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.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
Similar content being viewed by others
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.
Brierley, C. L., 1982, Microbiological mining, Sci. Am. 2: 44–53.
Brock, T. D., 1978, Thermophilic Microorganisms and Life at High Temperatures, Springer-Verlag, New York.
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.
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.
Cavanaugh, C. M., 1983, Symbiotic chemoautotrophic bacteria in marine invertebrates from sulfide-rich habitats, Nature 302: 58–61.
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.
Cedergren, R. J., LaRue, B., Sankoff, D., and Grosjean, H., 1981, The evolving tRNA molecule, Crit. Rev. Biochem. 11: 35–104.
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.
Delihas, N., and Andersen, J. 1982, Generalized structures of the 5S ribosomal RNAs, Nucleic Acids Res. 10: 7323–7344.
Demoulin, V., 1979, Protein and nucleic acid sequence data and phylogeny, Science 205: 1036–1039.
Donis-Keller, H., Maxam, A., and Gilbert, W., 1977, Mapping adenines, guanines, and pyrimidines in RNA, Nucleic Acids Res. 4: 2527–2538.
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.
Edmond, J. M., and Von Damm, K., 1983, Hot springs on the ocean floor, Sci. Am. 248: 78–93.
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.
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.
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.
Felsenstein, J., 1982, Numerical methods for inferring evolutionary trees, Q. Rev. Biol. 57: 379–404.
Fitch, W. M., 1976, The molecular evolution of cytochrome c in eukaryotes, J. Mol. Evol. 8: 13–40.
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.
Fitch, W. M., and Smith, T. F., 1983, Optimal sequence alignments, Proc. Natl. Acad. Sci. USA 80: 1382–1386.
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.
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.
Garrett, R. A., 1979, The structure, assembly, and function of ribosomes, Crit. Rev. Biochem. 25: 121–177.
Gauss, D. H., and Sprinzl, M., 1984, Compilation of tRNA sequences, Nucleic Acids Res. 12 (suppl.): r1 - r58.
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.
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.
Goodman, M. (ed.), 1982, Macromolecular Sequences in Systematic and Evolutionary Biology, Plenum Press, New York.
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.
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.
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.
Ingraham, J. L., Maalbe, O., and Neidhardt, F. C., 1983, Growth of the Bacterial Cell, Sinauer, Sunderland, Massachusetts.
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.
Jannasch, H. W., and Wirsen, C. O., 1979, Chemosynthetic primary production at east Pacific sea floor spreading centers, Bioscience 29: 592–598.
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.
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.
Kandler, O. (ed.), 1982, First workshop on archaebacteria, Munich, 1981, Bakteriol. Zentralbl. Hug. I Abt. Orig. C3 1982:1–161.
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.
Lane, D. J., 1983, 5S rRNA phylogenetic analyses of certain free-living and symbiotic sulfuroxidizing chemolithotrophs, Thesis, Health Sciences Center, University of Colorado.
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.
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.
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.
Maniatis, T., Fritsch, E. F., and Sambrook, J., 1982, Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York.
Marrs, B., and Kaplan, S., 1970, 23S precursor ribosomal RNA of Rhodopseudomonas sphaeroides, J. Mol. BioL 49: 297–317.
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.
Nomura, M., Traub, P., and Bechman, H., 1968, Hybrid 30S ribosomal particles reconstituted from components of different bacterial origens, Nature 219: 793–799.
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.
Olsen, G. J., 1983, Comparative analysis of nucleotide sequence data, Thesis, Health Sciences Center, University of Colorado.
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.
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.
Parish, J. H., 1972, Principles and Practice of Experiments with Nucleic Acids, pp. 104–111, Longman, London.
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.
Peattie, D. A., 1979, Direct chemical method for sequencing RNA, Proc. NatL Acad. Sci. USA 76: 1760–1764.
Penny, D., 1976, Criteria for optimizing phylogenetic trees and the problem of determining the root of a tree, J. Mol Evol. 8: 95–116.
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.
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.
Sanger, F., Brownlee, G. G., and Barrell, B. G., 1965, A two-dimensional fractionation procedure for radioactive nucleotides, J. Mol. Biol. 13: 373–398.
Sanger, F., Nicklen, S., and Coulson, A. R., 1977, DNA sequencing with chain-terminating inhibitors, Proc. Natl. Acad. Sci. USA 74: 5463–5467.
Smith, T. F., Waterman, M. S., and Fitch, W. M., 1981, Comparative biosequence metrics, J. Mol. Evol. 18: 38–46.
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.
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.
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.
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.
Stetter, K. O., and Gaag, G., 1983, Reduction of molecular sulfur by methanogenic bacteria, Nature 305: 309–311.
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.
Walker, T. A., and Pace, N. R., 1983, 5.8S ribosomal RNA, Cell 33: 320–322.
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.
Wittmann, H. G., 1983, Architecture of prokaryotic ribosomes, Annu. Rev. Biochem. 52: 35–65.
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.
Woese, C. R., and Fox, G. E., 1977, The concept of cellular evolution, J. Mol. Evol. 10: 1–6.
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.
Zuckerkandl, E., and Pauling, L., 1965, Molecules as documents of evolutionary history, J. Theor. BioL 8: 357–366.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 1986 Springer Science+Business Media New York
About this chapter
Cite this chapter
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
Download citation
DOI: https://doi.org/10.1007/978-1-4757-0611-6_1
Publisher Name: Springer, Boston, MA
Print ISBN: 978-1-4757-0613-0
Online ISBN: 978-1-4757-0611-6
eBook Packages: Springer Book Archive