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The Analysis of Natural Microbial Populations by Ribosomal RNA Sequences

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Advances in Microbial Ecology

Part of the book series: Advances in Microbial Ecology ((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.

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References

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • Brierley, C. L., 1982, Microbiological mining, Sci. Am. 2: 44–53.

    Article  Google Scholar 

  • Brock, T. D., 1978, Thermophilic Microorganisms and Life at High Temperatures, Springer-Verlag, New York.

    Book  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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 

  • Cavanaugh, C. M., 1983, Symbiotic chemoautotrophic bacteria in marine invertebrates from sulfide-rich habitats, Nature 302: 58–61.

    Article  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • Cedergren, R. J., LaRue, B., Sankoff, D., and Grosjean, H., 1981, The evolving tRNA molecule, Crit. Rev. Biochem. 11: 35–104.

    Article  CAS  Google Scholar 

  • 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 

  • Delihas, N., and Andersen, J. 1982, Generalized structures of the 5S ribosomal RNAs, Nucleic Acids Res. 10: 7323–7344.

    Article  PubMed  CAS  Google Scholar 

  • Demoulin, V., 1979, Protein and nucleic acid sequence data and phylogeny, Science 205: 1036–1039.

    Article  PubMed  CAS  Google Scholar 

  • Donis-Keller, H., Maxam, A., and Gilbert, W., 1977, Mapping adenines, guanines, and pyrimidines in RNA, Nucleic Acids Res. 4: 2527–2538.

    Article  PubMed  CAS  Google Scholar 

  • 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 

  • Edmond, J. M., and Von Damm, K., 1983, Hot springs on the ocean floor, Sci. Am. 248: 78–93.

    Article  CAS  Google Scholar 

  • 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 

  • 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.

    Article  PubMed  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • Felsenstein, J., 1982, Numerical methods for inferring evolutionary trees, Q. Rev. Biol. 57: 379–404.

    Article  Google Scholar 

  • Fitch, W. M., 1976, The molecular evolution of cytochrome c in eukaryotes, J. Mol. Evol. 8: 13–40.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • Fitch, W. M., and Smith, T. F., 1983, Optimal sequence alignments, Proc. Natl. Acad. Sci. USA 80: 1382–1386.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • Garrett, R. A., 1979, The structure, assembly, and function of ribosomes, Crit. Rev. Biochem. 25: 121–177.

    CAS  Google Scholar 

  • Gauss, D. H., and Sprinzl, M., 1984, Compilation of tRNA sequences, Nucleic Acids Res. 12 (suppl.): r1 - r58.

    Article  PubMed  Google Scholar 

  • 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.

    Article  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • Goodman, M. (ed.), 1982, Macromolecular Sequences in Systematic and Evolutionary Biology, Plenum Press, New York.

    Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • Ingraham, J. L., Maalbe, O., and Neidhardt, F. C., 1983, Growth of the Bacterial Cell, Sinauer, Sunderland, Massachusetts.

    Google Scholar 

  • 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 

  • Jannasch, H. W., and Wirsen, C. O., 1979, Chemosynthetic primary production at east Pacific sea floor spreading centers, Bioscience 29: 592–598.

    Article  CAS  Google Scholar 

  • 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 

  • 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 

  • Kandler, O. (ed.), 1982, First workshop on archaebacteria, Munich, 1981, Bakteriol. Zentralbl. Hug. I Abt. Orig. C3 1982:1–161.

    Google Scholar 

  • 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.

    Chapter  Google Scholar 

  • 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 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • 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 

  • Marrs, B., and Kaplan, S., 1970, 23S precursor ribosomal RNA of Rhodopseudomonas sphaeroides, J. Mol. BioL 49: 297–317.

    Google Scholar 

  • 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 

  • Nomura, M., Traub, P., and Bechman, H., 1968, Hybrid 30S ribosomal particles reconstituted from components of different bacterial origins, Nature 219: 793–799.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    CAS  Google Scholar 

  • Olsen, G. J., 1983, Comparative analysis of nucleotide sequence data, Thesis, Health Sciences Center, University of Colorado.

    Google Scholar 

  • 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 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • Parish, J. H., 1972, Principles and Practice of Experiments with Nucleic Acids, pp. 104–111, Longman, London.

    Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • Peattie, D. A., 1979, Direct chemical method for sequencing RNA, Proc. NatL Acad. Sci. USA 76: 1760–1764.

    Article  PubMed  CAS  Google Scholar 

  • Penny, D., 1976, Criteria for optimizing phylogenetic trees and the problem of determining the root of a tree, J. Mol Evol. 8: 95–116.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • Sanger, F., Brownlee, G. G., and Barrell, B. G., 1965, A two-dimensional fractionation procedure for radioactive nucleotides, J. Mol. Biol. 13: 373–398.

    Article  PubMed  CAS  Google Scholar 

  • Sanger, F., Nicklen, S., and Coulson, A. R., 1977, DNA sequencing with chain-terminating inhibitors, Proc. Natl. Acad. Sci. USA 74: 5463–5467.

    Article  PubMed  CAS  Google Scholar 

  • Smith, T. F., Waterman, M. S., and Fitch, W. M., 1981, Comparative biosequence metrics, J. Mol. Evol. 18: 38–46.

    Article  PubMed  CAS  Google Scholar 

  • 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 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • Stetter, K. O., and Gaag, G., 1983, Reduction of molecular sulfur by methanogenic bacteria, Nature 305: 309–311.

    Article  CAS  Google Scholar 

  • 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 

  • Walker, T. A., and Pace, N. R., 1983, 5.8S ribosomal RNA, Cell 33: 320–322.

    Google Scholar 

  • 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.

    Article  PubMed  CAS  Google Scholar 

  • Wittmann, H. G., 1983, Architecture of prokaryotic ribosomes, Annu. Rev. Biochem. 52: 35–65.

    Article  PubMed  CAS  Google Scholar 

  • 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 

  • Woese, C. R., and Fox, G. E., 1977, The concept of cellular evolution, J. Mol. Evol. 10: 1–6.

    Article  PubMed  CAS  Google Scholar 

  • 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.

    PubMed  CAS  Google Scholar 

  • Zuckerkandl, E., and Pauling, L., 1965, Molecules as documents of evolutionary history, J. Theor. BioL 8: 357–366.

    Article  PubMed  CAS  Google Scholar 

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Pace, N.R., Stahl, D.A., Lane, D.J., Olsen, G.J. (1986). The Analysis of Natural Microbial Populations by Ribosomal RNA Sequences. In: Marshall, K.C. (eds) Advances in Microbial Ecology. Advances in Microbial Ecology, vol 9. Springer, Boston, MA. https://doi.org/10.1007/978-1-4757-0611-6_1

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  • DOI: https://doi.org/10.1007/978-1-4757-0611-6_1

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