1887

Abstract

A novel ikarugamycin-producing actinomycete, designated strain NEAU-Da3, was isolated from soybean root [ (L.) Merr.] and characterized using a polyphasic approach. 16S rRNA gene sequence similarity studies showed that strain NEAU-Da3 belonged to the genus , and was most closely related to NRRL B-16359 (99.5 %), VC-A46 (99.3 %) and MCCC 1A01550 (97.2 %); similarities to other type strains of species of the genus were lower than 97.1 %. The maximum-likelihood phylogenetic tree based on 16S rRNA gene sequences showed that the isolate formed a distinct phyletic line with NRRL B-16359, VC-A46 and MCCC 1A01550. This branching pattern was also supported by the tree reconstructed with the neighbour-joining method. A comparative study between strain NEAU-Da3 and the type strains of the closest related species of the genus revealed that it differed from them in morphological, physiological and biochemical characteristics. Therefore, it is proposed that strain NEAU-Da3 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is NEAU-Da3 ( = CGMCC 4.7047 = DSM 42076).

Funding
This study was supported by the:
  • NKPBR (Award 2010CB126102)
  • NNSF (Award 30771427 and 30971937)
  • National Outstanding Youth Foundation (Award 31225024)
  • Special Foundation for Scientific and Technological Innovation Research of Harbin (Award 011RFXXN038)
  • NSF of Heilongjiang Province (Award C201029)
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.050088-0
2013-10-01
2024-04-19
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/63/10/3579.html?itemId=/content/journal/ijsem/10.1099/ijs.0.050088-0&mimeType=html&fmt=ahah

References

  1. Bloemberg G. V., Lugtenberg B. J. J. ( 2001 ). Molecular basis of plant growth promotion and biocontrol by rhizobacteria. . Curr Opin Plant Biol 4, 343350. [View Article] [PubMed]
    [Google Scholar]
  2. Collins M. D. ( 1985 ). Isoprenoid quinone analyses in bacterial classification and identification. . In Chemical Methods in Bacterial Systematics, pp. 267284. Edited by Goodfellow M., Minnikin D. E. . London:: Academic Press;.
    [Google Scholar]
  3. Cui Y. S., Baek S.-H., Wang L., Lee H.-G., Cui C. C., Lee S.-T., Im W.-T. ( 2012 ). Streptomyces panacagri sp. nov., isolated from soil of a ginseng field. . Int J Syst Evol Microbiol 62, 780785. [View Article] [PubMed]
    [Google Scholar]
  4. De Ley J., Cattoir H., Reynaerts A. ( 1970 ). The quantitative measurement of DNA hybridization from renaturation rates. . Eur J Biochem 12, 133142. [View Article] [PubMed]
    [Google Scholar]
  5. Emmert E. A. B., Handelsman J. ( 1999 ). Biocontrol of plant disease: a (Gram-) positive perspective. . FEMS Microbiol Lett 171, 19. [View Article] [PubMed]
    [Google Scholar]
  6. Felsenstein J. ( 1981 ). Evolutionary trees from DNA sequences: a maximum likelihood approach. . J Mol Evol 17, 368376. [View Article] [PubMed]
    [Google Scholar]
  7. Felsenstein J. ( 1985 ). Confidence limits on phylogenies: an approach using the bootstrap. . Evolution 39, 783791. [View Article]
    [Google Scholar]
  8. Fischbach M. A., Walsh C. T. ( 2009 ). Antibiotics for emerging pathogens. . Science 325, 10891093. [View Article] [PubMed]
    [Google Scholar]
  9. Goodfellow M., Orchard V. A. ( 1974 ). Antibiotic sensitivity of some nocardioform bacteria and its value as a criterion for taxonomy. . J Gen Microbiol 83, 375387. [View Article] [PubMed]
    [Google Scholar]
  10. Gordon R. E., Barnett D. A., Handerhan J. E., Pang C. ( 1974 ). Nocardia coeliaca, Nocardia autotrophica, and the nocardin strain. . Int J Syst Bacteriol 24, 5463. [View Article]
    [Google Scholar]
  11. Hayakawa M., Nonomura H. ( 1987 ). Humic acid-vitamin agar, a new medium for the selective isolation of soil actinomycetes. . J Ferment Technol 65, 501509. [View Article]
    [Google Scholar]
  12. Huß V. A. R., Festl H., Schleifer K. H. ( 1983 ). Studies on the spectrophotometric determination of DNA hybridization from renaturation rates. . Syst Appl Microbiol 4, 184192. [View Article] [PubMed]
    [Google Scholar]
  13. Kelly K. L. ( 1964 ). Inter-Society Color Council – National Bureau of Standards Color Name Charts Illustrated with Centroid Colors. Washington, DC:: US Government Printing Office;.
    [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. & other authors ( 2012 ). Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. . Int J Syst Evol Microbiol 62, 716721. [View Article] [PubMed]
    [Google Scholar]
  15. Kimura M. ( 1980 ). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. . J Mol Evol 16, 111120. [View Article] [PubMed]
    [Google Scholar]
  16. Lechevalier M. P., Lechevalier H. A. ( 1980 ). The chemotaxonomy of actinomycetes. . In Actinomycete Taxonomy (Special Publication no.6), pp. 227291. Edited by Dietz A., Thayer J. . Arlington, VA:: Society for Industrial Microbiology;.
    [Google Scholar]
  17. Lechevalier M. P., Stern A. E., Lechevalier H. A. ( 1981 ). Phospholipids in the taxonomy of actinomycetes. . Zentralbl Bakteriol Hyg Abt 1 (Suppl 11), 111116.
    [Google Scholar]
  18. Lee Y. K., Kim H. W., Liu C. L., Lee H. K. ( 2003 ). A simple method for DNA extraction from marine bacteria that produce extracellular materials. . J Microbiol Methods 52, 245250. [View Article] [PubMed]
    [Google Scholar]
  19. Loqman S., Barka E. A., Clément C., Ouhdouch Y. ( 2009 ). Antagonistic actinomycetes from Moroccan soil to control the grapevine gray mold. . World J Microbiol Biotechnol 25, 8191. [View Article]
    [Google Scholar]
  20. Mandel M., Marmur J. ( 1968 ). Use of ultraviolet absorbance-temperature profile for determining the guanine plus cytosine content of DNA. . Methods Enzymol 12B, 195206. [View Article]
    [Google Scholar]
  21. McKerrow J., Vagg S., McKinney T., Seviour E. M., Maszenan A. M., Brooks P., Seviour R. J. ( 2000 ). A simple HPLC method for analysing diaminopimelic acid diastereomers in cell walls of Gram-positive bacteria. . Lett Appl Microbiol 30, 178182. [View Article] [PubMed]
    [Google Scholar]
  22. Minnikin D. E., Hutchinson I. G., Caldicott A. B., Goodfellow M. ( 1980 ). Thin-layer chromatography of methanolysates of mycolic acid-containing bacteria. . J Chromatogr A 188, 221233. [View Article]
    [Google Scholar]
  23. Minnikin D. E., O’Donnell A. G., Goodfellow M., Alderson G., Athalye M., Schaal A., Parlett J. K. ( 1984 ). An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. . J Microbiol Methods 2, 233241. [View Article]
    [Google Scholar]
  24. Saitou N., Nei M. ( 1987 ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. . Mol Biol Evol 4, 406425.[PubMed]
    [Google Scholar]
  25. Shirling E. B., Gottlieb D. ( 1966 ). Methods for characterization of Streptomyces species. . Int J Syst Bacteriol 16, 313340. [View Article]
    [Google Scholar]
  26. Shirling E. B., Gottlieb D. ( 1969 ). Cooperative description of type cultures of Streptomyces. IV. Species descriptions from the second, third and fourth studies. . Int J Syst Bacteriol 19, 391512. [View Article]
    [Google Scholar]
  27. 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, 27312739. [View Article] [PubMed]
    [Google Scholar]
  28. Taubes G. ( 2008 ). The bacteria fight back. . Science 321, 356361. [View Article] [PubMed]
    [Google Scholar]
  29. Walsh C. ( 2003 ). Where will new antibiotics come from?. Nat Rev Microbiol 1, 6570. [View Article] [PubMed]
    [Google Scholar]
  30. Wayne L. G., Brenner D. J., Colwell R. R., Grimont P. A. D., Kandler O., Krichevsky M. I., Moore L. H., Moore W. E. C., Murray R. G. E. & other authors ( 1987 ). International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. . Int J Syst Bacteriol 37, 463464. [View Article]
    [Google Scholar]
  31. Weller D. M. ( 1988 ). Biological control of soilborne plant pathogens in the rhizosphere with bacteria. . Annu Rev Phytopathol 26, 379407. [View Article]
    [Google Scholar]
  32. Wu C., Lu X., Qin M., Wang Y., Ruan J. ( 1989 ). Analysis of menaquinone compound in microbial cells by HPLC. Microbiology [English translation of Microbiology (Beijing)] 16, 176178.
    [Google Scholar]
  33. Xiang W. S., Liu C. X., Wang X. J., Du J., Xi L. J., Huang Y. ( 2011 ). Actinoalloteichus nanshanensis sp. nov., isolated from the rhizosphere of a fig tree (Ficus religiosa). . Int J Syst Evol Microbiol 61, 11651169. [View Article] [PubMed]
    [Google Scholar]
  34. Xu J., Wang Y., Xie S. J., Xu J., Xiao J., Ruan J. S. ( 2009 ). Streptomyces xiamenensis sp. nov., isolated from mangrove sediment. . Int J Syst Evol Microbiol 59, 472476. [View Article] [PubMed]
    [Google Scholar]
  35. Yokota A., Tamura T., Hasegawa T., Huang L. H. ( 1993 ). Catenuloplanes japonicus gen. nov., sp. nov., nom. rev., a new genus of the order Actinomycetales . . Int J Syst Bacteriol 43, 805812. [View Article]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.050088-0
Loading
/content/journal/ijsem/10.1099/ijs.0.050088-0
Loading

Data & Media loading...

Supplements

Supplementary material 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