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The Analysis of Natural Microbial Populations by Ribosomal RNA Sequences

  • Norman R. Pace
  • David A. Stahl
  • David J. Lane
  • Gary J. Olsen
Part of the Advances in Microbial Ecology book series (AMIE, volume 9)

Abstract

Recombinant DNA methodology and rapid nucleotide sequence determinations have changed the face of cell biology in the past few years. This technology offers powerful new tools to the microbial ecologist as well. In this chapter we describe technical strategies we are developing which use these methods to analyze phylogenetic and quantitative aspects of mixed, naturally occurring microbial populations.

Keywords

Microbial Population rRNA Sequence Sequence Position Recombinant Phage Translation Apparatus 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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References

  1. Biggin, M. D., Gibson, T. J., and Hong, G. F., 1983, Buffer gradient gels and 35S label as an aid to rapid DNA sequence determination, Proc. Natl. Acad. Sci. USA 80: 3963–3965.PubMedCrossRefGoogle Scholar
  2. Brierley, C. L., 1982, Microbiological mining, Sci. Am. 2: 44–53.CrossRefGoogle Scholar
  3. Brock, T. D., 1978, Thermophilic Microorganisms and Life at High Temperatures, Springer-Verlag, New York.CrossRefGoogle Scholar
  4. Brosius, J., Palmer, M. L., Kennedy, R. J., and Noller, H. F., 1978, Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli, Proc. Natl. Acad. Sci. USA 75: 4801–4805.PubMedCrossRefGoogle Scholar
  5. Brosius, J., Dull, T. J., and Noller, H. F., 1980, Complete nucleotide sequence of a 23S ribosomal RNA gene from Escherichia coli, Proc. Natl. Acad. Sci. USA 77: 201–204.Google Scholar
  6. Cavanaugh, C. M., 1983, Symbiotic chemoautotrophic bacteria in marine invertebrates from sulfide-rich habitats, Nature 302: 58–61.CrossRefGoogle Scholar
  7. Cavanaugh, C. M., Gardiner, S., Jones, M. L., Jannasch, H. W., and Waterbury, J. B., 1981, Prokaryotic cells in the hydrothermal vent tubeworm Riftia pachyptila Jones: Possible chemoautotrophic symbionts, Science 213: 340–342.PubMedCrossRefGoogle Scholar
  8. Cedergren, R. J., LaRue, B., Sankoff, D., and Grosjean, H., 1981, The evolving tRNA molecule, Crit. Rev. Biochem. 11: 35–104.CrossRefGoogle Scholar
  9. Chambliss, G., Craven, G. R., Davies, J., Davis, K., Kahan, L., and Nomura, M. (eds.), 1980, Ribosomes: Structure, Function, and Genetics, University Park Press, Baltimore.Google Scholar
  10. Delihas, N., and Andersen, J. 1982, Generalized structures of the 5S ribosomal RNAs, Nucleic Acids Res. 10: 7323–7344.PubMedCrossRefGoogle Scholar
  11. Demoulin, V., 1979, Protein and nucleic acid sequence data and phylogeny, Science 205: 1036–1039.PubMedCrossRefGoogle Scholar
  12. Donis-Keller, H., Maxam, A., and Gilbert, W., 1977, Mapping adenines, guanines, and pyrimidines in RNA, Nucleic Acids Res. 4: 2527–2538.PubMedCrossRefGoogle Scholar
  13. Doolittle, W. F., 1973, Postmaturational cleavage of 23S ribosomal ribonucleic acid and its metabolic control in the blue-green alga Anacystis nidulans, J. Bacteriol. 113: 1256 1263.Google Scholar
  14. Edmond, J. M., and Von Damm, K., 1983, Hot springs on the ocean floor, Sci. Am. 248: 78–93.CrossRefGoogle Scholar
  15. Enquist, L., and Sternberg, N., 1979, In vitro packaging of A Dam vectors and their use in cloning DNA fragments, in Methods in Enzymology, Vol. 68 (R. Wu, ed.), pp. 281–298, Academic Press, New York.Google Scholar
  16. Erdmann, V A., Wolters, J., Huysmans, E., Vandenberghe, A., and De Wachter, R., 1984, Collection of published 5S and 5.8S ribosomal RNA sequences, Nucleic Acids Res. 12: r133 - r166.PubMedCrossRefGoogle Scholar
  17. Felbeck, H., Childress, J. J., and Somero, G. N., 1981, Calvin-Benson cycle and sulfide oxidation enzymes in animals from sulfide-rich habitats, Nature 293: 291–293.CrossRefGoogle Scholar
  18. Felsenstein, J., 1982, Numerical methods for inferring evolutionary trees, Q. Rev. Biol. 57: 379–404.CrossRefGoogle Scholar
  19. Fitch, W. M., 1976, The molecular evolution of cytochrome c in eukaryotes, J. Mol. Evol. 8: 13–40.PubMedCrossRefGoogle Scholar
  20. Fitch, W. M., and 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.PubMedCrossRefGoogle Scholar
  21. Fitch, W. M., and Smith, T. F., 1983, Optimal sequence alignments, Proc. Natl. Acad. Sci. USA 80: 1382–1386.PubMedCrossRefGoogle Scholar
  22. Fox, G. E., Stackebrandt, E., Hespell, R. B., Gibson, J., Maniloff, J., Dyer, T. A., Wolfe, R. S., Gupta, R., Bonen, L, Lewis, B. J., Stahl, D. A., Luehrson, K R., Chen, K N., and Woese, C. R., 1980, The phylogeny of prokaryotes, Science 209: 457–463.PubMedCrossRefGoogle Scholar
  23. Garber, R. C., and Yoder, O. C. 1983, Isolation of DNA from filamentous fungi and separation into nuclear, mitochondrial, ribosomal, and plasmid components, Anal. Biochem. 135: 416–422.PubMedCrossRefGoogle Scholar
  24. Garrett, R. A., 1979, The structure, assembly, and function of ribosomes, Crit. Rev. Biochem. 25: 121–177.Google Scholar
  25. Gauss, D. H., and Sprinzl, M., 1984, Compilation of tRNA sequences, Nucleic Acids Res. 12 (suppl.): r1 - r58.PubMedCrossRefGoogle Scholar
  26. Gibson, J., Stackebrandt, E., Zablen, L. B., Gupta, R., and Woese, C. R., 1979, A phylogenetic analysis of the purple photosynthetic bacteria, Curr. Microbiol. 3: 59–64.CrossRefGoogle Scholar
  27. Goad, W. B., and Kanehisa, M. I., 1982, Pattern recognition in nucleic acid sequences. I. A general method for finding local homologies and symmetries, Nucleic Acids Res. 10: 247–263.PubMedCrossRefGoogle Scholar
  28. Goodman, M. (ed.), 1982, Macromolecular Sequences in Systematic and Evolutionary Biology, Plenum Press, New York.Google Scholar
  29. Gupta, R., Lanter, J. M., and Woese, C. R., 1983, Sequence of the 16S ribosomal RNA from Halobacterium volcanii, an archaebacterium, Science 221: 656–659.PubMedCrossRefGoogle Scholar
  30. Harrison, A. P., Jr., 1982, Genomic and physiological diversity amongst strains of Thiobacillus ferrooxidans, and genomic comparison with Thiobacillus thiooxidans, Arch. Microbiol. 131: 68–76.CrossRefGoogle Scholar
  31. Hori, H., and Osawa, S., 1979, Evolutionary change in 5S RNA secondary structure and a phylogenetic tree of 54 5S RNA species, Proc. Natl. Acad. Sci. USA 76: 381–385.PubMedCrossRefGoogle Scholar
  32. Ingraham, J. L., Maalbe, O., and Neidhardt, F. C., 1983, Growth of the Bacterial Cell, Sinauer, Sunderland, Massachusetts.Google Scholar
  33. Jannasch, H. W., and Nelson, D. C., 1984, Recent progress in the microbiology of hydrothermal vents, in: Current Perspectives in Microbial Ecology ( M. J. and C. A. Reddy, eds.), pp. 170–176, American Society for Microbiology, Washington, D. C.Google Scholar
  34. Jannasch, H. W., and Wirsen, C. O., 1979, Chemosynthetic primary production at east Pacific sea floor spreading centers, Bioscience 29: 592–598.CrossRefGoogle Scholar
  35. Jones, M. L., 1981, Riftia pachyptila, new genus, new species, the vestimentiferan worm from the Galapagos rift geothermal vents (Pogonophora), Proc. Biol. Soc. Wash. 94: 1295–1313.Google Scholar
  36. Jukes, T. H., and Cantor, C. R., 1969, Evolution of protein molecules, in: Mammalian Protein Metabolism ( H. N. Munro, ed.), pp. 21–132, Academic Press, New York.Google Scholar
  37. Kandler, O. (ed.), 1982, First workshop on archaebacteria, Munich, 1981, Bakteriol. Zentralbl. Hug. I Abt. Orig. C3 1982:1–161.Google Scholar
  38. Karp, R. M., 1972, Reducibility among combinatorial problems, in: Complexity of Computer Computations, ( R. E. Miller and J. W. Thatcher eds.), pp. 85–103, Plenum Press, New York.CrossRefGoogle Scholar
  39. Lane, D. J., 1983, 5S rRNA phylogenetic analyses of certain free-living and symbiotic sulfuroxidizing chemolithotrophs, Thesis, Health Sciences Center, University of Colorado.Google Scholar
  40. Lane, D. J., Stahl, D. A., Olsen, G. J., Heller, D., and Pace, N. R., 1985, Phylogenetic analysis of the genera Thiobacillus and Thiomicrospira by 55 rRNA sequences, J. BacterioL. 163: 75–81.PubMedGoogle Scholar
  41. Luehrsen, K. R., Nicholson, D. E., Eubanks, D. C., and Fox, G. E., 1981, An archaebacterial 5S rRNA contains a long insertion sequence, Nature 293: 755–756.PubMedCrossRefGoogle Scholar
  42. Mackay, R. M., Spencer, D. F., Schnare, M. N., Doolittle, W. F., and Gray, M. W., 1982, Comparative sequence analysis as an approach to evolving structure, function, and evolution of 5S and 5.8S ribosomal RNAs, Can. J. Biochem. 60: 480–485.PubMedGoogle Scholar
  43. Maniatis, T., Fritsch, E. F., and Sambrook, J., 1982, Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York.Google Scholar
  44. Marrs, B., and Kaplan, S., 1970, 23S precursor ribosomal RNA of Rhodopseudomonas sphaeroides, J. Mol. BioL 49: 297–317.Google Scholar
  45. Messing, J., 1983, New M13 vectors for cloning, in: Methods in Enzymology, Vol. 101, ( R. Wu, L. Grossman, and K. Moldave, eds. ), pp. 70–78.Google Scholar
  46. Nomura, M., Traub, P., and Bechman, H., 1968, Hybrid 30S ribosomal particles reconstituted from components of different bacterial origins, Nature 219: 793–799.PubMedCrossRefGoogle Scholar
  47. Norris, P. R., Brierley, J. A., and Kelly, D. P., 1980, Physiological characteristics of twofacultatively thermophilic mineral-oxidizing bacteria, FEMS Microbiol. Lett. 7: 119–122.Google Scholar
  48. Olsen, G. J., 1983, Comparative analysis of nucleotide sequence data, Thesis, Health Sciences Center, University of Colorado.Google Scholar
  49. Palleroni, N., 1981, Introduction to the family Pseudomonadaceae, in: The Prokaryotes ( M. P. Starr, H. Stolp, H. G. Truper, A. Balows, and H. G. Schlegel, eds.), pp. 655–669, Springer-Verlag, New York.Google Scholar
  50. Papanicolaou, C., Gouy, M., and Ninio, J., 1984, An energy model that predicts the correct folding of both the tRNA and the 5S RNA molecules, Nucleic Acids Res. 12: 31–44.PubMedCrossRefGoogle Scholar
  51. Parish, J. H., 1972, Principles and Practice of Experiments with Nucleic Acids, pp. 104–111, Longman, London.Google Scholar
  52. Pavlakis, G. N., Jordan, B. R., Wurst, R. M., and Voumakis, J. N., 1979, Sequence and secondary structure of Drosophila melanogaster 5.8S and 2S rRNAs and of the processing site between them, Nucleic Acids Res. 7: 2213–2238.PubMedCrossRefGoogle Scholar
  53. Peattie, D. A., 1979, Direct chemical method for sequencing RNA, Proc. NatL Acad. Sci. USA 76: 1760–1764.PubMedCrossRefGoogle Scholar
  54. Penny, D., 1976, Criteria for optimizing phylogenetic trees and the problem of determining the root of a tree, J. Mol Evol. 8: 95–116.PubMedCrossRefGoogle Scholar
  55. Pieler, T., and Erdmann, V. A., 1982, Three-dimensional structural model of eubacterial 5S rRNA that has functional implications, Proc. Natl. Acad. Sci. USA 15: 4599–4603.CrossRefGoogle Scholar
  56. Ruby, E. G., and Jannasch, H. W., 1982, Physiological characteristics of Thiomicrospira sp. strain L-12 isolated from deep-sea hydrothermal vents, J. Bacteriol. 149: 161–165.PubMedGoogle Scholar
  57. Sanger, F., Brownlee, G. G., and Barrell, B. G., 1965, A two-dimensional fractionation procedure for radioactive nucleotides, J. Mol. Biol. 13: 373–398.PubMedCrossRefGoogle Scholar
  58. Sanger, F., Nicklen, S., and Coulson, A. R., 1977, DNA sequencing with chain-terminating inhibitors, Proc. Natl. Acad. Sci. USA 74: 5463–5467.PubMedCrossRefGoogle Scholar
  59. Smith, T. F., Waterman, M. S., and Fitch, W. M., 1981, Comparative biosequence metrics, J. Mol. Evol. 18: 38–46.PubMedCrossRefGoogle Scholar
  60. Stackebrandt, E., and Woese, C. R., 1981, The evolution of prokaryotes, in: Molecular and Cellular Aspects of Microbial Evolution ( M. J. Carlisle, J. R. Collins, and B. E. B. Moseley, eds.), pp. 1–31, Cambridge University Press, Cambridge.Google Scholar
  61. Stahl, D. A., Luehrsen, K. R., Woese, C. R., and Pace, N. R., 1981, An unusual 5S rRNA, from Sulfolobus acidocaldarius, and its implications for a general 5S rRNA structure, Nucleic Acids Res. 9: 6129–6137.PubMedCrossRefGoogle Scholar
  62. Stahl, D. A., Lane, D. J., Olsen, G. J., and Pace, N. R., 1984. Analysis of hydrothermal vent-associated symbionts by ribosomal RNA sequences, Science 224: 409–411.PubMedCrossRefGoogle Scholar
  63. Stahl, D. A., Lane, D. J., Olsen, G. J., and Pace, N. R., 1985, Characterization of a yellow-stone hot spring microbial community by 5S rRNA sequences, Appl. Environ. MicrobioL 49: 1379–1384.PubMedGoogle Scholar
  64. Stetter, K. O., and Gaag, G., 1983, Reduction of molecular sulfur by methanogenic bacteria, Nature 305: 309–311.CrossRefGoogle Scholar
  65. Stetter, K. O., and Zillig, W., 1985, Thermoplasma and the thermophilic sulfur-dependent Archaebacteria, in: The Bacteria, Vol. 8 (C. R. Woese and R. S. Wolfe eds.), pp. 85–170, Academic Press, New York.Google Scholar
  66. Walker, T. A., and Pace, N. R., 1983, 5.8S ribosomal RNA, Cell 33: 320–322.Google Scholar
  67. Waterman, M. S., 1983, Sequence alignments in the neighborhood of the optimum with general application to dynamic programming, Proc. Natl. Acad. Sci. USA 80: 3123–3124.PubMedCrossRefGoogle Scholar
  68. Wittmann, H. G., 1983, Architecture of prokaryotic ribosomes, Annu. Rev. Biochem. 52: 35–65.PubMedCrossRefGoogle Scholar
  69. Woese, C. R., 1972, The evolution of cellular tape reading processes and macromolecular complexity, in: Evolution of Genetic Systems, Brookhaven Symp. Biol. 23: 326–365.Google Scholar
  70. Woese, C. R., and Fox, G. E., 1977, The concept of cellular evolution, J. Mol. Evol. 10: 1–6.PubMedCrossRefGoogle Scholar
  71. Woese, C. R., Gutell, R. R., Gupta, R., and Noller, H. F., 1983, A detailed analysis of the higher-order structure of 16S-like ribosomal RNAs, Microbiol. Rev. 47: 621–669.PubMedGoogle Scholar
  72. Zuckerkandl, E., and Pauling, L., 1965, Molecules as documents of evolutionary history, J. Theor. BioL 8: 357–366.PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 1986

Authors and Affiliations

  • Norman R. Pace
    • 1
  • David A. Stahl
    • 1
  • David J. Lane
    • 1
  • Gary J. Olsen
    • 1
  1. 1.Department of Biology and Institute for Molecular and Cellular BiologyIndiana UniversityBloomingtonUSA

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