1887

Abstract

The taxonomic position of ten acidophilic actinomycetes isolated from an acidic rice-field soil was established using a polyphasic approach. 16S rRNA gene sequences determined for the isolates were aligned with corresponding sequences of representatives of the genera , and and phylogenetic trees were inferred using four tree-making algorithms. The isolates had identical sequences and formed a distinct branch at the periphery of the 16S rRNA gene tree. The chemotaxonomic and morphological properties of representative isolates were consistent with their assignment to the genus . The isolates shared nearly identical phenotypic profiles that readily distinguished them from representatives of the established species of . It is evident from the genotypic and phenotypic data that the isolates form a homogeneous group that corresponds to a novel species in the genus . The name proposed for this new taxon is sp. nov.; the type strain is strain TH49 (=CGMCC 4.2012=JCM 13271).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.64165-0
2006-06-01
2019-12-06
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/56/6/1257.html?itemId=/content/journal/ijsem/10.1099/ijs.0.64165-0&mimeType=html&fmt=ahah

References

  1. Collins, M. D. ( 1985; ). Isoprenoid quinone analysis in classification and identification. In Chemical Methods in Bacterial Systematics, pp. 267–289. Edited by M. Goodfellow & D. E. Minnikin. London: Academic Press.
  2. Felsenstein, J. ( 1981; ). Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17, 368–376.[CrossRef]
    [Google Scholar]
  3. Felsenstein, J. ( 1985; ). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783–791.[CrossRef]
    [Google Scholar]
  4. Felsenstein, J. ( 1993; ). phylip (phylogeny inference package), version 3.5c. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle, USA.
  5. Fitch, W. M. ( 1971; ). Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20, 406–416.[CrossRef]
    [Google Scholar]
  6. Fitch, W. M. & Margoliash, E. ( 1967; ). Construction of phylogenetic trees: a method based on mutation distances as estimated from cytochrome c sequences is of general applicability. Science 155, 279–284.[CrossRef]
    [Google Scholar]
  7. Goodfellow, M. & Dawson, D. ( 1978; ). Qualitative and quantitative studies of bacteria colonizing Picea sitchensis litter. Soil Biol Biochem 10, 303–307.[CrossRef]
    [Google Scholar]
  8. Groth, I., Schütze, B., Boettcher, T., Pullen, C. B., Rodriguez, C., Leistner, E. & Goodfellow, M. ( 2003; ). Kitasatospora putterlickiae sp. nov., isolated from rhizosphere soil, transfer of Streptomyces kifunensis to the genus Kitasatospora as Kitasatospora kifunensis comb. nov., and emended description of Streptomyces aureofaciens Duggar 1948. Int J Syst Evol Microbiol 53, 2033–2040.[CrossRef]
    [Google Scholar]
  9. Groth, I., Rodriguez, C., Schütze, B., Schmitz, P., Leistner, E. & Goodfellow, M. ( 2004; ). Five novel Kitasatospora species from soil: Kitasatospora arboriphila sp. nov., K. gansuensis sp. nov., K. nipponensis sp. nov., K. paranensis sp. nov. and K. terrestris sp. nov. Int J Syst Evol Microbiol 54, 2121–2129.[CrossRef]
    [Google Scholar]
  10. 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]
  11. Hopkins, D. W., MacNaughton, S. J. & O'Donnell, A. G. ( 1991; ). A dispersal and differential centrifugation technique for representatively sampling microorganisms from soil. Soil Biol Biochem 23, 217–225.[CrossRef]
    [Google Scholar]
  12. Hopwood, D. A., Bibb, M. J., Chater, K. F., Kieser, T. C. J., Kieser, H. M., Lydiate, D. J., Smith, C. P., Ward, J. M. & Schrempf, H. ( 1985; ). Genetic Manipulation of Streptomyces. A Laboratory Manual. Norwich: The John Innes Foundation.
  13. Huang, Y., Cui, Q., Wang, L., Rodriguez, C., Quintana, E., Goodfellow, M. & Liu, Z. ( 2004; ). Streptacidiphilus jiangxiensis sp. nov., a novel actinomycete isolated from acidic rhizosphere soil in China. Antonie van Leeuwenhoek 86, 159–165.[CrossRef]
    [Google Scholar]
  14. 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]
  15. Jukes, T. H. & Cantor, C. R. ( 1969; ). Evolution of protein molecules. In Mammalian Protein Metabolism, vol. 3, pp. 21-213. Edited by H. N. Munro. New York: Academic Press.
  16. Kawato, M. & Shinobu, R. ( 1959; ). On Streptomyces herbaricolor sp. nov., supplement: a single technique for microscopical observation. Mem Osaka Unit Lib Arts Educ B Nat Sci 8, 114–119 (in Japanese).
    [Google Scholar]
  17. Kelly, K. L. ( 1958; ). Centroid notations for the revised ISCC-NBS color name blocks. J Res Nat Bur Standards U S A 61, 427.[CrossRef]
    [Google Scholar]
  18. Kim, S. B., Falconer, C., Williams, E. & Goodfellow, M. ( 1998; ). Streptomyces thermocarboxydovorans sp. nov. and Streptomyces thermocarboxydus sp. nov., two moderately thermophilic carboxydotrophic species from soil. Int J Syst Bacteriol 48, 59–68.[CrossRef]
    [Google Scholar]
  19. Kim, S. B., Lonsdale, J., Seong, C.-N. & Goodfellow, M. ( 2003; ). Streptacidiphilus gen. nov., acidophilic actinomycetes with wall chemotype I and emendation of the family Streptomycetaceae ( Waksman and Henrici 1943 AL) emend. Rainey et al. 1997. Antonie van Leeuwenhoek 83, 107–116.[CrossRef]
    [Google Scholar]
  20. Kim, S. B., Seong, C. N., Jeon, S. J., Bae, K. S. & Goodfellow, M. ( 2004; ). Taxonomic study of neutrotolerant acidophilic actinomycetes isolated from soil and description of Streptomyces yeochonensis sp. nov. Int J Syst Evol Microbiol 54, 211–214.[CrossRef]
    [Google Scholar]
  21. Kroppenstedt, R. M. ( 1985; ). Fatty acid and menaquinone analysis of actinomycetes and related organisms. In Chemical Methods in Bacterial Systematics, pp. 173–199. Edited by M. Goodfellow & D. E. Minnikin. London: Academic Press.
  22. Küster, E. ( 1959; ). Outline of a comparative study of criteria used in characterization of the actinomycetes. Int Bull Bacteriol Nomencl Taxon 9, 97–104.
    [Google Scholar]
  23. Küster, E. & Williams, S. T. ( 1964; ). Selection media for isolation of streptomycetes. Nature 202, 928–929.[CrossRef]
    [Google Scholar]
  24. Lechevalier, M. P. & Lechevalier, H. A. ( 1980; ). The chemotaxonomy of actinomycetes. In Actinomycete Taxonomy (Special Publication 6), pp. 277–284. Edited by A. Dietz & D. W. Thayer. Arlington, VA: Society for Industrial Microbiology.
  25. Lechevalier, M. P., De Bièvre, C. & Lechevalier, H. A. ( 1977; ). Chemotaxonomy of aerobic actinomycetes: phospholipid composition. Biochem Syst Evol 5, 249–260.[CrossRef]
    [Google Scholar]
  26. McIlvaine, T. C. ( 1921; ). A buffer solution for colorimetric comparison. J Biol Chem 49, 183–186.
    [Google Scholar]
  27. 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 isoprenoid quinones and polar lipids. J Microbiol Methods 2, 233–241.[CrossRef]
    [Google Scholar]
  28. National Bureau of Standards ( 1964; ). ISCC-NBS Color Manual Charts Illustrated with Centroid Colors. Supplement to NBS Circular 553. Washington, DC: US Government Printing Office.
  29. Saitou, N. & Nei, M. ( 1987; ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–425.
    [Google Scholar]
  30. Sembiring, L., Ward, A. C. & Goodfellow, M. ( 2000; ). Selective isolation and characterisation of members of the Streptomyces violaceusniger clade associated with the roots of Paraserianthes falcataria. Antonie van Leeuwenhoek 78, 353–366.[CrossRef]
    [Google Scholar]
  31. Seong, C. N., Goodfellow, M., Ward, A. C. & Hah, Y. C. ( 1993; ). Numerical classification of acidiphilic actinomycetes isolated from acid soil in Korea. Kor J Microbiol 31, 355–363.
    [Google Scholar]
  32. Shirling, E. B. & Gottlieb, D. ( 1966; ). Methods for characterization of Streptomyces species. Int J Syst Bacteriol 16, 313–340.[CrossRef]
    [Google Scholar]
  33. Van de Peer, Y. & de Wachter, R. ( 1994; ). treecon for windows: a software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment. Comput Appl Biosci 10, 569–570.
    [Google Scholar]
  34. Waksman, S. A. & Henrici, A. T. ( 1943; ). The nomenclature and classification of the actinomycetes. J Bacteriol 46, 337–341.
    [Google Scholar]
  35. Williams, S. T. & Khan, M. R. ( 1974; ). Antibiotics – a soil microbiologist's viewpoint. Postepy Hig Med Dosw 28, 395–408.
    [Google Scholar]
  36. Williams, S. T. & Robinson, C. S. ( 1981; ). The role of streptomycetes in decomposition of chitin in acidic soils. J Gen Microbiol 127, 55–63.
    [Google Scholar]
  37. Williams, S. T., Davies, F. L., Mayfield, C. I. & Khan, M. R. ( 1971; ). Studies on the ecology of actinomycetes in soil. II. The pH requirements of streptomycetes from two acid soils. Soil Biol Biochem 3, 187–195.[CrossRef]
    [Google Scholar]
  38. 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]
  39. 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, 176–178.
    [Google Scholar]
  40. Xu, C., Wang, L., Cui, Q., Huang, Y., Liu, Z., Zheng, G. & Goodfellow, M. ( 2006; ). Neutrotolerant acidophilic Streptomyces species isolated from acidic soils in China: Streptomyces guanduensis sp. nov., Streptomyces paucisporeus sp. nov., Streptomyces rubidus sp. nov. and Streptomyces yanglinensis sp. nov. Int J Syst Evol Microbiol 56, 1109–1115.[CrossRef]
    [Google Scholar]
  41. Zhang, J., Liu, Z. & Goodfellow, M. ( 2003; ). Nocardia cashijiensis 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.0.64165-0
Loading
/content/journal/ijsem/10.1099/ijs.0.64165-0
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