1887

Abstract

An actinomycete strain, designated CP2R9-1, was isolated from root internal tissues of upland rice (). Based on a polyphasic approach, strain CP2R9-1 was characterized as a member of the genus Diaminopimelic acid and 3-OH-diaminopimelic acid were present in the cell-wall peptidoglycan. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannosides, two unidentified phospholipids and four unidentified polar lipids. Predominant menaquinones were MK-9(H), MK-9(H) and MK-10(H). Whole-cell sugars consisted of ribose, xylose, arabinose and glucose. Phylogenetic analysis of the nearly complete 16S rRNA gene sequence suggested that strain CP2R9-1 was closely related to 232617 (99.32 % similarity), DSM 43168 (99.18 %) and MA-2 (99.16 %). Strain CP2R9-1 was distinct from its closest relatives based on low levels of DNA–DNA relatedness (21.3 ± 0.1–41.7 ± 0.7 %) and phenotypic differences. The results presented in this study showed that strain CP2R9-1 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is CP2R9-1 ( = BCC 67266 = NBRC 110007).

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2015-11-01
2020-11-26
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References

  1. Arai T. ( 1975). Culture Media for Actinomycetes Tokyo: The Society for Actinomycetes;.
    [Google Scholar]
  2. Collins M. D., Pirouz T., Goodfellow M., Minnikin D. E. ( 1977;). Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 100 221230 [CrossRef] [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 224229 [CrossRef].
    [Google Scholar]
  4. Fang B., Liu C., Guan X., Song J., Zhao J., Liu H., Li C., Ning W., Wang X., Xiang W. ( 2015;). Two new species of the genus Micromonospora, Micromonospora palomenae sp. nov. and Micromonospora harpali sp. nov. isolated from the insects. Antonie van Leeuwenhoek 108 141150 [CrossRef] [PubMed].
    [Google Scholar]
  5. Felsenstein J. ( 1981;). Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17 368376 [CrossRef] [PubMed].
    [Google Scholar]
  6. Felsenstein J. ( 1985;). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39 783791 [CrossRef].
    [Google Scholar]
  7. Fitch W. M. ( 1971;). Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20 406416 [CrossRef].
    [Google Scholar]
  8. Garcia L. C., Martínez-Molina E., Trujillo M. E. ( 2010;). Micromonospora pisi sp. nov., isolated from root nodules of Pisum sativum . Int J Syst Evol Microbiol 60 331337 [CrossRef] [PubMed].
    [Google Scholar]
  9. Gordon R. E., Barnett D. A., Handerhan J. E., Pang C. H. N. ( 1974;). Nocardia coeliaca, Nocardia autotrophica, and the nocardin strain. Int J Syst Bacteriol 24 5463 [CrossRef].
    [Google Scholar]
  10. Itoh T., Kudo T., Parenti F., Seino A. ( 1989;). Amended description of the genus Kineosporia, based on chemotaxonomic and morphological studies. Int J Syst Bacteriol 39 168173 [CrossRef].
    [Google Scholar]
  11. Jongrungruangchok S., Tanasupawat S., Kudo T. ( 2008;). Micromonospora krabiensis sp. nov., isolated from marine soil in Thailand. J Gen Appl Microbiol 54 127133 [CrossRef] [PubMed].
    [Google Scholar]
  12. Kämpfer P., Kroppenstedt R. M. ( 1996;). Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. Can J Microbiol 42 9891005 [CrossRef].
    [Google Scholar]
  13. Kawamoto I., Oka T., Nara T. ( 1981;). Cell wall composition of Micromonospora olivoasterospora, Micromonospora sagamiensis, and related organisms. J Bacteriol 146 527534 [PubMed].
    [Google Scholar]
  14. Kelly K. L. ( 1964). Inter-Society Color Council – National Bureau of Standard Color Name Charts Illustrated with Centroid Colors Washington, DC: US Government Printing Office;.
    [Google Scholar]
  15. Kim O. S., Cho Y. J., Lee K., Yoon S. H., Kim M., Na H., Park S. C., Jeon Y. S., Lee J. H., 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 [CrossRef] [PubMed].
    [Google Scholar]
  16. Kimura M. ( 1980;). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16 111120 [CrossRef] [PubMed].
    [Google Scholar]
  17. Komagata K., Suzuki K. I. ( 1987;). Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 19 161207 [CrossRef].
    [Google Scholar]
  18. Lane D. J. ( 1991;). 16S/23S rRNA sequencing. . In Nucleic Acid Techniques in Bacterial Systematics, pp. 115175. Edited by Stackebrandt E., Goodfellow M. Chichester: Wiley;.
    [Google Scholar]
  19. Martínez-Hidalgo P., Galindo-Villardón P., Trujillo M. E., Igual J. M., Martínez-Molina E. ( 2014;). Micromonospora from nitrogen fixing nodules of alfalfa (Medicago sativa L.). A new promising Plant Probiotic Bacteria. Sci Rep 4 6389 [CrossRef] [PubMed].
    [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 159167 [CrossRef].
    [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 233241 [CrossRef].
    [Google Scholar]
  22. Nimaichand S., Zhang Y. G., Cheng J., Li L., Zhang D. F., Zhou E. M., Dong L., Ningthoujam D. S., Li W. J. ( 2013;). Micromonospora kangleipakensis sp. nov., isolated from a sample of limestone quarry. Int J Syst Evol Microbiol 63 45464551 [CrossRef] [PubMed].
    [Google Scholar]
  23. Ørskov J. ( 1923). Investigations into the Morphology of the Ray Fungi Copenhagen: Levin and Munksgaard;.
    [Google Scholar]
  24. Raaijmakers J. M., Mazzola M. ( 2012;). Diversity and natural functions of antibiotics produced by beneficial and plant pathogenic bacteria. Annu Rev Phytopathol 50 403424 [CrossRef] [PubMed].
    [Google Scholar]
  25. Ren J., Li L., Wei B., Tang Y. L., Deng Z. X., Sun M., Hong K. ( 2013;). Micromonospora wenchangensis sp. nov., isolated from mangrove soil. Int J Syst Evol Microbiol 63 23892395 [CrossRef] [PubMed].
    [Google Scholar]
  26. Saitou N., Nei M. ( 1987;). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4 406425 [PubMed].
    [Google Scholar]
  27. Sasser M. ( 1990;). Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. Newark, DE: MIDI Inc:.
  28. Schleifer K. H., Kandler O. ( 1972;). Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 36 407477 [PubMed].
    [Google Scholar]
  29. Shirling E. B., Gottlieb D. ( 1966;). Methods for characterization of Streptomyces species. Int J Syst Bacteriol 16 313340 [CrossRef].
    [Google Scholar]
  30. Stackebrandt E., Rainey F. A., Ward-Rainey N. L. ( 1997;). Proposal for a new hierarchic classification system, Actinobacteria classis nov.. Int J Syst Bacteriol 47 479491 [CrossRef].
    [Google Scholar]
  31. Staneck J. L., Roberts G. D. ( 1974;). Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 28 226231 [PubMed].
    [Google Scholar]
  32. Supong K., Suriyachadkun C., Pittayakhajonwut P., Suwanborirux K., Thawai C. ( 2013;). Micromonospora spongicola sp. nov., an actinomycete isolated from a marine sponge in the Gulf of Thailand. J Antibiot (Tokyo) 66 505509 [CrossRef] [PubMed].
    [Google Scholar]
  33. Tamaoka J. ( 1994;). Determination of DNA base composition. . In Chemical Methods in Prokaryotic Systematics, pp. 463470. Edited by Goodfellow M., O'Donnell A. G. Chichester: Wiley;.
    [Google Scholar]
  34. Tamura K., Stecher G., Peterson D., Filipski A., Kumar S. ( 2013;). mega6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30 27252729 [CrossRef] [PubMed].
    [Google Scholar]
  35. 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 46734680 [CrossRef] [PubMed].
    [Google Scholar]
  36. Uchida K., Aida K. ( 1984;). An improved method for the glycolate test for simple identification of the acyl type of bacterial cell walls. J Gen Appl Microbiol 30 131134 [CrossRef].
    [Google Scholar]
  37. Verlander C. P. ( 1992;). Detection of horseradish peroxidase by colorimetry. [CrossRef] In Nonisotopic DNA Probe Techniques, pp. 185201. Edited by Kricka L. J. New York: Academic Press;.
    [Google Scholar]
  38. 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 [CrossRef].
    [Google Scholar]
  39. Weisburg W. G., Barns S. M., Pelletier D. A., Lane D. J. ( 1991;). 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173 697703 [PubMed].
    [Google Scholar]
  40. Williams S. T., Cross T. ( 1971;). Actinomycetes. . In Methods in Microbiology, pp. 295334. Edited by Booth C. vol. 4 London: Academic Press;.
    [Google Scholar]
  41. Xiang W., Yu C., Liu C., Zhao J., Yang L., Xie B., Li L., Hong K., Wang X. ( 2014;). Micromonospora polyrhachis sp. nov., an actinomycete isolated from edible Chinese black ant (Polyrhachis vicina Roger). Int J Syst Evol Microbiol 64 495500 [CrossRef] [PubMed].
    [Google Scholar]
  42. Xie Q. Y., Qu Z., Lin H. P., Li L., Hong K. ( 2012;). Micromonospora haikouensis sp. nov., isolated from mangrove soil. Antonie van Leeuwenhoek 101 649655 [CrossRef] [PubMed].
    [Google Scholar]
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