Distribution of microbial-selected populations in Lake North Mamry by fluorescent in situ hybridization

• Autorzy: Skowronska A
• Języki publikacji: EN

Abstrakty

EN

Fluorescent in situ hybridization (FISH) with rRNA -targeted oligonucleotide probes has become one of the major techniques in environmental microbiology, allowing rapid and reliable definition of prokaryotes and quantification of population sizes. The aim was to demonstrate the applicability of the FISH method to study bacterioplankton composition in North Mamry Lake, and to follow the dynamics of two populations of common bacteria. We analyzed the phylogenetic composition of free-living bacterioplankton assemblage using oligonucleotide probes specific for Bacteria as well as for β-Proteobacteria and Cytophaga-Flavobacterium groups. Up to 53% of bacteria detected with DA PI could be detected via FISH by applying the universal bacterial probe for domain Bacteria (Eub338). Percentage of Cytophaga-Flavobacterium cluster did not exceed 20%. Members of the β –Proteobacteria appeared to be the most abundant group.

Słowa kluczowe

EN

community composition; rRNA-target oligonucleotide probe; fluorescent in situ hybridization; Lake North Mamry; bacterial community

• Wydawca: -
• Czasopismo: Polish Journal of Environmental Studies
• Rocznik: 2007
• Tom: 16
• Numer: 1
• Opis fizyczny: p.123-128,fig.,ref.

Twórcy

autor

Skowronska A

• University of Warmia and Mazury, Prawochenskiego 1, 10-957 Olsztyn-Kortowo, Poland

Bibliografia

• 1. ALFREIDER A., PERNTHALER J., AMANN R., SATTLER B., GLOCKNER F.O., WILLE A., PSENNER R. Community analysis of the bacterial assemblages in the winter cover and pelagic layers of a high mountain lake by in situ hybridization. Appl. Environ. Microbiol. 62, 2138, 1996.
• 2. AMANN R. I., BINDER B. J., OLSON R.J., CHISHOLM S. W., DEVEREUX R., STAHL D. A., Combination of 16Stargeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl. Environ. Microbiol. 56, 1919, 1990.
• 3. AMANN R., LUDWIG W., SCHLEIFER K. H., Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59, 143, 1995.
• 4. AMANN R., GLÕCKNER F. O., NEEF A., Modern methods in subsurface microbiology-in situ identification of microorganisms with nucleic acid probes. FEM S Microbiol. Rev. 20, 191, 1997.
• 5. AMANN R., LUDWIG W., Ribosomal RNA -targeted nucleic acid probes for studies in microbial ecology. FEM S Microbiol. Rev. 24, 555, 2000.
• 6. AMANN R., FUCHS B. M., BEHREN S S., The identification of microorganisms by fluorescence in situ hybridization. Current Opinion in Biotechnology 12, 231, 2001.
• 7. BOBROW M. N., HARRIS T. D., SHAUGHNESSY K. J., LITT G. J., Catalyzed reporter deposition, a novel method of signal amplification. J. Immunol. Methods 125, 279, 1989.
• 8. BOUVIER T. C., DEL GIORGIO P. A. Compositional changes in free-living bacterial communities along salinity gradient in two temperature estuaries. Limnol. Oceanogr. 47, 453, 2002.
• 9. CHROST R. J., SIUDA W. Microbial production, utilization, and enzymatic degradation of organic mater in upper tropogenic water layer in the pelagial zone of lakes along the eutrophication gradient. Limnol. Oceanogr. 50, 4, 2005.
• 10. DELONG E. F., WICKHMAN G. S., PACE N. R. Phylogenetic stains: ribosomal RNA -based probes for the identification of single cells. Science 243, 1360, 1989.
• 11. DELONG E. F., TAYLOR T. T., MARSH T. L., PRESTON C. M. Visualization and enumeration of marine planktonic Archaea and Bacteria by using polirybonucleotide probes and fluorescent in situ hybridization. Appl. Environ. Microbiol. 65, 5554, 1999.
• 12. DEL GIORGIO P.A., BOUVIER T. C. Linking the physiologic and phylogenetic successions in free-living bacterial communities along an estuarine salinity gradient. Limnol. Oceanogr. 47, 471, 2002.
• 13. EILER S H., PERNTHALER J., GLÖCKNER F. O., AMANN R. Culturability and in situ abundance of pelagic bacteria from the North Sea. Appl. Environ. Microbiol. 66, 3044, 2000.
• 14. FUCHS B. M., GLÖCKNER F. O., WÜLF J., AMANN R. Unlabeled helper oligonucleotides increase the in situ accessibility to 16S rRNA of fluorescently labeled oligonucleotide probes. Appl. Environ. Microbiol. 66, 3603, 2000.
• 15. GIOVANONNI S. J., BRITSCHGIT. B., MOYER C.L., FIELD K. G., Genetic diversity in Sargasso Sea bacterioplankton. Nature 345, 60, 1990.
• 16. GLÖCKNER F-O., AMANN R., ALFREIDER A .,.PERNTHALER J., PSENNER R., TREBESIUS R., SCHLEIFER K.-H. An in situ hybridization protocol for detection and identification of planktonic bacteria. System. Appl. Microbiol. 19, 403, 1996.
• 17. GLÖCKNER F-O., FUCHS B. M., AMANN R. Bacterioplankton compositions of lakes and oceans: a first comparison based on fluorescence in situ hybridization. Appl. Environ. Microbiol. 65, 3721, 1999.
• 18. GLÖCKNER F-O., ZAICHIKOV E, BELKOVA N., DENISSOWA L., PRENTHALER J., PERNTHALER A., AMANN R. Comparative 16S rRNA analysis of lake bacterioplankton reveals globally distributed phylogenetic clusters including an abundant group of actinobacteria. Appl. Environ. Microbiol. 66, 5053, 2000.
• 19. HEAD I. M., SAUNDER S J. R., PICKU P R. W. Microbial evolution, diversity and ecology: a decade of ribosomal RNA analysis of uncultivated microorganisms. Microbial Ecol. 35, 1, 1998.
• 20. KIRCHMAN D. L., DITTEL A. I., FINDLAY S. E. G., FISHER D. Changes in bacterial activity and community structure in response to dissolved organic matter in the Hudson River. Microb. Ecol. 35, 243, 2004.
• 21. KLAMMER S., POSH T., SONNTAG B., GRIEBLER CH., MINDL B., PSENNER R. Dynamics of bacterial abundance, biomass, activity, and community composition in the oligotrophic Traunsee and the Traun River Austria. Water, Air and Soil Pollution 2, 137, 2002.
• 22. KUFEL L. Uncoupling of chlorophyll and nutrients in lakespossible reasons, expected consequences. Hydrobiologia 443, 59, 2001.
• 23. LOY A., HORN M., WAGNER M. probeBase: an online resource for rRNA-targeted oligonucleotide probes. Nucleic Acids Res. 31 (1), 514, 2003.
• 24. MANZ W., AMANN R., LUDWIG W., WAGNER M., SCHLEIFER K. H., Phylogenetic oligonucleotide probes fort the major subclasses of Proteobacteria: Problems and solutions. Syst. Appl. Microbiol. 15, 593, 1992.
• 25. MANZ W., AMANN R., VAN CANNEYT M., SCHLEIFER K-H. 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 140, 2849, 1996.
• 26. METHE B. A., HIORNS W. D., ZEHR J. P. Contrast between marine and freshwater bacterial community composition: analyses of communities in Lake George and six other Adirondack lakes. Limnol. Oceanogr. 43, 368, 1998.
• 27. MOTER A., GÖBEL U. B., Fluorescence in situ hybridization (FISH) for direct visualization of microorganisms. J. Microbiol. Methods 41, 85, 2000.
• 28. NEEF A., Anwendynng der in situ –Einzelzell-identifizierung von bakterien zur populationsanalyse in komplexen mikrobiellen biozonosen. Ph. D. Thesis. Technische Universitat Munchen, Munich, Germany, 1997.
• 29. OLSEN R. A. BAKKEN L.R. Viability of soil bacteria, optimization of plate-counting technique and comparison between total counts and plate counts within different size groups. Microb. Ecol. 13, 59, 1987.
• 30. OUVERNEY C. C., FUHRMAN J. A. Increase in fluorescence intensity of 16S rRNA in situ hybridization in natural samples treated with chloramfenicol. Appl. Environ. Microbiol 63, 235, 1997.
• 31. PERNTHALER J., GLÖCKNER F-O., UNTERHOLZNER S., ALFREIDER A., PSENNER R., AMANN R. Seasonal community and population dynamics of pelagic Bacteria and Archaea in a high mountain lake. Appl. Environ. Microbiol. 64, 4299, 1998.
• 32. PERNTHALER J., GLÕCKNER F-O., SCHONHUBER W., AMANN R. Fluorescence in situ hybridization with rRNA - targeted oligonucleotide probes. Methods in Microbiology 30, 207, 2001.
• 33. PERNTHALER A., PRESTOM C. M., PERNTHALER J., DELONG E. F., AMANN R. A comparison of fluorescently labeled oligonucleotide and polynucleotide probes for detection of pelagic marine bacteria and Arachaea. Appl. Environ. Microbiol. 68, 661, 2002.
• 34. PERNTHALER A., PERNTHALER J., AMANN R. Fluorescence in situ hybridization and catalyzed reporter deposition fort he identification of marine bacteria. Appl. Environ. Microbiol. 68, 3094, 2002.
• 35. PERNTHALER J., ZOLLNER E., WARNECKE F., JURGEN S K. Bloom of filamentous bacteria in a mesotrophic lake identity and potential controlling mechanism. Appl. Environ. Microbiol. 70, 6272, 2005.
• 36. PINHASSI J., HAGSTRÖM A. Seasonal succession in marine bacterioplankton. Aquat. Microb. Ecol. 24, 245, 2000.
• 37. PORTER K. G., FEIG Y. S., The use of DA PI for identifying and counting aquatic microflora. Limnol. Oceanogr. 25, 943, 1980.
• 38. SEKAR R., PERNTHALER A., PERNTHALER J., WARNECKE F., POSH T., AMANN R. An improved protocol for quantification of freshwater Actinobacteria by fluorescence in situ hybridization. Appl. Environ. Microbiol 69, 2928, 2003.
• 39. SCHÖNHUBER W., FUCHS B., JURETSCHKO S., AMANN R. Improved sensitivity of whole-cell hybridization by the combination of horseradish peroxidase-labeled oligonucleotides and tyramide signal amplification. Appl. Environ. Microbiol 63, 3268, 1997.
• 40. SEKAR R., PERNTHALER A., PERNTHALER J., WARNECKE F., POSH T., AMANN R. An improved protocol for quantification of freshwater Actinobacteria by fluorescence in situ hybridization. Appl. Environ. Microbiol 69, 2928, 2003.
• 41. SKOWROŃSKA A., Application of molecular methods to investigate biodiversity of bacterioplankton in lake water. Doctoral thesis, Biblioteka Główna UW-M w Olsztynie p. 82, 2004. [In Polish]
• 42. WAGNER M., AMANN R., LEMMER H., SCHLEIFER K.-H. Probing activated sludge with oligonucleotides specific for Proteobacteria: inadequacy of culture-dependent methods for describing community structure. Appl. Environ. Microbiol. 59, 1520, 1993.
• 43. WAGNER M., HORN M., DAIM S H., Fluorescence in situ hybridization for the identification and characterization of prokaryotes. Current Opinion in Microbiology 6, 302, 2003.
• 44. WALLNER G., AMANN R., BEISKER W., Optimizing fluorescent in situ hybridization with rRNA -targeted oligonucleotide probes for flow cytometric identification of microorganisms. Cytometry 14, 136, 1993.
• 45. WARD D. M., WELLER R., BATESON M. M., 16S rRNA sequences reveals numerous uncultured microorganisms in a natural community. Nature (London) 345, 63, 1990.
• 46. WORDEN CHISHOLM s. W., BINDER B. J. In situ hybridization of Prochlorococcus and Synechococcus spp. Marine cyanobacteria with rRNA-targeted peptide nucleic acid probes. Appl. Environ. Microbiol. 66, 284, 2000