1887

Abstract

A novel actinomycete strain YIM 33361 was isolated from a soil sample collected from Yunnan, China. Comparative 16S rRNA gene sequencing showed that the strain constituted a distinct subclade within the genus , displaying more than 3 % sequence divergence from established species. Based on its morphological, chemotaxonomic, phenotypic and genotypic characteristics, strain YIM 33361 (=CCTCC AA 204004=KCTC 19027) is proposed as the type strain of a novel species, sp. nov.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.63352-0
2005-07-01
2019-10-20
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/55/4/ijs551465.html?itemId=/content/journal/ijsem/10.1099/ijs.0.63352-0&mimeType=html&fmt=ahah

References

  1. Albuquerque de Barros, E. V. S., Manfio, G. P., Ribeiro Maitan, V., Mendes Bataus, L. A., Kim, S. B., Maldonado, L. A. & Goodfellow, M. ( 2003; ). Nocardia cerradoensis sp. nov., a novel isolate from Cerrado soil in Brazil. Int J Syst Evol Microbiol 53, 29–33.[CrossRef]
    [Google Scholar]
  2. Altschul, S. F., Madden, T. L., Schäffer, A. A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D. J. ( 1997; ). Gapped blast and psi-blast: a new generation of protein database search programs. Nucleic Acids Res 25, 3389–3402.[CrossRef]
    [Google Scholar]
  3. Becker, B., Lechevalier, M. P. & Lechevalier, H. A. ( 1965; ). Chemical composition of cell-wall preparation from strains of various form-genera of aerobic actinomycetes. Appl Microbiol 13, 236–243.
    [Google Scholar]
  4. Chun, J. & Goodfellow, M. ( 1995; ). A phylogenetic analysis of the genus Nocardia with 16S rRNA gene sequences. Int J Syst Bacteriol 45, 240–245.[CrossRef]
    [Google Scholar]
  5. Collins, M. D., Pirouz, T., Goodfellow, M. & Minnikin, D. E. ( 1977; ). Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 100, 221–230.[CrossRef]
    [Google Scholar]
  6. Felsenstein, J. ( 1985; ). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783–791.[CrossRef]
    [Google Scholar]
  7. Felsenstein, J. ( 1993; ). phylip – Phylogeny Inference Package, version 3.5c. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle, USA.
  8. Goodfellow, M. ( 1971; ). Numerical taxonomy of some nocardioform bacteria. J Gen Microbiol 69, 33–80.[CrossRef]
    [Google Scholar]
  9. Goodfellow, M. ( 1992; ). The family Nocardiaceae. In The Prokaryotes, 2nd edn, pp. 1188–1213. Edited by A. Balows, H. G. Trüper, M. Dworkin, W. Harder & K. H. Schleifer. New York: Springer.
  10. Goodfellow, M. ( 1998; ). Nocardia and related genera. In Topley and Wilson's Microbiology and Microbial Infections, 9th edn, vol. 2, Systematic Bacteriology, pp. 463–489. Edited by A. Balows & B. I. Duerden. London: Arnold.
  11. Goodfellow, M. & Lechevalier, M. P. ( 1989; ). Genus Nocardia Trevisan 1889, 9AL. In Bergey's Manual of Systematic Bacteriology, vol. 2, pp. 1458–1471. Edited by S. T. Williams, M. E. Sharpe & J. G. Holt. Baltimore: Williams & Wilkins.
  12. Goodfellow, M. & Orchard, V. A. ( 1974; ). Antibiotic sensitivity of some nocardioform bacteria and its value as a criterion for taxonomy. J Gen Microbiol 83, 375–387.[CrossRef]
    [Google Scholar]
  13. Goodfellow, M., Isik, K. & Yates, E. ( 1999; ). Actinomycete systematics: an unfinished synthesis. Nova Acta Leopold NF80(312), 47–82.
    [Google Scholar]
  14. Gordon, R. E. ( 1967; ). The taxonomy of soil bacteria. In The Ecology of Soil Bacteria, pp. 293–321. Edited by T. R. G. Gray & D. Parkinson. Liverpool: Liverpool University Press.
  15. Gordon, R. E. & Mihm, J. M. ( 1957; ). A comparative study of some strains received as nocardiae. J Bacteriol 73, 15–27.
    [Google Scholar]
  16. Gordon, R. E. & Mihm, J. M. ( 1962; ). The type species of the genus Nocardia. J Gen Microbiol 27, 1–10.[CrossRef]
    [Google Scholar]
  17. 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, 54–63.[CrossRef]
    [Google Scholar]
  18. Hayakawa, M. & Nonomura, H. ( 1987; ). Humic acid-vitamin agar, a new medium for the selective isolation of soil actinomycetes. J Ferment Technol 65, 501–509.[CrossRef]
    [Google Scholar]
  19. Jiang, L. Y., Li, M. G., Li, W. J., Cui, X. L., Xu, L. H. & Jiang, C. L. ( 2001; ). Study on the application of quantitative analysis of cell-wall amino acids in actinomycetes. Acta Microbiol Sin 41, 270–277.
    [Google Scholar]
  20. Jones, K. L. ( 1949; ). Fresh isolates of actinomycetes in which the presence of sporogenous aerial mycelia is a fluctuating characteristic. J Bacteriol 57, 141–145.
    [Google Scholar]
  21. Kageyama, A., Poonwan, N., Yazawa, K., Mikami, Y. & Nishimura, K. ( 2004a; ). Nocardia asiatica sp. nov., isolated from patients with nocardiosis in Japan and clinical specimens from Thailand. Int J Syst Evol Microbiol 54, 125–130.[CrossRef]
    [Google Scholar]
  22. Kageyama, A., Yazawa, K., Nishimura, K. & Mikami, Y. ( 2004b; ). Nocardia inohanensis sp. nov., Nocardia yamanashiensis sp. nov. and Nocardia niigatensis sp. nov., isolated from clinical specimens. Int J Syst Evol Microbiol 54, 563–569.[CrossRef]
    [Google Scholar]
  23. Kämpfer, P. & Kroppenstedt, R. M. ( 1996; ). Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. Can J Microbiol 42, 989–1005.[CrossRef]
    [Google Scholar]
  24. Kämpfer, P., Buczolits, S., Jäckel, U., Grün-Wollny, I. & Busse, H.-J. ( 2004; ). Nocardia tenerifensis sp. nov. Int J Syst Evol Microbiol 54, 381–383.[CrossRef]
    [Google Scholar]
  25. 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.
  26. 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]
  27. Kimura, M. ( 1983; ). The Neutral Theory of Molecular Evolution. Cambridge: Cambridge University Press.
  28. Kumar, S., Tamura, K., Jakobsen, I. B. & Nei, M. ( 2001; ). mega2: Molecular Evolutionary Genetics Analysis software. Bioinformatics 17, 1244–1245.[CrossRef]
    [Google Scholar]
  29. Lechevalier, M. P. ( 1976; ). The taxonomy of the genus Nocardia: some light at the end of the tunnel? In The Biology of the Nocardiae, pp. 1–33. Edited by M. Goodfellow, G. H. Brownell & J. A. Serrano. London: Academic Press.
  30. Lechevalier, M. P. & Lechevalier, H. A. ( 1970; ). Chemical composition as a criterion in the classification of aerobic actinomycetes. Int J Syst Bacteriol 20, 435–443.[CrossRef]
    [Google Scholar]
  31. Lechevalier, M. P. & Lechevalier, H. A. ( 1980; ). The chemotaxonomy of actinomycetes. In Actinomycete Taxonomy, Special Publication no. 6, pp. 227–291. Edited by A. Dietz & J. Thayer. Arlington, VA: Society for Industrial Microbiology.
  32. Lechevalier, M. P., De Bièvre, C. & Lechevalier, H. A. ( 1977; ). Chemotaxonomy of aerobic actinomycetes: phospholipid composition. Biochem Syst Ecol 5, 249–260.[CrossRef]
    [Google Scholar]
  33. Lechevalier, M. P., Stern, A. E. & Lechevalier, H. A. ( 1981; ). Phospholipids in the taxonomy of actinomycetes. Zentralbl Bakteriol Hyg Abt 1 Suppl 11, 111–116.
    [Google Scholar]
  34. Maldonado, L., Hookey, J. V., Ward, A. C. & Goodfellow, M. ( 2000; ). The Nocardia salmonicida clade, including descriptions of Nocardia cummidelens sp. nov., Nocardia fluminea sp. nov. and Nocardia soli sp. nov. Antonie van Leeuwenhoek 78, 367–377.[CrossRef]
    [Google Scholar]
  35. Mandel, M. & Marmur, J. ( 1968; ). Use of ultraviolet absorbance temperature profile for determining the guanine plus cytosine content of DNA. Methods Enzymol 12B, 195–206.
    [Google Scholar]
  36. Marmur, J. ( 1961; ). A procedure for the isolation of deoxyribonucleic acid from microorganisms. J Mol Biol 3, 208–218.[CrossRef]
    [Google Scholar]
  37. McNeil, M. M. & Brown, J. M. ( 1994; ). The medically important aerobic actinomycetes: epidemiology and microbiology. Clin Microbiol Rev 7, 357–417.
    [Google Scholar]
  38. Minnikin, D. E., Alshamaony, L. & Goodfellow, M. ( 1975; ). Differentiation of Mycobacterium, Nocardia and related taxa by thin-layer chromatographic analysis of whole-organism methanolysates. J Gen Microbiol 88, 200–204.[CrossRef]
    [Google Scholar]
  39. Mordarska, H., Mordarski, M. & Goodfellow, M. ( 1972; ). Chemotaxonomic characters and classification of some nocardioform bacteria. J Gen Microbiol 71, 77–86.[CrossRef]
    [Google Scholar]
  40. Orchard, V. A. & Goodfellow, M. ( 1980; ). Numerical classification of some named strains of Nocardia asteroides and related isolates from soil. J Gen Microbiol 118, 295–312.
    [Google Scholar]
  41. Orchard, V. A., Goodfellow, M. & Williams, S. T. ( 1977; ). Selective isolation and occurrence of Nocardiae in soil. Soil Biol Biochem 9, 233–238.[CrossRef]
    [Google Scholar]
  42. Saintpierre-Bonaccio, D., Maldonado, L. A., Amir, H., Pineau, R. & Goodfellow, M. ( 2004; ). Nocardia neocaledoniensis sp. nov., a novel actinomycete isolated from a New-Caledonian brown hypermagnesian ultramafic soil. Int J Syst Evol Microbiol 54, 599–603.[CrossRef]
    [Google Scholar]
  43. Saitou, N. & Nei, M. ( 1987; ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–425.
    [Google Scholar]
  44. Sasser, M. ( 1990; ). Identification of bacteria by gas chromatography of cellular fatty acids. USFCC Newsl 20, 1–6.
    [Google Scholar]
  45. Shirling, E. B. & Gottlieb, D. ( 1966; ). Methods for characterization of Streptomyces species. Int J Syst Bacteriol 16, 313–340.[CrossRef]
    [Google Scholar]
  46. Society for American Bacteriologists ( 1957; ). Manual of Microbiological Methods. New York: McGraw-Hill.
  47. 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, 479–491.[CrossRef]
    [Google Scholar]
  48. Tatusova, T. A. & Madden, T. L. ( 1999; ). blast 2 sequences – a new tool for comparing protein and nucleotide sequences. FEMS Microbiol Lett 174, 247–250.[CrossRef]
    [Google Scholar]
  49. 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]
  50. Tsukamura, M. ( 1966; ). Adansonian classification of mycobacteria. J Gen Microbiol 45, 253–273.[CrossRef]
    [Google Scholar]
  51. Waksman, S. A. ( 1961; ). The Actinomycetes, vol. 2, Classification, Identification and Descriptions of Genera and Species. Baltimore: Williams & Wilkins.
  52. Wang, L., Zhang, Y., Lu, Z., Shi, Y., Liu, Z., Maldonado, L. & Goodfellow, M. ( 2001; ). Nocardia beijingensis sp. nov., a novel isolate from soil. Int J Syst Evol Microbiol 51, 1783–1788.[CrossRef]
    [Google Scholar]
  53. Williams, S. T., Goodfellow, M., Alderson, G., Wellington, E. M. H., Sneath, P. H. A. & Sackin, M. J. ( 1983; ). Numerical classification of Streptomyces and related genera. J Gen Microbiol 129, 1743–1813.
    [Google Scholar]
  54. Xu, P., Li, W. J., Zhang, Y. G., Tang, S. K., Gao, H. Y., Xu, L. H., He, B. K. & Jiang, C. L. ( 2003a; ). Molecular screening and distribution of polyketide antibiotics producers from Actinomycetes. J Chin Antibiot 28, 321–324.
    [Google Scholar]
  55. Xu, P., Li, W. J., Xu, L. H. & Jiang, C. L. ( 2003b; ). A microwave based method for genomic DNA extraction from actinomycetes. Microbiology 30, 82–84 (in Chinese).
    [Google Scholar]
  56. Yassin, A. F., Rainey, A. F. & Steiner, U. ( 2001; ). Nocardia cyriacigeorgici sp. nov. Int J Syst Evol Microbiol 51, 1419–1423.
    [Google Scholar]
  57. Zhang, J. L., Liu, Z. & Goodfellow, M. ( 2003; ). Nocardia caishijiensis sp. nov., a novel soil actinomycete. Int J Syst Evol Microbiol 53, 999–1004.[CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.63352-0
Loading
/content/journal/ijsem/10.1099/ijs.0.63352-0
Loading

Data & Media loading...

Most Cited This Month

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