1887

Abstract

Comparisons of 5S ribosomal ribonucleic acid (rRNA) nucleotide sequences were used for the phylogenetic characterization of a number of “morphologically conspicuous” sulfide-oxidizing eubacteria and certain of their non-sulfide oxidizing counterparts. Nucleotide sequences were determined for 5S rRNAs isolated from sp., B18LD, JP2, strain 30 (a -like organism), B23SS, L1401-7, V. ATCC 15551, VT1, and (Stokes). All 5S rRNAs characterized in this study, except that of sp., belong to either the gamma or beta subdivisions of the “purple bacteria,” which form 1 of the 10 major eubacterial divisions so far defined by 16S rRNA oligonucleotide catalog analysis. Although its 5S rRNA is clearly eubacterial in character, sp. appears to have no specific relatives among the eubacteria presently represented in the 5S rRNA data collection.

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1987-04-01
2024-03-28
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References

  1. Dams E., Vandenberghe A., De Wachter R. 1983; Nucleotide sequences of the 5S rRNAs of Azotobacter vinelandii, Pseudomonas aeruginosa, and Pseudomonas fluorescens with some notes on 5S RNA secondary structure. Nucleic Acids Res. 11:1245–1252
    [Google Scholar]
  2. Delihas N., Andersen J. 1982; Generalized structures of the 5S ribosomal RNAs. Nucleic Acids Res. 10:7323–7344
    [Google Scholar]
  3. Donis-Keller H., Maxam A., Gilbert W. 1977; Mapping adenines, guanines, and pyrimidines in RNA. Nucleic Acids Res. 4:2527–2538
    [Google Scholar]
  4. Crombach W. H., Van Veen W. L., van der Vlies A. W., Bots W. C. 1974; DNA base composition of some sheathed bacteria. Antonie van Leeuwenhoek J. Microbiol. Serol 40:217–220
    [Google Scholar]
  5. Elwood H. J., Olsen G. J., Sogin M. L. 1985; The smallsubunit ribosomal RNA gene sequences from the hypotrichous ciliates Oxytricha nova and Stylonychia pustulata. Mol. Biol. Evol 2:399–410
    [Google Scholar]
  6. Erdmann V. A., Wolters J., Huysmans E., De Wachter R. 1. Collection of published 5S, 5.8S, and 4.5S ribosomal RNA sequences. Nucleic Acids Res 13:rl05–rl53
    [Google Scholar]
  7. Felbeck H., Childress J. J., Somero G. M. 1981; Calvin-Benson cycle and sulphide oxidation enzymes in animals from sulphide-rich habitats. Science 293:291–293
    [Google Scholar]
  8. Fitch W. M., Margoliash E. 1967; Construction of phylogenetic trees: a method based on mutational distances as estimated from cytochrome c sequences is of general applicability. Science 155:279–284
    [Google Scholar]
  9. Fox G. E., Stackebrandt E., Hespell R. B., Gibson J., Maniloff J., Dyer T. A., Wolfe R. S., Balch W. E., Tanner R. S., Magrum L. J., Zablen L. B., Blakemore R., Gupta R., Bonen L., Lewis B. J., Stahl D. A., Luehrsen K. R., Chen K. N., Woese C. R. 1980; The phylogeny of prokaryotes. Science 209:457–463
    [Google Scholar]
  10. Gude H., Strohl W. R., Larkin J. M. 1979; Mixotrophic and heterotrophic growth of Beggiatoa alba in continuous culture. Arch. Microbiol. 129:357–360
    [Google Scholar]
  11. Hassur S. M., Whitlock H. W. 1974; UV shadowing–a new and convenient method for the location of ultravioletabsorbing species in polyacrylamide gels. Anal. Biochem. 59:162–164
    [Google Scholar]
  12. Hori H., Osawa S. 1979; Evolutionary change in 5S RNA secondary structure and a phylogenetic tree of 54 5S rRNA species. Proc. Natl. Acad. Sci. USA 76:381–385
    [Google Scholar]
  13. Imhoff J. R., Triiper H. G., Pfennig N. 1984; Rearrangement of the species and genera of the phototrophic “purple nonsulfur bacteria.”. Int. J. Syst. Bacteriol. 34:340–343
    [Google Scholar]
  14. Jukes T. M., Cantor C. R. 1969 Evolution of protein molecules. 21–132 Munro H. N.ed Mammalian protein metabolism Academic Press, Inc.; New York:
    [Google Scholar]
  15. Kimura M., Ohta T. 1972; On the stoachastic model for estimation of mutational distance between homologous proteins. J. Mol. Evol. 2:87–90
    [Google Scholar]
  16. Kuenen J. G. 1975; Colourless sulfur bacteria and their role in the sulfur cycle. Plant Soil 43:49–76
    [Google Scholar]
  17. Lane D. J., Pace B., Olsen G. J., Stahl D. A., Sogin M. L., Pace N. R. 1985; Rapid determination of 16S ribosomal RNA sequences of phylogenetic analyses. Proc. Natl. Acad. Sci. USA 82:6955–6959
    [Google Scholar]
  18. Lane D. J., Stahl D. A., Olsen G. J., Heller D. J., Pace N. R. 1985; Phylogenetic analysis of the genera Thiobacillus and Thiomicrospira by 5S ribosomal RNA sequences. J. Bacteriol. 163:75–81
    [Google Scholar]
  19. la Riviere J. W. M., Schmidt K. 1981 Morphologically conspicuous sulfur-oxidizing eubacteria. 1037–1048 Starr M. P., Stolp H., Triiper H. G., Balows A., Schlegel H. G.ed The prokaryotes–a handbook on habitats, isolation, and identification of bacteria I Springer-Verlag; New York:
    [Google Scholar]
  20. Larkin J. M., Shinabarger D. L. 1983; Characterization of Thiothrix nivea. Int. J. Syst. Bacteriol. 33:841–846
    [Google Scholar]
  21. Larkin J. M., Strohl W. R. 1983; Beggiatoa, Thiothrix, and Thioploca. Annu. Rev. Microbiol. 37:341–367
    [Google Scholar]
  22. Leadbetter E. R. 1974 Order II. Cytophagales nomen novum. 99 Buchanan R. E., Gibbons N. E.ed Bergey’s manual of determinative bacteriology, 8th. The Williams and Wilkins Co.; Baltimore:
    [Google Scholar]
  23. Mulder E. G., Deinema M. H. 1981 The sheathed bacteria. 425–440 Starr M. P., Stolp H., Triiper H. G., Balows A., Schlegel H. G.ed The prokaryotes–a handbook on habitats, isolation, and identification of bacteria I Springer-Verlag; New York:
    [Google Scholar]
  24. Nelson D. C., Jannasch H. W. 1983; Chemoautotrophic growth of a marine Beggiatoa in sulfide-gradient cultures. Arch. Microbiol. 136:262–269
    [Google Scholar]
  25. Olsen G. J., Lane D. J., Giovannoni S. J., Pace N. R., Stahl D. A. 1986; Microbial ecology and evolution: a ribosomal RNA approach. Annu. Rev. Microbiol. 40:337–365
    [Google Scholar]
  26. Pace N. R., Stahl D. A., Lane D. J., Olsen G. J. 1986; The analysis of natural microbial populations by ribosomal RNA sequences. Adv. Microb. Ecol. 9:1–55
    [Google Scholar]
  27. Pate J. L., Chang L. E. 1979; Evidence that gliding motility in prokaryotic cells is driven by rotary assemblies in the cell envelopes. Curr. Microbiol. 2:59–64
    [Google Scholar]
  28. Peattie D. A. 1979; Direct chemical method for sequencing RNA. Proc. Natl. Acad. Sci. USA 76:1760–1764
    [Google Scholar]
  29. Pringsheim E. G. 1949; The relationship between bacteria and Myxophyceae. Bacteriol. Rev. 13:47–91
    [Google Scholar]
  30. Reichenbach H. 1981; Taxonomy of the gliding bacteria. Annu. Rev. Microbiol. 35:339–364
    [Google Scholar]
  31. Reichenbach H., Dworkin M. 1981 Introduction to the gliding bacteria. 315–327 Starr M. P., Stolp H., Triiper H. G., Balows A., Schlegel H. G.ed The prokaryotes– a handbook on habitats, isolation, and identification of bacteria I Springer-Verlag; New York:
    [Google Scholar]
  32. Stackebrandt E., Woese C. R. 1981 The evolution of prokaryotes. 1–31 Carlisle M. J., Collins J. R., Moseley B. E. B.ed Molecular and cellular aspects of microbial evolution Cambridge University Press; Cambridge:
    [Google Scholar]
  33. Stahl D. A., Lane D. J., Olsen G. J., Pace N. R. 1984; Analysis of hydrothermal vent-associated symbionts by ribosomal RNA sequences. Science 224:409–411
    [Google Scholar]
  34. Stahl D. A., Lane D. J., Olsen G. J., Pace N. R. 1985; Characterization of a Yellowstone hot spring microbial community by 5S ribosomal RNA sequences. Appl. Environ. Microbiol. 49:1379–1384
    [Google Scholar]
  35. Strohl W. R., Larkin J. M. 1978; Cell division and trichome breakage in beggiatoa. Curr. Microbiol. 1:151–155
    [Google Scholar]
  36. Strohl W. R., Schmidt T. M., Lawry N. H., Mezzino M. J., Larkin J. M. 1986; Characterization of Vitreoscilla beggiatoides and V.filiformis sp. nov., nom. rev., and comparison to V. stercoraria and Beggiatoa. Int. J. Syst. Bacteriol. 36:302–313
    [Google Scholar]
  37. Williams T. M., Unz R. F. 1985; Filamentous sulfur bacteria of activated sludge: characterization of Thiothrix, Beggiatoa, and Eikelboom type 021N strains. Appl. Environ. Microbiol. 49:887–898
    [Google Scholar]
  38. Wirsen C. O., Jannasch H. W. 1978; Physiological and morphological observations on Thiovulum sp. J. Bacteriol. 136:765–774
    [Google Scholar]
  39. Woese C. R. 1985 Why study evolutionary relationships among bacteria?. 1–30 Schleifer K. H., Stackebrandt E.ed Evolution of prokaryotes Academic Press, Inc.; New York:
    [Google Scholar]
  40. Woese C. R., Stackebrandt E., Macke T. J., Fox G. E. 1985; A phylogenetic definition of the major eubacterial taxa, syst. Appl. Microbiol. 6:143–151
    [Google Scholar]
  41. Woese C. R., Stackebrandt E., Weisburg W. G., Paster B. J., Madigan M. R., Fowler V. J., Hahn C. M., Blanz P., Gupta R., Nealson K. H., Fox G. E. 1984; The phylogeny of purple bacteria: the alpha subdivision. Syst. Appl. Microbiol. 5:315–326
    [Google Scholar]
  42. Woese C. R., Weisburg W., Hahn C. M., Paster B., Zablen L. B., Lewis B. J., Ludwig W., Stackebrandt E. 1984; The phylogeny of purple bacteria: the gamma subdivision. Syst. Appl. Microbiol. 6:25–33
    [Google Scholar]
  43. Woese C. R., Weisburg W. G., Paster B. J., Hahn C. M., Tanner R. S., Krieg N. R., Koops H. P., Harms H., Stackebrandt E. 1984; The phylogeny of purple bacteria: the beta subdivision. Syst. Appl. Microbiol. 5:327–336
    [Google Scholar]
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