In situ detection of bacteria in continuous-flow cultures of seawater sediment suspensions with fluorescently labelled rRNA-directed oligonucleotide probes

Microbiology

Volumn 144, Issue 10, 1998, Pages 2783-2790

  Bruns, Alke ^a   Berthe Corti, Luise ^a  

^a UNIVERSITY OF OLDENBURG   (Germany)

Author keywords

In situ hybridization; Intertidal sediment suspension; Population structure; rRNA targeted oligonucleotide probes

Indexed keywords

BACTERIAL RNA; HEXADECANE; RIBOSOME RNA; SEA WATER;

ARTICLE; BACTERIAL COUNT; BACTERIUM CULTURE; BACTERIUM DETECTION; DESULFOVIBRIO VULGARIS; FLAVOBACTERIUM; FLEXIBACTERACEAE; IN SITU HYBRIDIZATION; NONHUMAN; OLIGONUCLEOTIDE PROBE; PRIORITY JOURNAL; RHODOSPIRILLUM RUBRUM; SEDIMENT; SUSPENSION;

BACTERIA (MICROORGANISMS); COMAMONAS TESTOSTERONI; CYTOPHAGA; DESULFOVIBRIO; DESULFOVIBRIO VULGARIS SUBSP. VULGARIS; FLAVOBACTERIA; FLAVOBACTERIUM; FLEXIBACTERACEAE; GAMMAPROTEOBACTERIA; PROTEOBACTERIA; RHODOSPIRILLUM RUBRUM;

EID: 0031734971     PISSN: 13500872     EISSN: None     Source Type: Journal    
DOI: 10.1099/00221287-144-10-2783     Document Type: Article

References (36)

1. Amann, R. I., Krumholz, L. & Stahl, D. A. (199Oa). Fluorescent-oligonucleotide probing of whole cells for determinative, phylogenetic, and environmental studies in microbiology. J Bacterial 172, 762-770.
2. Amann, R. I., Binder, B. J., Oison, R. J., Chrisholm, S. W., Devereux, R. & Stahl, D. A. (199Ob). Combination of 16S rRNA targeted oligonucleotide probes with How cytometry for analyzing mixed microbial populations. Appl Environ Microbiol 56, 1919-1925.
3. Amann, R. I., Springer, N., Ludwig, W., Görtz, H.-D. & Schleifer, K.-H. (1991). Identification in situ and phylogeny of uncultured bacterial endosymbionts. Nature 351, 161-164.
4. Amann, R. L, Ludwig, W. & Schleifer, K.-H. (1995). Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59, 143-169.
5. Austin, B. (1988). Methods in Aquatic Bacteriology. New York: Wiley.
6. Berthe-Corti, L., Bruns, A. & Hulsch, R. (1997). Semi-continuous-flow cultures with marine sediment suspensions containing non-polar carbon sources - culture control by a pneumatic sediment suspension dosage system. J Microbiol Methods 29, 129-137.
7. Brosius, J., Dull, T. J., Sleeter, D. D. & Noller, H. F. (1981). Gene organisation and primary structure of a ribosomal RNA operon from Escherichia coli. J Mol Biol 148, 107-127.
8. Coleman, A. W. (1980). Enhanced detection of bacteria in natural environments by fluorochrome staining of DNA. Limnol Oceanogr 25, 948-951.
9. Cote, R. J. & Gherna, R. L. (1994). Nutrition and media. In Methods for General and Molecular Bacteriology, pp. 155-178. Edited by P. Gerhardt, R. G. E. Murray, W. A. Wood & N. R. Krieg. Washington, DC: American Society for Microbiology.
10. DeLong, E. F., Wickham, G. S. & Pace, N. R. (1989). Phylogenetic stains: ribosomal RNA-based probes for the identification of single microbial cells. Science 243, 924-934.
11. Fredrickson, J. K., Balkwill, D. L., Zachara, J. M., Li, S.-M. W., Brockman, F. J. & Simmons, M. A. (1991). Physiological diversity and distributions of heterotrophic bacteria in deep cretaceous sediments of the Atlantic coastal plain. Appl Environ Microbiol 57, 402-411.
12. Frischer, M. E., Floriani, P. J. & Nierzwkki-Bauer, S.A. (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. Grasshoff, K. (1983). Methods of Seawater Analysis. Weinheim: Verlag Chemie.
14. Hahn, D., Amann, R. I., Ludwig, W., Akkermans, A. D. L. & Schleifer, K.-H. (1992). Detection of micro-organisms in soil after in situ hybridization with rRNA-targeted, fluorescently labelled oligonucleotides. J Gen Microbiol 138, 879-887.
15. Hicks, R. E., Amann, R. I. & Stahl, D. A. (1992). Dual staining of natural bacterioplankton with 4′,6-diamidino-2-phenylindole and fluorescent oligonucleotide probes targeting kingdom-level 16S rRNA sequences. Appl Environ Microbiol 58, 2158-2163.
16. Kapuscinski, J. (1995). DAPI: a DNA-specific fluorescent probe. Biotech Histochem 70, 220-233.
17. Leahy, J. G. & Colwell, R. R. (1990). Microbial degradation of hydrocarbons in the environment. Microbiol Rev 54, 305-315.
18. Manz, W., Amann, R., Ludwig, W., Wagner, M. & Schleifer, K.-H. (1992). Phylogenetic oligodeoxynucleotide probes for the major subclasses of Proteobacteria: problems and solutions. Syst Appl Microbiol 15, 593-600.
19. McKay, A. M. (1992). Viable but non-culturable forms of potentially pathogenic bacteria in water. Lett Appl Microbiol 14, 129-135.
20. Manz, W., Wagner, M., Amann, R. & Schleifer, K.-H. (1994). In situ characterization of the microbial consortia active in two waste-water treatment plants. Water Res 28, 1715-1723.
21. Manz, W., Amann, R., Ludwig, W., Vancanneyt, M. & Schleifer, K.-H. (1996). Application of a suite of 16S rRNA-specific oligonucleotide probes designed to investigate bacteria of the phylum cytophaga-flavobacter-bacteroides in the natural environment. Microbiology 142, 1097-1106.
22. Oliver, J. D. & Colwell, R. R. (1973). Extractable lipids of gram-negative marine bacteria : fatty acid composition. Int J Syst Bacterial 23, 442-458.
23. Porter, K. G. & Feig, Y. S. (1980). The use of DAPI for identifying and counting aquatic microflora. Limnol Oceanogr 25, 943-945.
24. Radwan, S. S. & Sorkhoh, N. A. (1993). Lipids of n-alkane-utilizing microorganisms and their application potential. Adv Appl Microbiol 39, 29-90.
25. Ritz, K. & Griffiths, B. S. (1994). Potential application of a community hybridization technique for assessing changes in the population structure of soil microbial communities. Soil Biol Biochem 26, 963-971.
26. Roszak, D. B. & Colwell, R. R. (1987). Survival strategies of bacteria in the natural environment. Microbiol Rev 51, 365-379.
27. Rüger, H.-J. & Krambeck, H.-J. (1994). Evaluation of the Biolog substrate metabolism system for classification of marine bacteria. Syst Appl Microbiol 17, 281-288.
28. Snaidr, J., Amann, R., Huber, I., Ludwig, W. & Schleifer, K.-H. (1997). Phylogenetic analysis and in situ identification of bacteria in activated sludge. Appl Environ Microbiol 63, 2884-2896.
29. Spring, S., Amann, R., Ludwig, W., Schleifer, K.-H. & Petersen, N. (1992). Phylogenetic diversity and identification of nonculturable magnetotactic bacteria. Syst Appl Microbiol 15, 116-122.
30. Staley, J. T. & Konopka, A. (1985). Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats. Annu Rev Microbiol 39, 321-346.
31. Wagner, M., Amann, R., Lemmer, H. & 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.
32. Wagner, M., Amann, R., Kämpfer, P., Assmus, B., Hartmann, A., Hutzler, P., Springer, N. & Schleifer, K.-H. (1994). Identification and in situ detection of gram-negative filamentous bacteria in activated sludge. Syst Appl Microbiol 17, 405-417.
33. Wallner, G. & Amann, R. (1993). Fluorescence in situ hybridization for the detection and identification of microbial cells by fluorescence microscopy and flow cytometry. In Ribosomal RNA-targeted Oligonncleottde Probes. Workshop on Water Microbiology for the 21st Century, 21-22 September, MacQuarie University, pp. 1-12.
34. Wallner, G., Amann, R. & Beisker, W. (1993). Optimizing fluorescent in situ hybridization with rRNA-targeted oligonucleotide probes for flow cytometric identification of microorganisms. Cytometry 14, 136-143.
35. Ward, D. M., Weller, R. & Bateson, M. M. (1990). 16S rRNA sequences reveal numerous uncultured microorganisms in a natural community. Nature 345, 63-65.
36. Zweifel, U. L. & Hagström, A. (1995). Total counts of marine bacteria include a large fraction of non-nucleoid-containing bacteria (ghosts). Appl Environ Microbiol 61, 2180-2185.