1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 46, Issue 2

Analysis of Thermophilic Clades within the Genus by 16S Ribosomal DNA Sequence Comparisons Free

Abstract

Almost complete sequences of the 16S rRNA genes of eight representative thermophilic streptomycetes were determined following the isolation and cloning of the amplified genes. These sequences were aligned with those of representative mesophilic streptomycetes, and phylogenetic trees were inferred by using four tree-making algorithms. The thermophilic streptomycetes formed two distinct clades that were supported by high bootstrap values based on 1,000 resamplings. One clade encompassed and related species, and the second clade included and allied taxa. The relationships between the organisms were not markedly influenced by the different tree-making methods, but the rooting of the tree was sensitive to the choice of the outgroup strain. It is evident from this study that the thermophilic streptomycetes do not merit recognition as a distinct taxon within the genus

  • Published Online:
Copyright © 1996 International Union of Microbiological Societies
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/00207713-46-2-581
1996-04-01
2024-04-23
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/46/2/ijs-46-2-581.html?itemId=/content/journal/ijsem/10.1099/00207713-46-2-581&mimeType=html&fmt=ahah

References

  1. Agre N. S. 1983 Genera Streptomyces, Streptoverticillium, and Chainia,. 52–71 Gause T. F., Preobrazhenskaya T. P., Sveshnikova M. A., Terekhova L. P., Maksimova T. S.ed A guide for the determination of actinomycetes Nauka; Moscow: In Russian
    [Google Scholar]
  2. Bergey D. H., Harrison F. C., Breed R. S., Hammer B. W., Huntoon F. M. 1923 Bergey’s manual of determinative bacteriology, 1st ed The Williams and Wilkins Co.; Baltimore:
     [Google Scholar]
  3. Brosius J., Palmer M. L., Kennedy P. J., Noller H. F. 1978; Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli. Proc. Natl. Acad. Sci. USA 75:4801–4805
     [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
     [Google Scholar]
  5. Corbaz R., Gregory P. H., Lacey M. E. 1963; Thermophilic and mesophilic actinomycetes in mouldy hay. J. Gen. Microbiol 32:449–456
     [Google Scholar]
  6. Craveri R., Pagani H. 1962; Thermophilic micro-organisms among actinomycetes in the soil. Ann. Microbiol 12:115–130
     [Google Scholar]
  7. Desai A. J., Dhala S. A. 1967; Streptomyces thermonitnficans sp. n., a thermophilic streptomycete. Antonie Leeuwenhoek 33:137–144
     [Google Scholar]
  8. Felsenstein J. 1981; Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol 17:368–376
     [Google Scholar]
  9. Felsenstein J. 1985; Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791
     [Google Scholar]
  10. Felsenstein J. 1993 PHYLIP (phylogenetic inference package), version 3.5c Department of Genetics; University of Washington, Seattle:
     [Google Scholar]
  11. 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
     [Google Scholar]
  12. Goodfellow M., Lacey J., Todd C. 1987; Numerical classification of thermophilic streptomycetes. J. Gen. Microbiol 133:3135–3149
     [Google Scholar]
  13. Henssen A. 1957; Uber die Bedeutung der thermophilen Mikroorganismen fiir der Zersetzung des Stallmistes. Arch. Mikrobiol 27:63–81
     [Google Scholar]
  14. Huelsenbeck J. P., Hillis D. M. 1993; Success of phylogenetic methods in the four-taxon case. Syst. Biol 42:247–264
     [Google Scholar]
  15. 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]
  16. Jukes T. H., Cantor C. R. 1969 Evolution of protein molecules. 21–132 Munro H. N.ed Mammalian protein metabolism Academic Press; New York:
     [Google Scholar]
  17. Kim E., Kim H., Kang K. H., Kho Y. H., Park Y. H. 1991; Complete nucleotide sequence of a 16S ribosomal RNA gene from Streptomyces griseus subsp. griseus. Nucleic Acids Res 19:1149
     [Google Scholar]
  18. Kim J. 1993; Improving the accuracy of phylogenetic estimation by combining different methods. Syst. BioL 42:331–340
     [Google Scholar]
  19. Kluge A. G., Farris F. S. 1969; Quantitative phyletics and the evolution of anurans. Syst. Zool 18:1–32
     [Google Scholar]
  20. Krassilnikov N. A., Agre N. S., Dorokhova L. A., Sokolov A. A. 1968; Three new species of thermophilic actinomycetes. Mikrobiologiya 37:75–83 In Russian.
    [Google Scholar]
  21. Kiister E., Locci R. 1963; Studies on peat and peat micro-organisms. I. Taxonomic studies on thermophilic actinomycetes isolated from peat. Arch. Mikrobiol 45:188–197
     [Google Scholar]
  22. Lane D. J. 1991 16S/23S rRNA sequencing. 115–175 Stackebrandt E., Goodfellow M.ed Nucleic acid techniques in bacterial systematics John Wiley and Sons; Chichester, United Kingdom:
     [Google Scholar]
  23. Li W. H., Gouy M. 1990; Statistical tests of molecular phylogenies. Methods Enzymol 183:645–659
     [Google Scholar]
  24. Maidak B. L., Larsen N., McCaughey M. J., Overbeek R., Olsen G. J., Fogel K., Blandy J., Woese C. R. 1994; The Ribosomal Database Project. Nucleic Acids Res 22:3485–3487
     [Google Scholar]
  25. Mehling A., Wehmeier U., Piepersberg W. Unpublished data
  26. Nakagaito Y., Shimazu A., Yokota A., Hasegawa T. 1992; Proposal of Streptomyces atroaurantiacus sp. nov. and Streptomyces kifunensis sp. nov. and transferring Kitasatosporia cystarginea Kusakabe and Isono to the genus Streptomyces as Streptomyces cystargineus comb. nov. J. Gen. Appl. Microbiol 38:627–633
     [Google Scholar]
  27. Ochi K. 1995; A taxonomic study of the genus Streptomyces by analysis of ribosomal protein AT-L30. Int. J. Syst. Bacteriol 45:507–514
     [Google Scholar]
  28. Ochi K., Hiranuma H. 1994; A taxonomic review of the genera Kitasatosporia and Streptoverticillium by analysis of ribosomal protein AT-L30. Int. J. Syst. Bacteriol 44:285–292
     [Google Scholar]
  29. Olsen G. J., Matsuda H., Hagstrom R., Overbeek R. 1994; FastDNAml: a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood. Comput. Appl. Biol. Sci 10:41–48
     [Google Scholar]
  30. Omura S., Takahashi Y., Iwai Y., Tanaka H. 1982; Kitasatosporia, a new genus of the order Actinomycetales. J. Antibiot 35:1013–1019
     [Google Scholar]
  31. Pernodet J. L., Boccard F., Alegre M. T., Gagnat J., Guerineau M. 1989; Organization and nucleotide sequence analysis of a ribosomal RNA gene cluster from Streptomyces ambofaciens. Gene 79:33–46
     [Google Scholar]
  32. Pitcher D. G., Saunders N. A., Owen R. J. 1989; Rapid extraction of bacterial genomic DNA with guanidium thiocyanate. Lett. Appl. Microbiol 8:151–156
     [Google Scholar]
  33. Pridham T. G., Tresner H. D. 1974 Family VIL Streptomycetaceae Waksman and Henrici 1943, 339. 747–748 Buchanan R. E., Gibbons N. E.ed Bergey’s manual of determinative bacteriology, 8th. Williams and Wilkins; Baltimore:
     [Google Scholar]
  34. Saitou N., Nei M. 1987; The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol 4:406–425
     [Google Scholar]
  35. Sambrook J., Fritsch E. F., Maniatis T. 1989 Molecular cloning: a laboratoiy manual, 2nd. Cold Spring Harbor Laboratory Press; Cold Spring Harbor, N.Y:
     [Google Scholar]
  36. Stackebrandt E., Goebel B. M. 1994; A place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int. J. Syst. Bacterio1 44:846–849
     [Google Scholar]
  37. Stackebrandt E., Liesack W., Witt D. 1992; Ribosomal RNA and rDNA sequence analyses. Gene 115:255–260
     [Google Scholar]
  38. Stackebrandt E., Witt D., Kemmerling C., Kroppenstedt R. M., Liesack W. 1991; Designation of streptomycete 16S and 23S rRNA-based target regions of oligonucleotide probes. Appl. Environ. Microbiol 57:1468–1477
     [Google Scholar]
  39. Swofford D. L., Olsen G. J. 1990 Phylogenetic reconstruction. 411–501 Hillis D., Moritz C.ed Molecular systematics Sinauer Associates; Sunderland, Mass:
     [Google Scholar]
  40. Van Wezel G. P., Vijgenboom E., Bosch L. 1991; A comparative study of the ribosomal RNA operons of Streptomyces coelicolor A3(2) and sequence analysis of rmA. Nucleic Acids Res 19:4399–4403
     [Google Scholar]
  41. Waksman S. A., Lechevalier H. A.ed 1953 Guide to the classification and identification of the actinomycetes and their antibiotics The Williams and Wilkins Co.; Baltimore:
     [Google Scholar]
  42. Waksman S. A., Curtis R. E. 1916; The actinomycetes of the soil. Soil Sci 1:99–134
     [Google Scholar]
  43. Waksman S. A., Henrici A. T. 1943; The nomenclature and classification of the actinomycetes. J. Bacteriol 46:337–341
     [Google Scholar]
  44. Waksman S. A., Henrici A. T. 1948 Family III Streptomycetaceae Waksman and Henrici. 929–980 Breed R. S., Murray E. G. D., Hitchens P.ed Bergey’s manual of determinative bacteriology, 6th. The Williams and Wilkins Co.; Baltimore:
     [Google Scholar]
  45. Waksman S. A., Umbreit W. W., Cordon T. C. 1939; Thermophilic actinomycetes and fungi in soils and in corn posts. Soil Sci 47:37–61
     [Google Scholar]
  46. Wellington E. M. H., Stackebrandt E., Sanders D., Wolstrup J., Jorgensen N. O. G. 1992; Taxonomic status of Kitasatosporia and proposed unification with Streptomyces on the basis of phenotypic and 16S rRNA analysis and emendation of Streptomyces Waksman and Henrici 1943, 339AL Int. J. Syst. Bacteriol 42:156–160
     [Google Scholar]
  47. Williams S. T., Goodfellow M., Alderson G. 1989 Genus Streptomyces Waksman and Henrici 1943, 339AL. 2452–2492 Williams S. T., Sharpe M. E., Holt J. G.ed Bergey’s manual of systematic bacteriology 4 Williams and Wilkins; Baltimore:
     [Google Scholar]
  48. 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]
  49. Witt D., Stackebrandt E. 1990; Unification of the genera Streptoverticillium and Streptomyces, and amendation of Streptomyces Waksman and Henrici 1943, 339AL. Syst. Appl. Microbiol 13:361–371
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/00207713-46-2-581
Loading
Analysis of Thermophilic Clades within the Genus Streptomyces by 16S Ribosomal DNA Sequence Comparisons
Int J Syst Evol Microbiol 46, 581 (1996); https://doi.org/10.1099/00207713-46-2-581
/content/journal/ijsem/10.1099/00207713-46-2-581
/content/journal/ijsem/10.1099/00207713-46-2-581
Loading

Data & Media loading...

Most cited 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