1887

Abstract

The sequences of the 16S rRNA genes of 20 isolates were determined to a high fidelity by using automated DNA sequencing and fluorescent-dye-labelled primers. The strains tested included members of the three validly named species and representatives of major taxonomic clusters defined previously for this genus. The parsimony method was used to reconstruct the phylogeny of the strains from the aligned sequences, and a bootstrap analysis revealed a number of well-supported clades. Our results are not consistent with groupings inferred from numerical taxonomy data but support the conjecture that the genus contains more species than the three currently recognized species.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/00207713-43-4-754
1993-10-01
2024-04-17
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/43/4/ijs-43-4-754.html?itemId=/content/journal/ijsem/10.1099/00207713-43-4-754&mimeType=html&fmt=ahah

References

  1. Achenbach-Richter L., Gupta R., Stetter K. O., Woese C. R. 1987; Were the original eubacteria thermophiles?. Syst. Appl. Microbiol 9:34–39
    [Google Scholar]
  2. Applied Biosystems 1988; DNA synthesizer user bulletin 49. Applied Biosystems Foster City, Calif.
    [Google Scholar]
  3. Bateson M. M., Thibault K. J., Ward D. M. 1990; Comparative analysis of 16S ribosomal RNA sequences of Thermus species. Syst. Appl. Microbiol. 13:8–13
    [Google Scholar]
  4. Borges K. M., Bergquist P. L. 1993; Genomic restriction map of the extremely thermophilic bacterium Thermus thermo-philus HB8. J. Bacteriol. 175:103–110
    [Google Scholar]
  5. Brock T. D., Freeze H. 1969; Thermus aquaticus gen. n. and sp. n., a non-sporulating extreme thermophile. J. Bacteriol. 98:289–297
    [Google Scholar]
  6. Clark A. G., Whittam T. S. 1992; Sequencing errors and molecular evolution analysis. Mol. Biol. Evol. 4:744–752
    [Google Scholar]
  7. Degryse E., Glansdorff N., Pierard A. 1978; A comparative analysis of extreme thermophilic bacteria belonging to the genus Thermus. Arch. Microbiol. 117:189–196
    [Google Scholar]
  8. DeLong E. F., Wickham G. S., Pace N. R. 1989; Phylogenetic stains: ribosomal RNA-based probes for the identification of single cells. Science 243:1360–1362
    [Google Scholar]
  9. Devereux J., Haeberli P., Smithies O. 1990; A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res. 12:387–395
    [Google Scholar]
  10. Donato M. M., Seleiro E. A., Da Costa M. S. 1990; Polar lipid and fatty acid composition of strains of the genus Thermus. Syst. Appl. Microbiol. 13:234–239
    [Google Scholar]
  11. Ehresmann C., Stiegler P., Fellner P., Ebel J.-P. 1972; The determination of the primary structure of the 16S ribosomal RNA of Escherichia coli. II. Nucleotide sequences of products from partial enzymatic hydrolysis. Biochimie 54:901–967
    [Google Scholar]
  12. Felsenstein J. 1985; Confidence limits on phylogeny and approach using the bootstrap. Evolution 39:783–791
    [Google Scholar]
  13. Felsenstein J. 1989; PHYLIP—phylogeny inference package (version 3.2). Cladistics 5:164–166
    [Google Scholar]
  14. Feng D.-F., Doolittle R. F. 1987; Progressive sequence alignment as a prerequisite to correct phylogenetic trees. J. Mol. Evol. 25:351–360
    [Google Scholar]
  15. Garnier T., Canard B., Cole S. T. 1991; Cloning, mapping, and molecular characterization of the rRNA operons of Clostridium. J. Bacteriol. 173:5431–5438
    [Google Scholar]
  16. Green C. J., Stewart G. C., Hollis M. A., Void B. S., Bott K. F. 1985; Nucleotide sequence of the Bacillus subtilis ribosomal RNA operon, rmB. Gene 37:261–266
    [Google Scholar]
  17. Hartmann R. K., Wolters J., Kroeger B., Schultz S., Specht T., Erdmann V. A. 1989; Does Thermus represent another deep eubacterial branching?. Syst. Appl. Microbiol. 11:243–249
    [Google Scholar]
  18. Hensel R., Dernharter W., Kandler O., Kroppenstedt R. M., Stackebrandt E. 1986; Chemotaxonomic and molecular-genetic studies of the genus Thermus: evidence for a phylogenetic relationship of Thermus aquaticus and Thermus ruber to the genus Deinococcus. Int. J. Syst. Bacteriol. 36:444–453
    [Google Scholar]
  19. Hudson J. A. 1986; The taxonomy and ecology of the genus Thermus. Ph.D. thesis. University of Waikato, Hamilton, New Zealand
    [Google Scholar]
  20. Hudson J. A., Morgan H. W., Daniel R. M. 1986; A numerical classification of some Thermus isolates. J. Gen. Microbiol. 132:531–540
    [Google Scholar]
  21. Hudson J. A., Morgan H. W., Daniel R. M. 1987; Thermus filiformis sp. nov., a filamentous caldoactive bacterium. Int. J. Syst. Bacteriol. 37:431–436
    [Google Scholar]
  22. Hudson J. A., Morgan H. W., Daniel R. M. 1989; Numerical classification of Thermus isolates from globally distributed hot springs. Syst. Appl. Microbiol. 11:250–256
    [Google Scholar]
  23. Janssen P. H., Parker L. E., Morgan H. W. 1991; Filament formation in Thermus species in the presence of some D-amino acids or glycine. Antonie van Leeuwenhoek 59:147–154
    [Google Scholar]
  24. Jones C. J., Morgan H. W., Daniel R. M. 1988; Aspects of protease production by a Thermus strain OK6 and other NZ isolates. J. Gen. Microbiol. 134:191–198
    [Google Scholar]
  25. Koyama Y., Hoshino T., Tomizuka N., Furukawa K. 1986; Genetic transformation of the extreme thermophile Thermus thermophilus and other Thermus spp. J. Bacteriol. 166:338–340
    [Google Scholar]
  26. Kumano M., Tomioka N., Shinozaki K., Sugiura M. 1986; Analysis of the promoter region in the rmA operon from a blue-green alga, Anacystis nidulans 6301. Mol. Gen. Genet. 202:173–178
    [Google Scholar]
  27. Loginova L. G., Egorova L. A. 1975; An obligately thermophilic bacterium Thermus ruber from Hot Springs in Kamchatka. Mikrobiologiya 44:661–665
    [Google Scholar]
  28. Maniatis T., Fritsch E. F., Sambrook J. 1982 Molecular cloning: a laboratoiy manual Cold Spring Harbor Laboratory; Cold Spring Harbor, N.Y.:
    [Google Scholar]
  29. Messing J. 1983; New M13 vectors for cloning. Methods Enzymol. 101:20–78
    [Google Scholar]
  30. Murzina N., Vorozheikina P., Matvienko N. 1988; Nucleotide sequence of Thermus thermophilus HB8 gene coding 16S rRNA. Nucleic Acids Res. 16:81–72
    [Google Scholar]
  31. Oshima T., Imahori K. 1974; Description of Thermus thermophilus (Yoshima and Oshima) comb, nov., a nonsporu- lating thermophilic bacterium from a Japanese thermal spa. Int. J. Syst Bacteriol. 24:104–112
    [Google Scholar]
  32. Pamilo P., Nei M. 1988; Relationship between gene trees and species trees. Mol. Biol. Evol. 5:568–583
    [Google Scholar]
  33. Peek K., Janssen P. H., Morgan H. W., Daniel R. M. 1990; Enhancement of in vitro stability and recovery of a proteinase produced by an extreme thermophile. p. 97–102 In Yu P.-L. (ed.) Fermentation technologies—industrial applications Elsever Applied Science; London:
    [Google Scholar]
  34. Rodrigo A. G. Calculating the bootstrap test of monophyly. Int. J. Parasitol. in press
    [Google Scholar]
  35. Rodrigo A. G., Kelly-Borges M., Bergquist P. R., Bergquist P. L. A randomization test of the null hypothesis that two cladograms are sample estimates of a parametric phylogenetic trees. N. Z. J. Bot. in press
    [Google Scholar]
  36. Saiki T., Kimura R., Arima K. 1972; Isolation and characterization of extremely thermophilic bacteria from hot springs. Agric. Biol. Chem. 34:2357–2366
    [Google Scholar]
  37. Saito H., Miura K. 1963; Preparation of transforming deoxyribonucleic acid by phenol treatment. Biochim. Biophys. Acta 72:619–629
    [Google Scholar]
  38. Saitou N., Nei M. 1987; The neighbour joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406–425
    [Google Scholar]
  39. Sanderson M. J. 1989; Confidence limits on phylogenetics: the bootstrap revisited. Cladistics 5:113–129
    [Google Scholar]
  40. Santos M. A., Williams R. A. D., DaCosta M. S. 1989; Numerical taxonomy of Thermus isolates from hot springs in Portugal. Syst. Appl. Microbiol. 12:310–315
    [Google Scholar]
  41. Saravani G. A. 1985; Caldolase: an alkaline serine protease from Thermus strain Tok3. Ph.D. thesis. University of Waikato, Hamilton, New Zealand
    [Google Scholar]
  42. Sharp R. J., Williams R. A. D. 1988; Properties of Thermus ruber strains isolated from Icelandic hot springs and DNA:DNA homology of Thermus ruber and Thermus aquati-cus. Appl. Environ. Microbiol. 54:2049–2053
    [Google Scholar]
  43. Stahl D. A., Amann R. 1991; Development and application of nucleic acid probes. p. 205–248 In Stackebrandt E., Goodfellow M. (ed.) Nucleic acid techniques in bacterial systematics John Wiley & Sons, Ltd.; Chichester, United Kingdom:
    [Google Scholar]
  44. Swofford D. L. 1990; PAUP: phylogenetic analysis using parsimony, version 3.0. Complete program and manual. Illinois Natural History Survey, Champaign.
    [Google Scholar]
  45. Swofford D. L., Olsen G. J. 1990; Phylogeny reconstruction. p. 411–501 In Hills D. M., Moritz C. (ed.) Molecular systematics Sinauer Associates, Inc.; Sunderland, Mass.:
    [Google Scholar]
  46. Weisberg W. G., Giovannoni S. J., Woese C. R. 1989; The Deinococcus-Thermus phylum and the effect of rRNA composition on phylogenetic tree construction. Syst. Appl. Microbiol. 11:128–134
    [Google Scholar]
  47. Wiley E. O. 1981 Phylogenetics: the theory and practice of phylogenetic systematics Wiley Interscience; New York:
    [Google Scholar]
  48. Williams R. A. D. 1989; Biochemical taxonomy of the genus Thermus. p. 82–97 In DaCosta M. S., Duarte J. C., Williams R. A. D. (ed.) Microbiology of extreme environments and its potential for biotechnology Elsevier Applied Science; London:
    [Google Scholar]
  49. Williams R. A. D., De Costa M. S. 1991; The genus Thermus and related organisms. p. 3732–3744 In Balows A., Triiper H. G., Dworkin M., Harder W., Schleifer K.-H. (ed.) The prokaryotes, 2nd ed. Springer-Verlag; Berlin:
    [Google Scholar]
  50. Yanisch-Perron C., Vieira J., Messing J. 1985; Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mpl8 and pUC19 vectors. Gene 33:103–119
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/00207713-43-4-754
Loading
/content/journal/ijsem/10.1099/00207713-43-4-754
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