1887

Abstract

Four moderately thermophilic, carboxydotrophic streptomycetes were the subject of a comparative taxonomic investigation designed to establish their taxonomic relationships. Almost complete sequences of the 16S rRNA genes of the test strains were determined following the isolation and direct sequencing of the amplified genes. The resultant nucleotide sequences were aligned with the sequences of previously studied streptomycetes, and phylogenetic trees generated by using the neighbour-joining, Fitch-Margoliash, maximum-likelihood and maximum-parsimony methods. It was evident from the phylogenetic analyses that strains AT50, AT51 and AT52 were most closely related to DSM 40573 and strain AT37 to DSM 40716 and NRRL 3985. Random DNA amplification profiles clearly distinguished strains AT50, AT51 and AT52 from and from strain AT37. The molecular systematic evidence, together with phenotypic data derived from this and previous studies, indicate that the test strains merit species status within the genus . The name sp. nov. is proposed for strains AT50, AT51 and AT52 (type strain) and sp. nov. for strain AT37.

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1998-01-01
2024-11-14
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References

  1. Bell J. M., Falconer C., Colby J., Williams E. 1987; CO metabolism by a thermophilic actinomycete, Streptomyces strain G26. J Gen Microbiol 133:3445–3456
    [Google Scholar]
  2. Bell J. M., Colby J., Williams E. 1988; CO oxidoreductase from Streptomyces strain G26 is a molybdenum hydroxylase. Biochem J 250:605–612
    [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. 1995 Computer-assisted classification and identification of actinomycetes. PhD thesis, University of Newcastle upon Tyne;
    [Google Scholar]
  5. 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]
  6. Craveri R., Pagani H. 1962; Thermophilic micro-organisms among actinomycetes in the soil. Ann Microbiol 12:115–130
    [Google Scholar]
  7. Falconer C. 1988 The isolation, physiology and taxonomy of carboxydotrophic actinomycetes. PhD thesis, University of Newcastle upon Tyne;
    [Google Scholar]
  8. Felsenstein J. 1993 phylip (Phylogeny Inference Package) version 3.5.1. Department of Genetics University of Washington; Seattle, USA:
    [Google Scholar]
  9. 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]
  10. Gadkari D., Schricker K., Acker G., Kroppenstedt R. M., Meyer O. 1990; Streptomyces thermoautotrophicus sp. nov., a thermophilic CO- and H2-oxidizing obligate chemo- lithotroph. Appl Environ Microbiol 56:3727–3734
    [Google Scholar]
  11. Gadkari D., Mörsdorf G., Meyer O. 1992; Chemo- lithoautotrophic assimilation of dinitrogen by Streptomyces thermoautotrophicus UBT1: identification of an unusual N2-fixing system. J Bacteriol 174:6840–6843
    [Google Scholar]
  12. Gerke C. W., McCune R. A., Gama-Sosa M. A., Ehrlich M., Kuo K. C. 1984; Quantitative reversed-phase high-performance liquid chromatography of major and modified nucleosides in DNA. J Chromatogr 301:199–219
    [Google Scholar]
  13. Goodfellow M., Lacey J., Todd C. 1987; Numerical classification of thermophilic streptomycetes. J Gen Micro-biol 133:3135–3149
    [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 J. 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. In Mammalian Protein Metabolism 321–132 Munro H. N. New York: Academic Press;
    [Google Scholar]
  17. Kim J. 1993; Improving the accuracy of phylogenetic estimation by combining different methods. Syst Biol 42:331–340
    [Google Scholar]
  18. 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]
  19. Kim D., Chun J., Sahin N., Hah Y. C., Goodfellow M. 1996; Analysis of thermophilic clades within the genus Streptomyces by 16S ribosomal DNA sequence comparisons. Int J Syst Bacteriol 46:581–587
    [Google Scholar]
  20. Kluge A. G., Farris F. S. 1969; Quantitative phyletics and the evolution of anurans. Syst Zool 18:1–32
    [Google Scholar]
  21. Labeda D. P. 1988; Kitasatosporia mediocidica sp. nov. Int J Syst Bacteriol 38:287–290
    [Google Scholar]
  22. Labeda D. P. 1993; DNA relatedness among strains of the Streptomyces lavendulae phenotypic cluster group. Int J Syst Bacteriol 43:822–825
    [Google Scholar]
  23. Labeda D. P. 1996; DNA relatedness among verticilforming Streptomyces species (formerly Streptoverticillium species). Int J Syst Bacteriol 46:699–703
    [Google Scholar]
  24. Labeda D. P., Lyons A. J. 1991; The Streptomyces violaceusniger cluster is heterogeneous in DNA relatedness among strains: emendation of the descriptions of S. violaceusniger and Streptomyces hygroscopicus. Int J Syst Bacteriol 41:398–401
    [Google Scholar]
  25. Labeda D. P., Lyons A. J. 1991; Deoxyribonucleic acid relatedness among species of the Streptomyces cyaneus cluster. Syst Appl Microbiol 14:158–164
    [Google Scholar]
  26. Li W. H., Gouy M. 1990; Statistical tests of molecular phylogenies. Methods Enzymol 183:645–659
    [Google Scholar]
  27. Maidak B. L., Olsen G. J., Larsen N., Overbeek R., McCaughey M. J., Woese C. R. 1996; The Ribosomal Database Project (RDP). Nucleic Acids Res 24:82–85
    [Google Scholar]
  28. Manfio G. P., Zakrzewska-Czerwinska J., Atalan E., Goodfellow M. 1995; Towards minimal standards for the description of Streptomyces species. Biotekhnologia 7-8:242–253
    [Google Scholar]
  29. Mehling A., Wehmeier U. F., Piepersberg W. 1995; Nucleotide sequences of streptomycete 16S ribosomal DNA: towards a specific identification system for streptomycetes using PCR. Microbiology 141:2139–2147
    [Google Scholar]
  30. Mehling A., Wehmeier U. F., Piepersberg W. 1995; Application of random amplified polymorphic DNA (RAPD) assays in identifying conserved regions of actino- mycete genomes. FEMS Microbiol Lett 128:119–125
    [Google Scholar]
  31. 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
    [Google Scholar]
  32. O'Donnell A. G., Falconer C., Goodfellow M., Ward A. C., Williams E. 1993; Biosystematics and diversity amongst novel carboxydotrophic actinomycetes. Antonie Leeuwenhoek 64:325–340
    [Google Scholar]
  33. 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]
  34. 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]
  35. Saitou N., Nei M. 1987; The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425
    [Google Scholar]
  36. Sambrook J., Fritsch E. F., Maniatis T. 1989 Molecular Cloning: a Laboratory Manual. , 2. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory;
  37. Shirling E. B., Gottlieb D. 1966; Methods for characterization of Streptomyces species. Int J Syst Bacteriol 16:313–340
    [Google Scholar]
  38. Shirling E. B., Gottlieb D. 1968; Cooperative description of type cultures of Streptomyces. II. Species descriptions from first studies. Int J Syst Bacteriol 18:69–189
    [Google Scholar]
  39. Shirling E. B., Gottlieb D. 1968; Cooperative description of type cultures of Streptomyces. III. Additional species descriptions from first and second studies. Int J Syst Bacteriol 18:279–392
    [Google Scholar]
  40. Shirling E. B., Gottlieb D. 1969; Cooperative description of type cultures of Streptomyces. IV. Species descriptions from the second, third and fourth studies. Int J Syst Bacteriol 19:391–512
    [Google Scholar]
  41. Shirling E. B., Gottlieb D. 1969; Cooperative description of type cultures of Streptomyces. V. Additional descriptions. Int J Syst Bacteriol 22:265–394
    [Google Scholar]
  42. 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]
  43. Stackebrandt E., Liesack W., Witt D. 1992; Ribosomal RNA and rRNA sequence analysis. Gene 115:255–260
    [Google Scholar]
  44. Swofford D. L., Olsen G. J. 1990 Phylogenetic reconstruction. In Molecular Systematics411–501 Hillis D., Moritz C. Sunderland, MA: Sinauer Associates;
    [Google Scholar]
  45. Takeuchi T., Sawada H., Tanaka F., Matsuda I. 1996; Phylogenetic analysis of Streptomyces spp. causing potato scab based on 16S rRNA sequences. Int Syst Bacterial 46:476–479
    [Google Scholar]
  46. Tamaoka J. 1994 Determination of DNA base composition. In Chemical Methods in Prokaryotic Systematics463–470 Goodfellow M., O’Donnell A. G. Chichester: Wiley;
    [Google Scholar]
  47. Trujillo M. E., Goodfellow M. 1997; Polyphasic taxonomic study of clinically significant actinomadurae including the description of Actinomadura latina sp. nov. Zentralbl Bakteriol 285:212–233
    [Google Scholar]
  48. 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 rRNA. Nucleic Acids Res 19:4399–4403
    [Google Scholar]
  49. 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]
  50. Williams S. T., Goodfellow M., Alderson G. 1989 Genus Streptomyces Waksman and Henrici 1943, 339AL. In Bergey's Manual of Systematic Bacteriology 42452–2492 Williams S. T., Sharpe M. E., Holt J. G. Baltimore: Williams & Wilkins;
    [Google Scholar]
  51. Wayne L. G., Brenner D. J., Colwell R. R., Grimont P. A. D., Kandler O., Krichevsky M. I., Moore L. H., Moore W. E. C., Murray R. G. E., Stackebrandt E., Starr M. P., Trüper H. G. 1987; Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463–464
    [Google Scholar]
  52. 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]
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