donghaksa temple in Daejeon, Republic of Korea. According to 16S rRNA gene sequence comparisons, strain THG-DN6.20 was found to be most closely related to IFO 15208 (97.6 % sequence similarity), HU1-AH51 (97.5 %) and LL02 (96.9 %). The DNA–DNA relatedness between strain THG-DN6.20 and its phylogenetically closest neighbours was below 60.0 %. The respiratory quinone and polyamine detected in strain THG-DN6.20 were ubiquinone Q-10 and spermidine, respectively. The DNA G+C content was 63.1 mol%. The major polar lipids were found to be phosphatidylethanolamine, diphosphatidylglycerol, sphingoglycolipid and phosphatidylcholine. The major fatty acids were identified as C, summed feature 3 (C 7 and/or Cω6), summed feature 8 (Cω7 and/or Cω6) and C 2-OH. These data supported the affiliation of strain THG-DN6.20 to the genus . Strain THG-DN6.20 could be distinguished from related species of the genus by physiological and biochemical characteristics. Therefore, the novel isolate represents a novel species, for which the name sp. nov. is proposed, with THG-DN6.20 as the type strain (=KACC 18541=CCTCC AB 2015354).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.001418
2016-11-01
2024-03-29
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/66/11/4729.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.001418&mimeType=html&fmt=ahah

References

  1. Busse J., Auling G. 1988; Polyamine pattern as a chemotaxonomic marker within the proteobacteria. Syst Appl Microbiol 11:1–8 [View Article]
    [Google Scholar]
  2. Collins M. D., Jones D. 1981; Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication. Microbiol Rev 45:316–354[PubMed]
    [Google Scholar]
  3. 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 [View Article]
    [Google Scholar]
  4. Felsenstein J. 1985; Confidence limit on phylogenies: an approach using the bootstrap. Evolution 39:783–791 [View Article]
    [Google Scholar]
  5. Gillis M., Ley J. D., Cleene M. D. 1970; The Determination of molecular weight of bacterial genome DNA from renaturation rates. Eur J Biochem 12:143–153 [View Article]
    [Google Scholar]
  6. Hall T. A. 1999; BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser 41:95–98
    [Google Scholar]
  7. Hiraishi A., Ueda Y., Ishihara J., Mori T. 1996; Comparative lipoquinone analysis of influent sewage and activated sludge by high-performance liquid chromatography and photodiode array detection. J Gen Appl Microbiol 42:457–469 [View Article]
    [Google Scholar]
  8. Huo Y. Y., You H., Li Z. Y., Wang C. S., Xu X. W. 2015; Novosphingobium marinum sp. nov., isolated from seawater. Int J Syst Evol Microbiol 65:676–680 [View Article][PubMed]
    [Google Scholar]
  9. Kampfer P., Young C. C., Busse H. J., Lin S. Y., Rekha P. D., Arun A. B., Chen W. M., Shen F. T., Wu Y. H. 2011; Novosphingobium soli sp. nov., isolated from soil. Int J Syst Evol Microbiol 61:259–263 [View Article][PubMed]
    [Google Scholar]
  10. Kampfer P., Martin K., McInroy J. A., Glaeser S. P. 2015; Proposal of Novosphingobium rhizosphaerae sp. nov., isolated from the rhizosphere. Int J Syst Evol Microbiol 65:195–200 [View Article][PubMed]
    [Google Scholar]
  11. Kim O. S., Cho Y. J., Lee K., Yoon S. H., Kim M., Na H., Park S. C., Jeon Y. S., Lee J. H. et al. 2012; Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62:716–721 [View Article][PubMed]
    [Google Scholar]
  12. Kimura M. 1983 The Neutral Theory of Molecular Evolution Cambridge: Cambridge University Press; [CrossRef]
    [Google Scholar]
  13. Lin S. Y., Hameed A., Liu Y. C., Hsu Y. H., Lai W. A., Huang H. I, Young C. C. 2014; Novosphingobium arabidopsis sp. nov., a DDT-resistant bacterium isolated from the rhizosphere of Arabidopsis thaliana. Int J Syst Evol Microbiol 64:594–598 [View Article][PubMed]
    [Google Scholar]
  14. McConaughy B. L., Laird C. D., McCarthy B. J. 1969; Nucleic acid reassociation in formamide. Biochem 8:3289–3295 [View Article]
    [Google Scholar]
  15. Mesbah M., Premachandran U., Whitman W. B. 1989; Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 39:159–167 [View Article]
    [Google Scholar]
  16. Minnikin D. E., O'Donnell A. G., Goodfellow M., Alderson G., Athalye M., Schaal A., Parleet J. H. 1984; An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. Journal Microbiol Methods 2:233–241 [View Article]
    [Google Scholar]
  17. Moore D. D., Dowhan D. 1995; Preparation and analysis of DNA. In Current Protocols in Molecular Biology , pp. 2–11 Edited by Ausubel F. W., Brent R., Kingston R. E., Moore D. D., Seidman J. G., Smith J. A., Struhl K. New York: Wiley;
    [Google Scholar]
  18. Saitou N., Nei M. 1987; The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Bio Evol 4:406–425
    [Google Scholar]
  19. Sasser M. 1990 Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids MIDI Technical Note vol. 101 Newark, DE: MIDI Inc;
    [Google Scholar]
  20. Singh H., Du J., Yang J. E., Yin C., Kook M., Yi T. H. 2015; Novosphingobium aquaticum sp. nov., isolated from lake water in Suwon, Republic of Korea. Antonie van Leeuwenhoek 108:851–858 [View Article][PubMed]
    [Google Scholar]
  21. Stabili L., Gravili C., Tredici S. M., Piraino S., Talà A., Boero F., Alifano P. 2008; Epibiotic Vibrio luminous bacteria isolated from some hydrozoa and bryozoa species. Microb Ecol 56:625–636 [View Article][PubMed]
    [Google Scholar]
  22. Stackebrandt E., Goebel B. M. 1994; Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Evol Microbiol 44:846–849 [View Article]
    [Google Scholar]
  23. Taibi G., Schiavo M. R., Gueli M. C., Calanni Rindina P., Muratore R., Nicotra C. M. A. 2000; Rapid and simultaneous high-performance liquid chromatography assay of polyamines and monoacetylpolyamines in biological specimens. J Chromatogr B: Biomed Sci Appl 745:431–437 [View Article]
    [Google Scholar]
  24. 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 [View Article]
    [Google Scholar]
  25. Tamaoka J., Katayama-Fujimura A., Kuraishi H. 1983; Analysis of bacterial menaquinone mixtures by high performance liquid chromatography. J Appl Bacteriol 54:31–36 [View Article]
    [Google Scholar]
  26. Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S. 2011; mega5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739 [View Article][PubMed]
    [Google Scholar]
  27. Thompson J. 1997; The clustal_x windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882 [View Article]
    [Google Scholar]
  28. Wayne L. G., Brenner D. J., Colwell R. R. 1987; International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463–464 [CrossRef]
    [Google Scholar]
  29. Weisburg W. G., Barns S. M., Pelletier D. A., Lane D. J. 1991; 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173:697–703 [View Article]
    [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., Sphingomonas capsulata comb. nov., and two genospecies of the genus Sphingomonas. Microbiol Immunol 34:99–119 [View Article][PubMed]
    [Google Scholar]
  31. Zhang L., Gao J. S., Kim S. G., Zhang C. W., Jiang J. Q., Ma X. T., Zhang J., Zhang X. X. 2016; Novosphingobium oryzae sp. nov., a potential plant-promoting endophytic bacterium isolated from rice roots. Int J Syst Evol Microbiol 66:302–307 [View Article][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.001418
Loading
/content/journal/ijsem/10.1099/ijsem.0.001418
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF
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