Microbial communities in a strongly anthropogenic affected stream

Dana Baudišová 1  and Andrea Benáková 1
  • 1 T. G. Masaryk Water Research Institute, Public Research Institute, Podbabská 30, 160 00 Prague 6, Czech Republic

Abstract

Microbiological indicators (total coliforms, faecal coliforms, E. coli and enterococci) and phylogenetic groups (domain Archaea, classes Alpha-, Beta-, Gammaproteobacteria and the Cytophaga-Flavobacterium group) detected by FISH were detected in profiles of a highly anthropogenically-affected stream (Luzická Nisa; Northern Bohemia, Czech Republic). This study aimed to assess the changes in the microbial communities of such a polluted stream, and possible relationships between “classic indicators” and the phylogenetic groups. One particular aim concerned a characterisation of the fluorescence in situ hybridization (FISH) method, the source of any uncertainty and its limit in terms of quality control (QA/QC). Of the phylogenetic groups studied, the Proteobacteria phylum was more abundant in comparison to the Cytophaga-Flavobacterium group or the Archaea domain. The profile Lucany (above the start of city urban areas) was very different from later downstream profiles, because of its very low faecal bacteria content, low counts of Gammaproteobacteria, and evident dominance of the Cytophaga-Flavobacterium group together with Betaproteobacteria. Later profiles did not show such large differences among themselves. The group of Gammaproteobacteria was very common mainly in profiles with high amounts of untreated faecal pollution. The repeatability of counting bacteria by the FISH method was 14 % on average, an “uncertainty” similar to that of cultivation methods.

If the inline PDF is not rendering correctly, you can download the PDF file here.

  • Amann R. (1995): In situ identification of microorganisms by whole cell hybridization with rRNA-targered nucleic acid probes, pp. 3.3.6./1-3.3.6./15. In Akerman A. D. L., van El sas J. D. & de Brui jn F. J. (eds): Molecular Microbial Ecology Manual. Kluwer Academic Publisher, Dordrecht, Netherlands.

  • Araya R., Tani K., Takagi T., Yamaguchi N. & Nasu M. (2003): Bacterial activity and community composition in stream water and biofilm from an urban river determined by fluorescence in situ hybridization and DGGE analysis. − FEMS Microbiol. Ecol. 43: 111-119.

  • Balasté E. & Blanch A. R. (2010): Persistance of Bacteriodes species populations in a river as measured by molecular and culture techniques. − Appl. Environ. Microbiol. 76: 7608-7616.

  • Baudišová D., Havel L. & Benáková A. (2008): The water quality in anthropogenically affected stream of Luzicka Nisa. Part 1 - Microbiological indicators. − VTEI 50(4/2008): 5-7.

  • Bouvier T. & del Giorgio P.A. (2003): Factors influencing the detection of bacerial cells using fluorescence in situ hybridization (FISH): A quantitative review of published reports. − FEMS Microbiol. Ecol. 44:3-15.

  • Brűmmer I. H. M., Fehr W. & Wagner-Dőbler I. (2000): Biofilm community Structure in Polluted rivers: Abundance of Dominant Phylogenetic groups over a Complete Annual Cycle. − Appl. Environ. Microbiol. 66(7): 3078-3082.

  • Kildare B. J., Leutenegger C. M., McSwain B. S., Bambic D. G., Rajal V. B. & Wuer tz S. (2007): 16 S r RNA-based assays for quantitative detection of universal, human-, cow-, and dog specific fecal Bacteriodales. A Bayesian approach. − Wat. Res. 41(16): 3701-3715.

  • Kirchmann D. L. (2002): The ecology of Cytophaga-Flavobacterium in aquatic environments. − FEMS Microbiol. Ecol. 39: 91-100.

  • Loy A., Maixner F., Wagner M. & Horn M. (2007): ProbeBase - an online resource for rRNA-targeted oligonucleotide probes: New features. − Nucl. Acids Res. 35: 800-804.

  • Neef A. (in litt): Anwendung der in situ Einzelzell-Identifizierung von Bakterien zur Populationsanalyse in komplexen mikrobiellen Biozönosen. (Ph.D. thesis). Technische Universität München, 1997.

  • Nielsen P. H., Daims H. & Lemmer H. (2009): FISH handbook for biological wastewater treatment, identification and quantification of microorganisms in activated sludge and biofilms by FISH. IWA Publishing, London, UK, 123 pp.

  • Manz W., Amann R., Ludwig W., Wagner M. & Schlei fer K.-H. (1992): Phylogenetic oligodeoxynucleotide probes for the major subclasses of Proteobacteria: problems and solutions. − Syst. Appl. Microbiol. 15: 593-600.

  • Manz W., Amann R., Ludwig W., Vancanneyt M. & Schlei fer , 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(5): 1097-1106.

  • Mlejnková H. & Sovová K. (2010): Impact of pollution and seasonal changes on microbial community structure in surface water. − Wat. Sci. Tech. 61(11): 2787-2795.

  • Raskin L., St romley J., M., Ri t tmann B. & E. & Stahl , D., A. (1994): Group-specific 16S rRNA hybridization probes to describe natural communities of methanogens. − Appl. Environ. Microbiol. 60: 1232-1240.

  • Sekar R., Pernthaler A., Pernthaler J., Warnecke F., Posch T. & Amann R. (2003): An improved protocol for quantification of freshwater Actinobacteria by fluorescence in situ hybridisation. − Appl. Environ. Microbiol. 69(5): 2928-2935.

  • Stahl D., A. & Amann., R. (1991): Development and application of nucleic acid probes, pp. 205-248. In E. Stackebrandt & M. Goodfel low (eds): Nucleic acid techniques in bacterial systematics. John Wiley & Sons Ltd., Chichester, England.

  • Tirodimos I., Haidich A.B., Dar ravess i s T. & Arvani t idou M. (2009): River research and applications 10.1002/rra1301.

  • Wagner M., Horn M., Daims H. (2003): Fluorescence in situ hybridisation for identification and characterisation of prokaryotes. − Current Opinion in Microbiology, 6:302-309.

OPEN ACCESS

Journal + Issues

Search