1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 66, Issue 11

sp. nov., with ginsenoside-converting activity, isolated from compost Free

Abstract

A Gram-stain-negative, strictly aerobic, non-motile, light yellow, short-rod bacterium (designated GJ30-7) isolated from compost, was characterized using a polyphasic approach, in order to clarify its taxonomic position. Strain GJ30-7 was observed to grow optimally at 30 °C and at pH 7.0 on R2A agar medium. Strain Gsoil GJ30-7 possessed β-glucosidase activity, which was responsible for its ability to transform ginsenosides Rb1 and Rc (the two main active components of ginseng) to ginsenoside F2. Phylogenetic analysis, based on 16S rRNA gene sequence similarities, indicated that GJ30-7 belongs to the genus of the family and was most closely related to JCM 30166 (92.6 %), KACC 18188 (92.6 %), and KCTC 23708 (92.0 %). The DNA G+C content was 43 mol% and MK-7 was the major isoprenoid quinone. The main polar lipids were phosphatidylethanolamine, one unidentified phospolipid and one unknown polar lipid. In contrast to standard and reference strains, unidentified sphingolipid was also present. The predominant fatty acids of strain GJ30-7 were iso-C, iso-C 3-OH, Cω7 and/or Cω6 (summed feature 3) and iso-Cω9 and/or C 10-methyl (summed feature 9), supporting the affiliation of strain GJ30-7 to the genus . However, strain GJ30-7 could be distinguished genotypically and phenotypically from species of the genus with validly published names. The novel isolate therefore represents a novel species, for which the name sp. nov. is proposed, with the type strain GJ30-7 (=KACC 18625=JCM 30948).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): 16S rRNA gene sequence , polyphasic taxomony and Sphingobacterium jejuense
© 2016 IUMS
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.001370
2016-11-01
2024-04-20
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/66/11/4433.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.001370&mimeType=html&fmt=ahah

References

  1. Ahmed I., Ehsan M., Sin Y., Paek J., Khalid N., Hayat R., Chang Y. H. 2014; Sphingobacterium pakistanensis sp. nov., a novel plant growth promoting rhizobacteria isolated from rhizosphere of Vigna mungo. Antonie Van Leeuwenhoek 105:325–333 [View Article][PubMed]
     [Google Scholar]
  2. Albert R. A., Waas N. E., Pavlons S. C., Pearson J. L., Ketelboeter L., Rosselló-Móra R., Busse H. J. 2013; Sphingobacterium psychroaquaticum sp. nov., a psychrophilic bacterium isolated from Lake Michigan water. Int J Syst Evol Microbiol 63:952–958 [View Article][PubMed]
     [Google Scholar]
  3. Ali A., Khalid R., Ali S., Akram Z., Hayat R. 2015; Characterization of plant growth promoting rhizobacteria isolated from Chickpea. BMRJ 6:32–40 [CrossRef]
     [Google Scholar]
  4. Atlas R. M. 1993 Handbook of Microbiological Media pp. 49 Boca Raton: CRC Press;
     [Google Scholar]
  5. Buck J. D. 1982; Nonstaining (KOH) method for determination of gram reactions of marine bacteria. Appl Environ Microbiol 44:992–993[PubMed]
     [Google Scholar]
  6. Dees S. B., Carlone G. M., Hollis D., Moss C. W. 1985; Chemical and phenotypic characteristics of Flavobacterium thalpophilum compared with those of other Flavobacterium and Sphingobacterium species. Int J Syst Bacteriol 35:16–22 [View Article]
     [Google Scholar]
  7. Du J., Singh H., Won K., Yang J. E., Jin F. X., Yi T. H. 2015; Sphingobacterium mucilaginosum sp. nov., isolated from rhizosphere soil of a rose. Int J Syst Evol Microbiol 65:2949–2954 [View Article][PubMed]
     [Google Scholar]
  8. Felsenstein J. 1985; Confidence limits on phylogenies:an approach using the bootstrap. Evolution 39:783–791 [View Article]
     [Google Scholar]
  9. Fitch W. M. 1971; Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20:406–416 [View Article]
     [Google Scholar]
  10. Hall T. A. 1999; BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95–98
     [Google Scholar]
  11. 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]
  12. Holmes B., Owen R. J., Hollis D. G. 1982; Flavobacterium spiritivorum, a new species isolated from human clinical specimens. Int J Syst Bacteriol 32:157–165 [View Article]
     [Google Scholar]
  13. Jiang S., Chen M., Su S., Yang M., Li A., Zhang C., Lin M., Zhang W., Luo X. 2014; Sphingobacterium arenae sp. nov., isolated from sandy soil. Int J Syst Evol Microbiol 64:248–253 [View Article][PubMed]
     [Google Scholar]
  14. 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]
  15. Kim J. K., Kang M. S., Park S. C., Kim K. M., Choi K., Yoon M. H., Im W. T. 2015; Sphingosinicella ginsenosidimutans sp. nov., with ginsenoside converting activity. J Microbiol 53:435–441 [View Article][PubMed]
     [Google Scholar]
  16. Kimura M. 1983 The Neutral Theory of Molecular Evolution Cambridge: Cambridge University Press; [CrossRef]
     [Google Scholar]
  17. Lee D. H., Hur J. S., Kahng H. Y. 2013; Sphingobacterium cladoniae sp. nov., isolated from lichen, Cladonia sp., and emended description of Sphingobacterium siyangense. Int J Syst Evol Microbiol 63:755–760 [View Article][PubMed]
     [Google Scholar]
  18. Liu J., Yang L. L., Xu C. K., Xi J. Q., Yang F. X., Zhou F., Zhou Y., Mo M. H., Li W. J. 2012; Sphingobacterium nematocida sp. nov., a nematicidal endophytic bacterium isolated from tobacco. Int J Syst Evol Microbiol 62:1809–1813 [View Article][PubMed]
     [Google Scholar]
  19. Marques A. P. G. C., Pires C., Moreira H., Rangel A. O. S. S., Castro P. M. L. 2010; Assessment of the plant growth promotion abilities of six bacterial isolates using Zea mays as indicator plant. Soil Biol Biochem 42:1229–1235 [View Article]
     [Google Scholar]
  20. 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]
  21. Minnikin D. E., O'Donnell A. G., Goodfellow M., Alderson G., Athalye M., Schaal A., Parlett J. H. 1984; An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2:233–241 [View Article]
     [Google Scholar]
  22. 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]
  23. Peng S., Hong D. D., Xin Y. B., Jun L. M., Hong W. G. 2014; Sphingobacterium yanglingense sp. nov., isolated from the nodule surface of soybean. Int J Syst Evol Microbiol 64:3862–3866 [View Article][PubMed]
     [Google Scholar]
  24. Saitou N., Nei M. 1987; The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425[PubMed]
     [Google Scholar]
  25. Sasser M. 1990; Identification of bacteria through fatty acid analysis. In Methods in Phytobacteriology pp. 199–204 Edited by Klement Z., Rudolph K., Sands D. C. Budapest: Akademiai Kaido;
     [Google Scholar]
  26. Schmidt V. S. J., Wenning M., Scherer S. 2012; Sphingobacterium lactis sp. nov. and Sphingobacterium alimentarium sp. nov., isolated from raw milk and a dairy environment. Int J Syst Evol Microbiol 62:1506–1511 [View Article][PubMed]
     [Google Scholar]
  27. Schädler S., Burkhardt C., Kappler A. 2008; Evaluation of electron microscopic sample preparation methods and imaging techniques for characterization of cell-mineral aggregates. Geomicrobiol J 25:228–239 [View Article]
     [Google Scholar]
  28. Shivaji S., Ray M. K., Rao S. N., Saisree L., Jagannadham M. V., Seshu Kumar G., Reddy G. S. N., Bhargava P. M. 1992; Sphingobacterium antarcticus sp. nov., a psychrotrophic bacterium from the soils of Schirmacher Oasis, Antarctica. Int J Syst Bacteriol 42:102–106 [View Article]
     [Google Scholar]
  29. Steyn P. L., Segers P., Vancanneyt M., Sandra P., Kersters K., Joubert J. J. 1998; Classification of heparinolytic bacteria into a new genus, Pedobacter, comprising four species: Pedobacter heparinus comb. nov., Pedobacter piscium comb. nov., Pedobacter africanus sp. nov. and Pedobacter saltans sp. nov. Proposal of the family Sphingobacteriaceae fam. nov. Int J Syst Bacteriol 48:165–177 [View Article][PubMed]
     [Google Scholar]
  30. Sun L. N., Zhang J., Chen Q., He J., Li S. P. 2013; Sphingobacterium caeni sp. nov., isolated from activated sludge. Int J Syst Evol Microbiol 63:2260–2264 [View Article][PubMed]
     [Google Scholar]
  31. Takeuchi M., Yokota A. 1992; Proposals of Sphingobacterium faecium sp. nov., Sphingobacterium piscium sp. nov., Sphingobacterium heparinum comb. nov., Sphingobacterium thalpophilum comb. nov. and two genospecies of the genus Sphingobacterium, and synonymy of Flavobacterium yabuuchiae and Sphingobacterium spiritivorum. J Gen Appl Microbiol 38:465–482 [View Article]
     [Google Scholar]
  32. Tamura K., Stecher G., Peterson D., Filipski A., Kumar S. 2013; mega6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729 [View Article][PubMed]
     [Google Scholar]
  33. Ten L. N., Im W. T., Kim M. K., Kang M. S., Lee S. T. 2004; Development of a plate technique for screening of polysaccharide-degrading microorganisms by using a mixture of insoluble chromogenic substrates. J Microbiol Methods 56:375–382 [View Article][PubMed]
     [Google Scholar]
  34. Thompson J. D., Gibson T. J., Plewniak F., Jeanmougin F., Higgins D. G. 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][PubMed]
     [Google Scholar]
  35. Wang J., Chou S., Xu L., Zhu X., Dong N., Shan A., Chen Z. 2015; High specific selectivity and Membrane-Active Mechanism of the synthetic centrosymmetric α-helical peptides with Gly-Gly pairs. Sci Rep 5:15963 [View Article][PubMed]
     [Google Scholar]
  36. Wauters G., Janssens M., De Baere T., Vaneechoutte M., Deschaght P. 2012; Isolates belonging to CDC group II-i belong predominantly to Sphingobacterium mizutaii Yabuuchi et al. 1983: emended descriptions of S. mizutaii and of the genus Sphingobacterium. Int J Syst Evol Microbiol 62:2598–2601 [View Article][PubMed]
     [Google Scholar]
  37. Yabe S., Aiba Y., Sakai Y., Hazaka M., Kawahara K., Yokota A. 2013; Sphingobacterium thermophilum sp. nov., of the phylum Bacteroidetes, isolated from compost. Int J Syst Evol Microbiol 63:1584–1588 [View Article][PubMed]
     [Google Scholar]
  38. Yabuuchi E., Kaneko T., Yano I., Moss C. W., Miyoshi N. 1983; Sphingobacterium gen. nov., Sphingobacterium spiritivorum comb. nov., Sphingobacterium multivorum comb. nov., Sphingobacterium mizutae sp. nov., and Flavobacterium indologenes sp. nov.: glucose-nonfermenting gram-negative rods in CDC groups IIK-2 and IIb. Int J Syst Bacteriol 33:580–598 [View Article]
     [Google Scholar]
  39. Zhao P., Zhou Z., Chen M., Lin W., Zhang W., Wei G. 2014; Sphingobacterium gobiense sp. nov., isolated from soil of the Gobi Desert. Int J Syst Evol Microbiol 64:3931–3935 [View Article][PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.001370
Loading
Sphingobacterium jejuense sp. nov., with ginsenoside-converting activity, isolated from compost
Int J Syst Evol Microbiol 66, 4433 (2016); https://doi.org/10.1099/ijsem.0.001370
/content/journal/ijsem/10.1099/ijsem.0.001370
/content/journal/ijsem/10.1099/ijsem.0.001370
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF

Most cited 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