1887

Abstract

The taxonomic position of a soil isolate, strain 276, was established using a polyphasic approach. The organism showed a range of chemical and morphological properties consistent with its classification in the genus . An almost complete 16S rRNA gene sequence determined for the strain was aligned with corresponding sequences of representatives of the genus and related taxa using three tree-making algorithms. The organism formed a distinct phyletic line within the evolutionary radiation occupied by the genus and was most closely related to the type strain of . However, the two strains shared a low DNA–DNA relatedness value and were readily distinguished using a combination of phenotypic properties. The combined genotypic and phenotypic data show that strain 276 should be assigned to the genus as a novel species. The name proposed for this new taxon is sp. nov. The type strain is 276 (=CGMCC 4.1860=JCM 12160).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.63133-0
2004-11-01
2024-04-19
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/54/6/ijs542301.html?itemId=/content/journal/ijsem/10.1099/ijs.0.63133-0&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., 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. 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]
  3. Chun J., Blackall L. L., Kang S.-O., Hah Y. C., Goodfellow M. 1997; A proposal to reclassify Nocardia pinensis Blackall et al . as Skermania piniformis gen. nov., comb. nov.. Int J Syst Bacteriol 47:127–131 [CrossRef]
    [Google Scholar]
  4. Collins M. D., Howarth O. W., Grund E., Kroppenstedt R. M. 1987; Isolation and structural determination of new members of the vitamin K2 series in Nocardia brasiliensis . FEMS Microbiol Lett 41:35–39 [CrossRef]
    [Google Scholar]
  5. De Ley J., Cattoir H., Reynaerts A. 1970; The quantitative measurements of DNA hybridization from renaturation rates. Eur J Biochem 12:133–142 [CrossRef]
    [Google Scholar]
  6. Felsenstein J. 1993 phylip (Phylogeny Inference Package), version 3.6. Distributed by the author Department of Genetics, University of Washington; Seattle, USA:
    [Google Scholar]
  7. Goodfellow M., Isik K., Yates E. 1999; Actinomycete systematics: an unfinished synthesis. Nova Acta Leopold NF 80:31247–82
    [Google Scholar]
  8. Hamid M. E., Maldonado L., Sharaf Eldin G. S., Mohamed M. F., Saeed N. S., Goodfellow M. 2001; Nocardia africana sp. nov., a new pathogen isolated from patients with pulmonary infections. J Clin Microbiol 39:625–630 [CrossRef]
    [Google Scholar]
  9. Hasegawa T., Takizawa M., Tanida S. 1983; A rapid analysis for chemical grouping of aerobic actinomycetes. J Gen Appl Microbiol 29:319–322 [CrossRef]
    [Google Scholar]
  10. Huß V. A. R., Festl H., Schleifer K. H. 1983; Studies on the spectrophotometric determination of DNA hybridization from renaturation rates. Syst Appl Microbiol 4:184–192 [CrossRef]
    [Google Scholar]
  11. Isik K., Chun J., Hah Y. C., Goodfellow M. 1999; Nocardia uniformis nom. rev. Int J Syst Bacteriol 49:1227–1230 [CrossRef]
    [Google Scholar]
  12. Jahnke K.-D. 1992; Basic computer program for evaluation of spectroscopic DNA renaturation data from a Gilford System 2600 spectrophotometer on a PC/XT/AT type personal computer. J Microbiol Methods 15:61–73 [CrossRef]
    [Google Scholar]
  13. 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]
  14. Kageyama A., Yazawa K., Nishimura K., Mikami Y. 2004b; Nocardia inohanaensis 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]
  15. 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]
  16. 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]
  17. Kinoshita N., Homma Y., Igarashi M., Ikeno S., Hori M., Hamada M. 2001; Nocardia vinacea sp. nov.. Actinomycetologica 151–5 [CrossRef]
    [Google Scholar]
  18. Lechevalier H. A., Lechevalier M. P. 1970; Chemical composition as a criterion in the classification of aerobic actinomycetes. Int J Syst Bacteriol 20:435–443 [CrossRef]
    [Google Scholar]
  19. Lechevalier M. P., Lechevalier H. A. 1980; The chemotaxonomy of actinomycetes. In Actinomycete Taxonomy , Special Publication 6 pp  227–291 Arlington, VA: Society for Industrial Microbiology;
    [Google Scholar]
  20. 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]
  21. Lu Z., Liu Z., Wang L., Zhang Y., Qi W., Goodfellow M. 2001; Saccharopolyspora flava sp. nov. and Saccharopolyspora thermophila sp. nov., novel actinomycetes from soil. Int J Syst Evol Microbiol 51:319–325
    [Google Scholar]
  22. 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]
  23. Marmur J., Doty P. 1962; Determination of base composition of deoxyribonucleic acid from its denaturation temperature. J Mol Biol 5:109–118 [CrossRef]
    [Google Scholar]
  24. 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]
  25. 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]
  26. Mordarska H., Mordarski M., Goodfellow M. 1972; Chemotaxonomic characters and classification of some nocardioform bacteria. J Gen Microbiol 71:77–86 [CrossRef]
    [Google Scholar]
  27. Orchard V. A. 1981; The ecology of Nocardia and related taxa. Zentbl Bakteriol Suppl 11:167–180
    [Google Scholar]
  28. 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]
  29. Rainey F. A., Ward-Rainey N., Kroppenstedt R. M., Stackebrandt E. 1996; The genus Nocardiopsis represents a phylogenetically coherent taxon and a distinct actinomycete lineage: proposal of Nocardiopsiaceae fam. nov. Int J Syst Bacteriol 46:28–96
    [Google Scholar]
  30. Saito H., Miura K.-I. 1963; Preparation of transforming deoxyribonucleic acid by phenol treatment. Biochim Biophys Acta 72:619–629 [CrossRef]
    [Google Scholar]
  31. Sasser M. 1990; Identification of bacteria by gas chromatography of cellular fatty acids . Technical Note 101: Newark, DE: Microbial ID;
    [Google Scholar]
  32. 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]
  33. 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]
  34. Wang Y., Zhang Z., Ruan J., Wang Y., Ali S. 1999; Investigations of actinomycete diversity in the tropical rainforests of Singapore. J Ind Microbiol Biotechnol 23:178–187 [CrossRef]
    [Google Scholar]
  35. Wang L., Zhang Y., Huang Y., Maldonado L. A., Liu Z., Goodfellow M. 2004; Nocardia pigrifrangens sp. nov., a novel actinomycete isolated from a contaminated plate. Int J Syst Evol Microbiol 54:1683–1686 [CrossRef]
    [Google Scholar]
  36. Wayne L. G., Brenner D. J., Colwell R. R. 9 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 37:463–464 [CrossRef]
    [Google Scholar]
  37. Whipple D. L., Le Febvre R. B., Andrews R. E. Jr, Thiermann A. B. 1987; Isolation and analysis of restriction endonuclease digestive patterns of chromosomal DNA from Mycobacterium paratuberculosis and other Mycobacterium species. J Clin Microbiol 25:1511–1515
    [Google Scholar]
  38. Wu C., Lu X., Qin M., Wang Y., Ruan J. 1989; Analysis of menaquinone compound in microbial cells by HPLC. Microbiology (English translation of Mikrobiologiya) 16176–178
    [Google Scholar]
  39. Yassin A. F., Rainey F. A., Mendroch U., Brzezinka H., Schaal K. P. 2000; Nocardia abscessus sp. nov. Int J Syst Evol Microbiol 50:1487–1493 [CrossRef]
    [Google Scholar]
  40. Yassin A. F., Rainey F. A., Steiner U. 2001a; Nocardia cyriacigeorgici sp. nov. Int J Syst Evol Microbiol 51:1419–1423
    [Google Scholar]
  41. Yassin A. F., Rainey F. A., Steiner U. 2001b; Nocardia ignorata sp. nov. Int J Syst Evol Microbiol 51:2127–2131 [CrossRef]
    [Google Scholar]
  42. Yassin A. F., Sträubler B., Schumann P., Schaal K. P. 2003; Nocardia puris sp. nov. Int J Syst Evol Microbiol 53:1595–1599 [CrossRef]
    [Google Scholar]
  43. Zhang J., Zhang Y., Xiao C., Liu Z., Goodfellow M. 2002; Rhodococcus maanshanensis sp. nov., a novel actinomycete from soil. Int J Syst Evol Microbiol 52:2121–2126 [CrossRef]
    [Google Scholar]
  44. Zhang J., 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.0.63133-0
Loading
/content/journal/ijsem/10.1099/ijs.0.63133-0
Loading

Data & Media loading...

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