Abstract
Nucleic acid probes have revolutionized rapid diagnostics of plant-, animal- and human-pathogenic viroids, viruses, bacteria and protozoa, and have complemented the spectrum of immunological and serological tests. Sequences of genes and rRNA, of proven potential for identification of taxa, are a valuable tool in that both the identity and the phylogenetic position of an isolate can be elucidated. On the other hand, this approach is still laborious and requires sophisticated equipment. Designation of probes does not require information about sequences, although such knowledge is extremely helpful in the formulation of highly specific oligonucleotide probes, e.g. in the case of rDNA probes, where target stretches containing variable sequences are rather short (about 10–30 nucleotides). The application of probe technologies in molecular environmental studies byin situ hybridization, screening of gene libraries and flow cytometry is in its infancy but a logical step towards reconfirmation of the identity of a species in its natural habitat.
Similar content being viewed by others
References
Alexander, M. (1961)Introduction to Soil Microbiology. New York: J. Wiley & Sons.
Amann, R.I., Binder, B.J., Olson, R.J., Chisholm, S.W., Devereux, R. and Stahl, D.A. (1990a) Combination of 16S rRNA-targeted oligonucelotide probes with flow cytometry for analyzing mixed microbial populations.Appl. Env. Microbiol. 56, 1919–25.
Amann, R.I., Krumholz, L. and Stahl, D.A. (1990b) Fluorescent-oligonucleotide probing of white cells for determinative, phylogenetic and environmental studies in microbiology.J. Bacteriol. 172, 762–70.
Amann, R., Springer, N., Ludwig, W., Görtz, H.-D. and Schleifer, K.-H. (1991) Identificationin situ and phylogeny of uncultured bacterial endoymbionts.Nature 351, 161–4.
Britschgi, T.B. and Giovannoni, S.J. (1991) Phylogenetic analysis of a natural marine bacterioplankton population by rRNA gene cloning and sequencing.Appl. Env. Microbiol. 57 1707–13.
Colwell, R.R., Brayton, P.R., Grimes, D.J., Roszak, D.B., Huq, S.A. and Palmer, L.M. (1985) Viable but non-culturableVibrio cholerae and related pathogens in the environment: implications for release of genetically engineered microorganisms.Biotech. 3, 817–20.
Delong, E.F. and Shah, J. (1990) Fluorescent, ribosomal RNA probes for clinical application: a research review.Diag. Clin. Test. 28, 41–4.
DeLong, E.F., Schmidt, T.M. and Pace, N.R. (1989a) Analysis of single cells and oligotrophic picoplankton populations using 16S rRNA sequences. InRecent Advances in Microbial Ecology (T. Hattori, Y. Ishida, Y. Maruyama, R.Y. Morita and A. Uchida, eds) pp. 697–701. Tokyo: Japan Science Society Press.
DeLong, E.F., Wickham, G.S. and Pace, N.R. (1989b) Phylogenetic stains; ribosomal RNA-based probes for the identification of single cells.Science 243, 1360–3.
Devereux, R., Winfrey, J., Winfrey, M.R. and Stahl, D.A. (1990) Application of 16S rRNA probes to correlate communities of sulfate-reducing bacteria with sulfate reduction and mercury methylation in a marine sediment.Abstr. 90th Ann. Mtg. Am. Soc. Microbiol. 328.
Distel, D.L., DeLong, E.F. and Waterbury, J.B. (1991) Phylogenetic characterization andin situ localization of the bacterial symbiont of shipworms (Teredinidae: bivalva) using 16S rRNA sequence analysis and oligodeoxynucleotide probe hybridization.Appl. Env. Microbiol. 57, 2376–82.
Gardes, M., White, T.J., Fortin, J.A., Bruns, T.D. and Taylor, J.W. (1991) Identification of indigenous and introduced symbiotic fungi in ectomycorrhizae by amplification of nuclear and mitochondrial ribosomal DNA.Can. J. Bot. 69, 180–90.
Giovannoni, S.J. (1991) The polymerase chain reaction. InNucleic Acid Techniques in Bacterial Systematics-Modern Microbiological Methods (E. Stackebrandt and M. Goodfellow, eds) pp. 177–203. Chichester: Academic Press.
Giovannoni, S.J., DeLong, E.F., Olsen, G.J. and Pace, N.R. (1988) Phylogenetic group-specific oligodeoxynucleotide probes for identification of single microbial cells.J. Bacteriol. 170, 720–6.
Giovannoni, S.J., Britschgi, T.B., Moyer, C.L. and Field, K.G. (1990) Genetic diversity in Sargasso Sea bacterioplankton.Nature 345, 60–3.
Hahn, D., Dorsch, M., Stackebrandt, E. and Akkermans, A.D.L. (1989) Synthetic oligonucleotide probes for identification ofFrankia strains.Plant Soil 118, 211–9.
Hahn, D., Starrenburg, M.J.C. and Akkermans, A.D.L. (1990) Oligonucleotide probes that hybridize with rRNA as a tool to studyFrankia strains in root nodules.Appl. Env. Microbiol. 56 1342–6.
Jannasch, H.W. (1979) Microbial ecology of aquatic low nutrient habitats. InStrategies of Microbial Life in Extreme Environments, (M. Shilo, ed.) pp. 243–60. Berlin: Dahlem Konferenzen.
Jannasch, H.W. and Jones, G.E. (1959) Bacterial populations in sea water as determined by different methods of enumeration.Limol. Oceanogr. 4 128–39.
Kemmerling, C., Witt, D., Liesack, W., Weyland, H. and Stackebrandt, E. (1990) Approaches for the molecular identification of streptomycetes in marine environment. InCurrent Topics in Marine Biotechnology (S. Miyachi, I. Karube and Y. Eshida, eds) pp. 423–6. Tokyo: Japan Society for Marine Biotechnology.
Lee, S. and Fuhrman, J.A. (1990) DNA hybridization to compare species compositions of natural bacterioplankton assemblages.Appl. Env. Microbiol. 56, 739–46.
Liesack, W., Ward, N. and Stackebrandt, E. (1991a) Strategies for molecular microbial ecological studies.Actinomycetes,2, 63–76.
Liesack, W., Sela, S., Bercovier, H. and Stackebrandt, E. (1991b) Complete nucleotide sequence of theMycobacterium leprae 23S and 5S rRNA genes plus flanking regions and their potential in designing diagnostic oligonucleotide probes.FEBS Letters 281, 114–8.
Liesack, W., Weyland, H. and Stackebrandt, E. (1991c) Potential risks of gene amplification by PCR as determined by 16S rDNA analysis of a mixed-culture of obligately barophilic bacteria.Microb. Ecol. 21, 188–201.
Liesack, W. and Stackebrandt, E. (1992) Occurrence of novel groups of the Domain Bacteria as revealed by analysis of genetic material isolated from an Australian terrestrial environment.J. Bacteriol. 174, 5072–8.
Moreno, E., Stackebrandt, E., Dorsch, M., Wolters, J., Busch, M. and Mayer, H. (1990)Brucella abortus 16S rRNA and lipid A reveal a phylogenetic relationship with members of the alpha-2 subdivision of the classProteobacteria.J. Bacteriol. 172, 3569–76.
Novitsky, J.A. and Morita, R.Y. (1978) Possible strategy for the survival of marine bacteria under starvation conditions.Marine Biol. 48, 289–95.
Ogram, A.V., Sayler, G.S. and Barkay, T. (1988) The extraction and purification of microbial DNA from sediments.J. Microbiol. Methods 7, 57–66.
Olsen, G.J., Lane, D.J., Giovannoni, S.J. and Pace, N.R. (1986) Microbial ecology and evolution: a ribosomal RNA approach.Ann. Rev. Microbiol. 40, 337–65.
Pelletier, D.A., Paster, B.J., Weisburg, W.G., Dewhirst, F.E., Dannenberg, S. and Schroeder, I. (1991)Cristispira phylogeny by 16S rRNA sequence comparison of amplified bacterial DNA from crystalline styles.Abstr. 91st Ann. Am. Soc. Microbiol. 243.
Relman, D.A., Loutit, J.S., Schmidt, T.M., Falkow, S. and Tompkins, L.S. (1990) The agent of bacillary angiomatosis: an approach to the identification of uncultured pathogens.New Engl. J. Med. 323, 1573–80.
Roszak, D.B. and Colwell, R.R. (1987) Survival strategies of bacteria in the natural environment.Microbiol. Rev. 51, 365–79.
Sambrook, J., Frtisch, E.F. and Maniatis, T. (1989)Molecular cloning: a laboratory manual. Cold Springs Harbor, NY: Cold Springs Harbor Laboratory Press.
Sayler, G.S. and Layton, A.C. (1990) Environmental application of nucleic acid hybridization.Ann. Rev. Microbiol. 44, 625–48.
Seewaldt, E. and Stackebrandt, E. (1982) Partial sequence of 16S ribosomal RNA and the phylogeny ofProchloron.Nature 295, 618–20.
Stackebrandt, E. and Liesack, W. (1993) Nucleic acids and classification. InThe new bacterial systematics (M. Goodfellow, ed.). London: Academic Press (in press).
Stackebrandt, E., Witt, D., Kemmerling, C., Kroppenstedt, R. and Liesack, W. (1991) Designation of streptomycete 16S and 23S rRNA-based target regions for oligonucleotide probes.Appl. Env. Microbiol. 57, 1468–77.
Stahl, D.A. and Amann, R. (1991) Development and application of nucleic acid probes. InNucleic Acid Techniques in Bacterial Systematics — Modern Microbiological Methods (E. Stackebrandt and M. Goodfellow, eds.) pp. 205–48. Chichester: Academic Press.
Stahl, D.A., Flesher, B., Mansfield, H. and Montgomery, R. (1988) Use of phylogenetically based hybridization probes for studies of ruminal microbial ecology.Appl. Env. Microbiol. 54, 1079–84.
Stahl, D.A., Lane, D.J., Olsen, G.J. and Pace, N.R. (1985) Characterization of a Yellowstone hot spring microbial community by 5S rRNA sequences.Appl. Env. Microbiol. 49, 1379–84.
Tsai, Y.L. and Olson, B.H. (1991) Rapid method for direct extraction of DNA from soil and sediments.Appl. Env. Microbiol. 57, 1070–4.
Unterman, B.M., Baumann, P. and McLean, D.L. (1989) Pea aphid symbiont relationships established by analysis of 16S rRNAs.J. Bacteriol. 171, 2970–4.
Ward, D.M., Tayne, T.A., Anderson, K.L. and Bateson, M.M. (1987) Community structure and interactions among community members in hot spring cyanobacterial mats.Sympos. Soc. Gen. Microbiol. 41, 179–210.
Ward, D.M., Weller, R. and Bateson, M.M. (1990a) 16S rRNA sequences reveal numerous uncultured microorganisms in a natural community.Nature 345, 63–5.
Ward, D.M., Weller, R. and Bateson, M.M. (1990b) 16S rRNA sequences reveal uncultured inhabitants of a well-studied thermal community.FEMS Microbiol. Rev. 75, 105–16.
Ward, D.M., Bateson, M.M., Weller, R. and Ruff-Roberts, A.L. (1992) Ribosomal RNA analysis of microorganisms as they occur in nature.Adv. Microbial Ecol. (in press).
Weisburg, W.G., Hatch, T.P. and Woese, C.R. (1986) Eubacterial origin of the chlamydiae.J. Bacteriol. 167, 570–4.
Weisburg, W.G., Barns, S.M., Pelletier, D.A. and Lane, D.J. (1991) 16S ribosomal DNA amplification for phylogenetic study.J. Bacteriol. 173, 697–703.
Weller, R., Weller, J.W. and Ward, D.M. (1991); 16S rRNA sequences of uncultivated hot spring cyanobacterial mat inhabitants retrieved as randomly primed cDNA.Appl. Env. Microbiol. 57, 1146–51.
Witt, D., Liesack, W. and Stackebrandt, E. (1989) Identification of streptomycetes by 16S rRNA sequences and oligonucleotide probes. InRecent Advances in Microbial Ecology (T. Hattori, Y. Ishida, Y. Maruyama, R. Y. Morita and A. Uchida, eds) pp. 679–84. Tokyo: Japan Scientific Society Press.
Woese, C.R. (1987) Bacterial Evolution.Microbiol. Rev. 51, 221–71.
Xu, H.-S., Roberts, N., Singleton, F.L., Attwell, Grimes, D.J. and Colwell, R.R. (1982) Survival and viabiity of nonculturableEsherichia coli andVibrio cholerae in the estuarine and marine environment.Microbial Ecol. 8, 313–23.
Young, J.P.W., Downer, H.L. and Eardly, B.D. (1991) Phylogeny of the photographicRhizobium strain BTAil by polymerase chain reaction-based sequencing of a 16S rRNA gene segment.J. Bacteriol. 173, 2271–7.
Author information
Authors and Affiliations
Rights and permissions
About this article
Cite this article
Liesack, W., Stackebrandt, E. Unculturable microbes detected by molecular sequences and probes. Biodivers Conserv 1, 250–262 (1992). https://doi.org/10.1007/BF00693763
Received:
Accepted:
Issue Date:
DOI: https://doi.org/10.1007/BF00693763