In this study, strain YIM 65004, isolated from roots of , was shown to represent a novel species of the genus by means of a polyphasic approach. Chemotaxonomic data gathered for peptidoglycan type, menaquinones, phospholipids and fatty acids strongly supported the classification of this strain within the genus : the cell-wall peptidoglycan contained lysine, glutamic acid, alanine, glycine and aspartic acid, the predominant menaquinones were MK-8(H) (66.97 %) and MK-7(H) (23.26 %), the phospholipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and an unknown ninhydrin-negative phospholipid, and the major cellular fatty acids were anteiso-C (61.98 %), iso-C (14.25 %) and iso-C (13.04 %). The G+C content of the genomic DNA was 71.7 mol%. A number of physiological features were found that clearly distinguished strain YIM 65004 from recognized species. DNA–DNA hybridization studies suggested that the novel strain represents a separate genomic species. Based on the above data, a novel species of the genus , sp. nov., is proposed, with the type strain YIM 65004 (=CCTCC AA 208060=DSM 21948).


Article metrics loading...

Loading full text...

Full text loading...



  1. Barrow, G. I. & Feltham, R. K. A.(1993).Cowan and Steel's Manual for the Identification of Medical Bacteria, 3rd edn. Cambridge: Cambridge University Press.
  2. Chen, H.-H., Zhao, G.-Z., Park, D.-J., Zhang, Y. Q., Xu, L.-H., Lee, J.-C., Kim, C.-J. & Li, W.-J.(2009).Micrococcus endophyticus sp. nov., isolated from surface-sterilized Aquilaria sinensis roots. Int J Syst Evol Microbiol 59, 1070–1075.[CrossRef] [Google Scholar]
  3. Christensen, H., Angen, O., Mutters, R., Olsen, J. E. & Bisgaard, M.(2000). DNA–DNA hybridization determined in micro-wells using covalent attachment of DNA. Int J Syst Evol Microbiol 50, 1095–1102.[CrossRef] [Google Scholar]
  4. Cohn, F.(1872). Untersuchungen über Bakterien. Beitr Biol Pflanz 1, 127–244 (in German). [Google Scholar]
  5. Coombs, J. T. & Franco, C. M.(2003). Isolation and identification of actinobacteria from surface-sterilized wheat roots. Appl Environ Microbiol 69, 5603–5608.[CrossRef] [Google Scholar]
  6. 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]
  7. Felsenstein, J.(1985). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783–791.[CrossRef] [Google Scholar]
  8. He, L., Li, W., Huang, Y., Wang, L. & Liu, Z.(2005).Streptomyces jietaisiensis sp. nov., isolated from soil in northern China. Int J Syst Evol Microbiol 55, 1939–1944.[CrossRef] [Google Scholar]
  9. Holliday, P.(1989).A Dictionary of Plant Pathology. Cambridge: Cambridge University Press.
  10. 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]
  11. Kloos, W. E., Tornabene, T. G. & Schleifer, K. H.(1974). Isolation and characterization of micrococci from human skin, including two new species: Micrococcus lylae and Micrococcus kristinae. Int J Syst Bacteriol 24, 79–101.[CrossRef] [Google Scholar]
  12. Kroppenstedt, R. M.(1982). Separation of bacterial menaquinones by HPLC using reverse phase (RP18) and a silver loaded ion exchanger as stationary phases. J Liq Chromatogr 5, 2359–2367.[CrossRef] [Google Scholar]
  13. Kumar, S., Tamura, K. & Nei, M.(2004).mega3: integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. Brief Bioinform 5, 150–163.[CrossRef] [Google Scholar]
  14. Li, W.-J., Xu, P., Schumann, P., Zhang, Y.-Q., Pukall, R., Xu, L.-H., Stackebrandt, E. & Jiang, C.-L.(2007).Georgenia ruanii sp. nov., a novel actinobacterium isolated from forest soil in Yunnan (China) and emended description of the genus Georgenia. Int J Syst Evol Microbiol 57, 1424–1428.[CrossRef] [Google Scholar]
  15. Liu, H., Xu, Y., Ma, Y. & Zhou, P.(2000). Characterization of Micrococcus antarcticus sp. nov., a psychrophilic bacterium from Antarctica. Int J Syst Evol Microbiol 50, 715–719.[CrossRef] [Google Scholar]
  16. Liu, X.-Y., Wang, B.-J., Jiang, C.-Y. & Liu, S.-J.(2007).Micrococcus flavus sp. nov., isolated from activated sludge in a bioreactor. Int J Syst Evol Microbiol 57, 66–69.[CrossRef] [Google Scholar]
  17. 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.[CrossRef] [Google Scholar]
  18. 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.[CrossRef] [Google Scholar]
  19. Moaledj, K.(1986). Comparison of Gram-staining and alternate methods, KOH test and aminopeptidase activity in aquatic bacteria: their application to numerical taxonomy. J Microbiol Methods 5, 303–310.[CrossRef] [Google Scholar]
  20. Ryan, R. P., Germaine, K., Franks, A., Ryan, D. J. & Dowling, D. N.(2008). Bacterial endophytes: recent developments and applications. FEMS Microbiol Lett 278, 1–9.[CrossRef] [Google Scholar]
  21. Saitou, N. & Nei, M.(1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–425. [Google Scholar]
  22. Schleifer, K. H. & Kandler, O.(1972). Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 36, 407–477. [Google Scholar]
  23. Schulz, B. & Boyle, C.(2006). What are endophytes? In Microbial Root Endophytes, pp. 1–13. Edited by B. J. E. Schulz, C. J. C. Boyle & T. N. Sieber. Berlin: Springer-Verlag.
  24. Smibert, R. M. & Krieg, N. R.(1994). Phenotypic characterization. In Methods for General and Molecular Bacteriology, pp. 607–654. Edited by P. Gerhardt, R. G. E. Murray, W. A. Wood & N. R. Krieg. Washington, DC: American Society for Microbiology.
  25. 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 Bacteriol 44, 846–849.[CrossRef] [Google Scholar]
  26. Stackebrandt, E., Koch, C., Gvozdiak, O. & Schumann, P.(1995). Taxonomic dissection of the genus Micrococcus: Kocuria gen. nov., Nesterenkonia gen. nov., Kytococcus gen. nov., Dermacoccus gen. nov., and Micrococcus Cohn 1872 emend. Int J Syst Bacteriol 45, 682–692.[CrossRef] [Google Scholar]
  27. Strobel, G., Daisy, B., Castillo, U. & Harper, J.(2004). Natural products from endophytic microorganisms. J Nat Prod 67, 257–268.[CrossRef] [Google Scholar]
  28. 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.[CrossRef] [Google Scholar]
  29. Wieser, M., Denner, E. B. M., Kämpfer, P., Schumann, P., Tindall, B., Steiner, U., Vybiral, D., Lubitz, W., Maszenan, A. M. & other authors(2002). Emended descriptions of the genus Micrococcus, Micrococcus luteus (Cohn 1872) and Micrococcus lylae (Kloos et al. 1974). Int J Syst Evol Microbiol 52, 629–637. [Google Scholar]

Data & Media loading...


Transmission electron micrograph of cells of strain YIM 65004 ( sp. nov.). [PDF](27 KB)


Comparative fatty acid compositions of strain YIM 65004 ( sp. nov.) and related species of the genus . [PDF](44 KB)


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