Flow cytometric analysis of the in situ accessibility of Escherichia coli 16S rRNA for fluorescently labeled oligonucleotide probes

Applied and Environmental Microbiology

Volumn 64, Issue 12, 1998, Pages 4973-4982

  Fuchs, Bernhard Maximilian ^a   Wallner, Günter ^b,d   Beisker, Wolfgang ^b   Schwippl, Ines ^c   Ludwig, Wolfgang ^c   Amann, Rudolf ^a,e  

^a MAX PLANCK INSTITUTE FOR MARINE MICROBIOLOGY   (Germany)

^b INSTITUTE OF EPIDEMIOLOGY   (Germany)

^c TECHNICAL UNIVERSITY OF MUNICH   (Germany)

^d SANOFI   (France)

^e UNIVERSITY OF BREMEN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL RNA; FLUORESCENT DYE; OLIGONUCLEOTIDE; RIBOSOME RNA; RNA 16S;

ARTICLE; ESCHERICHIA COLI; FLOW CYTOMETRY; FLUORESCENCE; IN SITU HYBRIDIZATION; NONHUMAN; NUCLEOTIDE SEQUENCE; OLIGONUCLEOTIDE PROBE; OPERON; RNA ANALYSIS; SEQUENCE ANALYSIS;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; NEGIBACTERIA;

EID: 0031789907     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/aem.64.12.4973-4982.1998     Document Type: Article

References (35)

1. Amann, R., W. Ludwig, R. Schulze, S. Spring, E. Moore, and K. H. Schleifer. 1996. rRNA-targeted oligonucleotide probes for the identification of genuine and former pseudomonads. Syst. Appl. Microbiol. 19:501-509.
2. Amann, R. Unpublished results.
3. Amann, R. I., B. J. Binder, R. J. Olson, S. W. Chisholm, R. Devereux, and D. A. Stahl. 1990. Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl. Environ. Microbiol. 56:1919-1925.
4. Amann, R. I., L. Krumholz, and D. A. Stahl. 1990. Fluorescent-oligonucleotide probing of whole cells for determinative, phylogenetic, and environmental studies in microbiology. J. Bacteriol. 172:762-770.
5. Amann, R. I., W. Ludwig, and K. H. Schleifer. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59:143-169.
6. Amann, R. I., J. Stromley, R. Devereux, R. Key, and D. A. Stahl. 1992. Molecular and microscopic identification of sulfate-reducing bacteria in multispecies biofilms. Appl. Environ. Microbiol. 58:614-623.
7. Beisker, W. 1994. A new combined integral-light and slit-scan data analysis system (DAS) for flow cytometry. Comput. Prog. Biomed. 42:15-26.
8. Brosius, J., T. J. Dull, D. D. Sleeter, and H. F. Noller. 1981. Gene organization and primary structure of a ribosomal RNA operon from Escherichia coli. J. Mol. Biol. 148:107-127.
9. DeLong, E. F., G. S. Wickham, and N. R. Pace. 1989. Phylogenetic stains: ribosomal RNA-based probes for the identification of single cells. Science 243:1360-1363.
10. Ehresmann, B., C. Ehresmann, P. Romby, M. Mougel, F. Baudin, E. Westhof, and J.-P. Ebel. 1990, Detailed structures of rRNAs: new approaches, p. 148-159. In W. E. Hill, A. Dahlberg, R. A. Garrett, P. B. Moore, D. Schlessinger, and J. R. Warner (ed.), The ribosome: structure, function, and evolution. American Society for Microbiology, Washington, D. C.
11. Erhart, R., D. Bradford, R. J. Seviour, R. Amann, and L. L. Blackall. 1997. Development and use of fluorescent in situ hybridization probes for the detection and identification of "Microthrix parvicella" in activated sludge. Syst. Appl. Microbiol. 20:310-318.
12. Frischer, M. E., P. J. Floriani, and S. A. Nierzwicki-Bauer. 1996. Differential sensitivity of 16S rRNA targeted oligonucleotide probes used for fluorescence in situ hybridization is a result of ribosomal higher order structure. Can. J. Microbiol. 42:1061-1071.
13. Gutell, R. R. 1994. Collection of small subunit (16S-and 16S-like) ribosomal RNA structures: 1994. Nucleic Acids Res. 22:3502-3507.
14. Hill, W. E., J. Weller, T. Gluick, C. Merryman, R. T. Marconi, A. Tassanakajohn, and W. E. Tapprich. 1990. Probing ribosome structure and function by using short complementary DNA oligomers, p. 253-264. In W. E. Hill, A. Dahlberg, R. A. Garrett, P. B. Moore, D. Schlessinger, and J. R. Warner (ed.), The ribosome: structure, function, and evolution. American Society for Microbiology, Washington, D.C.
15. Kämpfer, P., R. Erhart, C. Beimfohr, J. Böhringer, M. Wagner, and R. Amann. 1996. Characterization of bacterial communities from activated sludge: culture-dependent numerical identification versus in situ identification using group-and genus-specific rRNA-targeted oligonucleotide probes. Microb. Ecol. 32:101-121.
16. Lasater, L. S., H. McKuskie Olson, P. A. Cann, and D. G. Glitz. 1988. Complementary oligodeoxynucleotide probes of RNA conformation within the Escherichia coli small ribosomal subunit. Biochemistry 27:4687-4695.
17. Lodmell, J. S., and A. E. Dahlberg. 1997. A conformational switch in Escherichia coli 16S ribosomal RNA during decoding of messenger RNA. Science 277:1262-1267.
18. Maidak, B. L., G. J. Olsen, N. Larsen, R. Overbeek, M. J. McCaughey, and C. R. Woese. 1997. The RDP (Ribosomal Database Project). Nucleic Acids Res. 25:109-111.
19. Malhorta, A., and S. C. Harvey. 1994. A quantitative model of the Escherichia coli 16S RNA in the 30 S ribosomal subunit. J. Mol. Biol. 240:308-340.
20. Mobarry, B. K., M. Wagner, V. Urbain, B. E. Rittman, and D. A. Stahl. 1996. Phylogenetic probes for analyzing abundance and spatial organization of nitrifying bacteria. Appl. Environ. Microbiol. 62:2156-2162.
21. Olsen, G. J., D. J. Lane, S. J. Giovannoni, N. R. Pace, and D. A. Stahl. 1986. Microbial ecology and evolution: a ribosomal rRNA approach. Annu. Rev. Microbiol. 40:337-365.
22. Pommerening-Röser, A., G. Rath, and H.-P. Koops. 1996. Phylogenetic diversity within the genus Nitrosomonas. Syst. Appl. Microbiol. 19:344-351.
23. Rath, G. Personal communication.
24. Rossello-Mora, R. A., M. Wagner, R. Amann, and K.-H. Schleifer. 1995. The abundance of Zoogloea ramigera in sewage treatment plants. Appl. Environ. Microbiol. 61:702-707.
25. Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning: a laboratory manual, 2nd ed., vol. 3, p. 11-21. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
26. Schleifer, K.-H., R. Amann, W. Ludwig, C. Rothemund, N. Springer, and S. Dorn. 1992. Nucleic acid probes for the identification and in situ detection of pseudomonads, p. 127-134. In E. Galli, S. Silver, and B. Witholt (ed.), Pseudomonads: molecular biology and biotechnology. American Society for Microbiology, Washington, D.C.
27. Snaidr, J., R. Amann, I. Huber, W. Ludwig, and K.-H. Schleifer. 1997. Phylogenetic analysis and in situ identification of bacteria in activated sludge. Appl. Environ. Microbiol. 63:2884-2896.
28. Stahl, D. A., and R. Amann. 1991. Development and application of nucleic acid probes, p. 205-248. In E. Stackebrandt and M. Goodfellow (ed.), Nucleic acid techniques in bacterial systematics. John Wiley & Sons Ltd., Chichester, United Kingdom.
29. Strunk, O., O. Gross, B. Reichel, M. May, S. Hermann, N. Stuckmann, B. Nonhoff, T. Ginhart, A. Vilbig, M. Lenke, T. Ludwig, A. Bode, K.-H. Schleifer, and W. Ludwig. ARB: a software environment for sequence data. http://www.mikro.biologie.tu-muenchen.de. Department of Microbiology, Technische Universität München, Munich, Germany.
30. Suggs, S. V., T. Hirose, T. Miyake, E. H. Kawashima, M. J. Johnson, K. Itakura, and R. B. Wallace. 1981. Use of synthetic oligodeoxyribonucleotides for the isolation of specific cloned DNA sequences, p. 683-693. In D. Brown and C. F. Fox (ed.), Developmental biology using purified genes. Academic Press, Inc., New York, N.Y.
31. Van de Peer, Y., A. Caers, P. De Rijk, and R. De Wachter. 1998. Database on the structure of small ribosomal subunit RNA. Nucleic Acids Res. 26:179-182.
32. Wagner, M., R. Erhart, W. Manz, R. Amann, H. Lemmer, D. Wedi, and K.-H. Schleifer. 1994. Development of an rRNA-targeted oligonucleotide probe specific for the genus Acinetobacter and its application for in situ monitoring in activated sludge. Appl. Environ. Microbiol. 60:792-800.
33. Wallner, G., R. Amann, and W. Beisker. 1993. Optimizing fluorescent in situ hybridization with rRNA-targeted oligonucleotide probes for flow cytometric identification of microorganisms. Cytometry 14:136-143.
34. Wallner, G., B. Fuchs, S. Spring, W. Beisker, and R. Amann. 1997. Flow sorting of microorganisms for molecular analysis. Appl. Environ. Microbiol. 63:4223-4231.
35. Woese, C. R. 1987. Bacterial evolution. Microbiol. Rev. 51:221-271.