Differential sensitivity of 16S rRNA targeted oligonucleotide probes used for fluorescence in situ hyibridization is a result of ribosomal higher order structure

Canadian Journal of Microbiology

Volumn 42, Issue 10, 1996, Pages 1061-1071

  Frischer, Marc E ^a,b   Floriani, Peter J ^a,c   Nierzwicki Bauer, Sandra A ^a  

^a RENSSELAER POLYTECHNIC INSTITUTE   (United States)

^b SKIDAWAY INSTITUTE OF OCEANOGRAPHY   (United States)

^c NONE   (United States)

Author keywords

16S rRNA; In situ hybridization; Oligonucleotide probes

Indexed keywords

OLIGONUCLEOTIDE; RIBOSOME RNA; RNA 16S;

ARTICLE; BACTERIUM DETECTION; BACTERIUM IDENTIFICATION; CONTROLLED STUDY; DNA PROBE; FLUORESCENCE; IN SITU HYBRIDIZATION; NONHUMAN; PRIORITY JOURNAL;

BACTERIA (MICROORGANISMS); NEGIBACTERIA;

EID: 0029798084     PISSN: 00084166     EISSN: None     Source Type: Journal    
DOI: 10.1139/m96-136     Document Type: Article

References (50)

1. Amann, R.I., Binder, B.J., Olson, R.J., Chisholm, S.W., Devereux, R., and Stahl, D.A., 1990. Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl. Environ. Microbiol. 56: 1919-1925.
2. Amann, R.I., Zarda, B., Stahl, D.A., and Schleifer, K.-H. 1992. Identification of individual prokaryotic cells by using enzyme labeled, rRNA-targeted oligonucleotide probes. Appl. Environ. Microbiol. 58: 3007-3011.
3. Amann, R.I., Ludwig, W., and Schleifer, K.-H. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59:143-169.
4. Amy, P.S., Haldeman, D.L., Ringelberg, D., Hall, D.H., and Russell, C. 1992. Comparison of identification systems for classification of bacteria isolated from water and endolithic habitats within the deep subsurface. Appl. Environ. Microbiol. 58: 3367-3373.
5. Betzl, D., Ludwig, W., and Schleifer, K.-H. 1990. Identification of lactococci and enterococci by colony hybridization with 23S rRNA-targeted oligonucleotide probes. Appl. Environ. Microbiol. 56: 2927-2929.
6. Bohlool, B.B., and Schmidt, E.L. 1980. The immunofluorescence approach in microbial ecology. Adv. Microbiol. Ecol. 4: 203-241.
7. Braun-Howland, E.B., Danielsen, S.A., and Nierzwicki-Bauer, S.A. 1992. Development of a rapid method for detecting bacterial cells in situ using 16S rRNA-targeted probes. Biotechniques, 13: 928-934.
8. Braun-Howland, E.B., Vescio, P.A., and Nierzwicki-Bauer, S.A. 1993. Use of a simplified cell blot technique and 16S rRNA-directed probes for identification of common environmental isolates. Appl. Environ. Microbiol. 59: 3219-3224.
9. Brock, T.D., and Madigan, M.T. 1988. Biology of microorganisms. 5th ed. Prentice Hall, Inc., Englewood Cliffs, N.J.
10. Delong, E.F., Wickham, G.S., and Pace, N.R. 1989. Phylogenetic stains: ribosomal RNA-based probes for the identification of single cells. Science (Washington, D.C.), 243: 1360-1363.
11. De Rijk, P., Neefs, J.M., Vandepeer, Y., and De Wachter, R. 1992. Compilation of small ribosomal subunit RNA sequences. Nucleic Acids Res. 20(Suppl.): 2075-2089.
12. Devereux, R., Kane, M.D., Winfrey, J., and Stahl, D.A., 1992. Genus- and group-specific hybridization probes for determinative and environmental studies of sulfate-reducing bacteria. Syst. Appl. Microbiol. 15: 601-609.
13. Dumas, J.P., and Ninio, J. 1982. Efficient algorithms for folding and comparing nucleic acid sequences. Nucleic Acids Res. 10: 197-206.
14. Dumey, A.I. 1970. Indexing for rapid random access memory systems. Comput. Autom. 5: 6-9.
15. Floriani, P.J. 1994. Finding substrings of varying uniqueness in ribosomal RNA data. Ph.D. thesis, Rensselaer Polytechnic Institute, Troy, N.Y.
16. 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: 720-726.
17. Gutell, R.R., Larsen, N., and Woese, C.R. 1994. Lessons from an evolving rRNA: 16S and 23S rRNA structures from a comparative perspective. Microbiol. Rev. 58: 10-26.
18. Hahn, D., Amann, R.I., Ludwig, W., Akkermans, A.D.L., and Schleifer, K.-H. 1992. Detection of micro-organisms in soil after in situ hybridization with rRNA targeted, fluorescently labeled oligonucleotides. J. Gen. Microbiol. 138: 879-887.
19. Hazen, T.C., and Jimenez, L. 1988. Enumeration and identification of bacteria from environmental samples using nucleic acid probes. Microbiol. Sci. 5: 340-343.
20. Herrick, J.B., Madsen, E.L., Batt, C.A., and Ghiorse, W.C. 1993. Polymerase chain reaction amplification of napthalene-catabolic and 16S rRNA gene sequences from indigenous sediment bacteria. Appl. Environ. Microbiol. 59: 687-694.
21. Huq, A., Colwell, R.R., Rahman, R., Ali, A., Chowdhury, M.A.R., Parveen, S., Sack, D.A., and Russek-Cohen, E. 1990. Detection of Vibrio cholerae OI in the aquatic environment by fluorescent-monoclonal antibody and culture methods. Appl. Environ. Microbiol. 56: 2370-2373.
22. Kemp, P.F., Lee, S., and LaRoche, J. 1993. Estimating the growth rate of slowly growing marine bacteria from RNA content. Appl. Environ. Microbiol. 59: 2594-2601.
23. Lane, D.J., Pace, B., Olsen, G.J., Stahl, D.A., Sogin, M.L., and Pace, N.R. 1985. Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. Proc. Natl. Acad. Sci. U.S.A. 82: 6955-6959.
24. Larsen, N., Olsen, G.J., Maidak, B.L., McCaughey, M.J., Overbeek, R., Macke, T.J., Marsh, T.L., and Woese, C.R. 1993. The ribosomal database project. Nucleic Acids Res. 21: 3021-3023.
25. Lasater, L.S., Olson, H.M., Cann, P.A., and Glitz, D.G. 1988. Complementary oligodeoxynucleotide probes of RNA conformation within the Escherichia coli small ribosomal subunit. Biochemistry, 27: 4687-4695.
26. Lee, S., and Kemp, P.F. 1994. Single-cell RNA content of natural marine planktonic bacteria measured by hybridization with multiple 16S rRNA-targeted fluorescent probes. Limonol. Oceanogr. 34: 869-879.
27. Maaloe, O., and Kjellgard, N.O. 1966. Control of macromolecular synthesis. W.A. Benjamin, Inc., New York.
28. Manz, W., Szewzyk, U., Ericsson, P., Amann, R., Schleifer, K.-H., and Stenstrom, T.-A. 1993. In situ identification of bacteria in drinking water and adjoining biofilms by hybridization with 16S and 23S rRNA-directed fluorescent oligonucleotide probes. Appl. Environ. Microbiol. 59: 2293-2298.
29. Nizetic, D., Drmanac, R., and Lehrach, H. 1990. An improved bacterial colony lysis procedure enables direct DNA hybridisation using short (10, 11 bases) oligonucleotides to cosmids. Nucleic Acids Res. 19: 182.
30. Noller, H.F., Moazed, D., Stern, S., Powers, T., Allen, P.N., Robertson, J.M., Weiser, B., and Triman, K. 1990. Structure of rRNA and its functional interaction in translation. In The ribosome: structure, function, and evolution. Edited by W.E. Hill, A. Dahlberg, R.A. Garrett, P.B. Moore, D. Schlessinger, and J.R. Warner. American Society for Microbiology, Washington, D.C. p. 73-92.
31. Osterhout, G.J., Shull, V.H., and Dick, J.D. 1991. Identification of clinical isolates of Gram-negative nonfermentative bacteria by an automated cellular fatty acid identification system. J. Clin. Microbiol. 29: 1822-1830.
32. Paul, J.H. 1991. The advances and limitations of methodology in environmental microbiology. In Aquatic microbiology: an ecological approach. Edited by T. Ford. Blackwell Scientific Publication, Inc., Cambridge, Mass.
33. 2 fixation potential. Appl. Environ. Microbiol. 55: 2965-2975.
34. Postgate, J.R. 1984. The sulfate-reducing bacteria. 2nd ed. Cambridge University Press, Cambridge, U.K.
35. Poulsen, L.K., Ballard, G., and Stahl, D.A. 1993. Use of rRNA fluorescence in situ hybridization for measuring the activity of single cells in young and established biofilms. Appl. Environ. Microbiol. 59: 1354-1360.
36. Raskin, L., Stromley, J.M. Rittmann, B.E., and Stahl, D.A. 1994. Group-specific 16S rRNA hybridization probes to describe natural communities of methanogens. Appl. Environ. Microbiol. 60: 1232-1240.
37. Rodriquez, G.G., Phipps, D., Ishiguro, K., and Ridgway, H.F. 1992. Use of a fluorescent redox probe for direct visualization of actively respiring bacteria. Appl. Environ. Microbiol. 58: 1801-1808.
38. Sayler, G.S., and Layton, A.C. 1990. Environmental application of nucleic acid hybridization. Annu. Rev. Microbiol. 44: 625-648.
39. Sokal, R.R., and Rohlf, F.S. 1981. Biometry. 2nd ed. W.H. Freeman and Company, N.Y.
40. Spring, S., Amann, R., Ludwig, W., Schleifer, K.-H., Gemerden, H., and Petersen, K. 1993. Dominating role of an unusual magnetotactic bacterium in the microaerobic zone of a freshwater sediment. Appl. Environ. Microbiol. 59: 2397-2403.
41. Stahl, D.A., Flesher, B., Mansfield, H. R., and Montgomer, L. 1988. Use of phylogenetically based hybridization probes for studies of ruminal microbial ecology. Appl. Environ. Microbiol. 54: 1079-1084.
42. Tabor, P.S., and Neihof, R.A. 1982. Improved method for determination of respiring individual microorganisms in natural waters. Appl. Environ. Microbiol. 43: 1249-1255.
43. Vescio, P.A., and Nierzwicki-Bauer, S.A. 1995. Extraction and purification of PCR amplifiable DNA from lacustrine subsurface sediments. J. Microbiol. Methods, 21: 225-233.
44. Wagner, M., Amann, R., Lemmer, H., and Schleifer, K.-H. 1993. Probing activated sludge with oligonucleotides specific for proteobacteria: inadequacy of culture-dependent methods for describing microbial community structure. Appl. Environ. Microbiol. 59: 1520-1525.
45. Wagner, M.-H., Erhart, R., Manz, W., Amann, R., Lemmer, H., Wedi, D., and Schleifer, K.-H. 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.
46. Ward, B.B. 1990. Immunology in biological oceanography and marine ecology. Oceanography, April: 30-35.
47. R promoters by a cI repressor in a broad-host-range thermoregulated plasmid marker system. Appl. Environ. Microbiol. 55: 771-777.
48. Woese, C.R., 1994. There must be a prokaryote somewhere: microbiology's search for itself. Microbiol. Rev. 58: 1-9.
49. Zehr, J.P., Limberger, R.J., Ohki, K., and Fujita, Y. 1990. Antiserum to nitrogenase generated from an amplified DNA fragment from natural populations of Trichodesmium spp. Appl. Environ. Microbiol. 56: 3527-3531.
50. Zeph, L.R., and Stotzky, G. 1989. Use of a biotinylated DNA probe to detect bacteria transduced by bacteriophage P1 in soil. Appl. Environ. Microbiol. 55: 661-665.