1887

Abstract

SUMMARY: RNA-targeted and f luorescently labelled oligonucleotide probes were used to study the composition of natural bacterial populations in continuous-f low cultures of seawater sediment suspensions. The cultures were run as enrichment cultures with increasing dilution rates, and hexadecane as the sole carbon source. Total cell numbers were analysed by counting DAPI (4′,6- diamidino-2-phenylindole)-stained cells. To differentiate the population composition, oligonucleotide probes for eubacteria, for Cytophagd Flavobacteria, and for four subclasses of the Proteobacteria (a, b, y and 6) were used. About 4&80°/o of the DAPI-stained cells could be detected with the EUB338 probe. Moreover, it was possible to detect a shift in the composition of the natural bacterial population with increasing dilution rate of the continuous culture, from large amounts of CytophagdFlavobacteria to large numbers of members of the pProteobacteria. The cell recovery rate for bacteria labelled with specific oligonucleotide probes was analysed with defined cell numbers of Rhodospirillum nrbnrm, Cornamonas testosteroni and Desulfowibrio vulgaris subsp. vulgaris introduced into the seawater sediment suspension, and was determined to be 13*%33*5 %. The standard deviation determined for this method applied to sediment suspensions was 28.3 %. The results suggest that the application of the in situ hybridization technique allows a good insight into the structure of populations growing in sediment suspensions.

Loading

Article metrics loading...

/content/journal/micro/10.1099/00221287-144-10-2783
1998-10-01
2024-12-09
Loading full text...

Full text loading...

/deliver/fulltext/micro/144/10/mic-144-10-2783.html?itemId=/content/journal/micro/10.1099/00221287-144-10-2783&mimeType=html&fmt=ahah

References

  1. Amann R.I., Krumholz L., Stahl D.A. 1990a; Fluorescent-oligonucleotide probing of whole cells for determinative, phylogenetic, and environmental studies in microbiology.. J Bacteriol 172:762–770
    [Google Scholar]
  2. Amann R.I., Binder B.J., Olson R.J., Chrisholm S.W., Devereux R., Stahl D.A. 1990b; Combination of 16S rRNA- targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations.. Appl Environ Microbiol 56:1919–1925
    [Google Scholar]
  3. Amann R.I., Springer N., Ludwig W., Görtz H.-D., Schieifer K.-H. 1991; Identification in situ and phylogeny of uncultured bacterial endosymbionts.. Nature 351:161–164
    [Google Scholar]
  4. Amann R.I., Ludwig W., Schieifer K.-H. 1995; Phylogenetic identification and in situ detection of individual microbial cells without cultivation.. Microbiol Rev 59:143–169
    [Google Scholar]
  5. Austin B. 1988 Methods in Aquatic Bacteriology. New York: Wiley;
    [Google Scholar]
  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
    [Google Scholar]
  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
    [Google Scholar]
  8. Coleman A.W. 1980; Enhanced detection of bacteria in natural environments by fluorochrome staining of DNA.. Limnol Oceanogr 25:948–951
    [Google Scholar]
  9. Cote R.J., Gherna R.L. 1994; Nutrition and media. . In Methods for General and Molecular Bacteriology pp. 155–178 Gerhardt P., Murray R.G.E., Wood W.A., Krieg N.R. Edited by Washington, DC: American Society for Microbiology;
    [Google Scholar]
  10. De Long 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
    [Google Scholar]
  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
    [Google Scholar]
  12. Frischer M.E., Floriani P.J., Nierzwicki-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
    [Google Scholar]
  13. Grasshoff K. 1983 Methods of Seawater Analysis. Weinheim: Verlag Chemie;
    [Google Scholar]
  14. Hahn D., Amann R.I., Ludwig W., Akkermans A.D.L., Schieifer 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
    [Google Scholar]
  15. Hicks R.E., Amann R.I., Stahl D.A. 1992; Dual staining of natural bacterioplankton with 4ʹ,6-diamidino-2-phenylindole and fluorescent oligonucleotide probes targeting kingdom-level 16S rRNA sequences.. Appl Environ Microbiol 58:2158–2163
    [Google Scholar]
  16. Kapuscinski J. 1995; DAPI: a DNA-specific fluorescent probe.. Biotech Histochem 70:220–233
    [Google Scholar]
  17. Leahy J.G., Colwell R.R. 1990; Microbial degradation of hydrocarbons in the environment.. Microbiol Rev 54:305–315
    [Google Scholar]
  18. Manz W., Amann R., Ludwig W., Wagner M., Schieifer K.-H. 1992; Phylogenetic oligodeoxynucleotide probes for the major subclasses of Proteobacteria: problems and solutions.. Syst Appl Microbiol 15:593–600
    [Google Scholar]
  19. McKay A.M. 1992; Viable but non-culturable forms of potentially pathogenic bacteria in water.. Lett Appl Microbiol 14:129–135
    [Google Scholar]
  20. Manz W., Wagner M., Amann R., Schleifer K.-H. 1994; In situ characterization of the microbial consortia active in two wastewater treatment plants.. Water Res 28:1715–1723
    [Google Scholar]
  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
    [Google Scholar]
  22. Oliver J.D., Colwell R.R. 1973; Extractable lipids of gramnegative marine bacteria: fatty acid composition.. lnt J Syst Bacteriol 23:442–458
    [Google Scholar]
  23. Porter K.G., Feig Y.S. 1980; The use of DAPI for identifying and counting aquatic microflora.. Limnol Oceanogr 25:943–945
    [Google Scholar]
  24. Radwan S.S., Sorkhoh N.A. 1993; Lipids of n-alkane-utilizing microorganisms and their application potential.. Adv Appl Microbiol 39:29–90
    [Google Scholar]
  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
    [Google Scholar]
  26. Roszak D.B., Colwell R.R. 1987; Survival strategies of bacteria in the natural environment.. Microbiol Rev 51:365–379
    [Google Scholar]
  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
    [Google Scholar]
  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
    [Google Scholar]
  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
    [Google Scholar]
  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
    [Google Scholar]
  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
    [Google Scholar]
  32. Wagner M., Amann R., Kämpfer P., Assmus B., Hartmann A., Hutzier 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
    [Google Scholar]
  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 Oligonucleotide Probes. Workshop on Water Microbiology for the 21st Century 21-22 September MacQuarie University: pp. 1–12
    [Google Scholar]
  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
    [Google Scholar]
  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
    [Google Scholar]
  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
    [Google Scholar]
/content/journal/micro/10.1099/00221287-144-10-2783
Loading
/content/journal/micro/10.1099/00221287-144-10-2783
Loading

Data & Media loading...

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error