An improved protocol for quantification of freshwater Actinobacteria by fluorescence in situ hybridization

Applied and Environmental Microbiology

Volumn 69, Issue 5, 2003, Pages 2928-2935

  Sekar, Raju ^a   Pernthaler, Annelie ^a   Pernthaler, Jakob ^a   Warnecke, Falk ^a   Posch, Thomas ^b   Amann, Rudolf ^a  

^a MAX PLANCK INSTITUTE FOR MARINE MICROBIOLOGY   (Germany)

^b UNIVERSITY OF INNSBRUCK   (Austria)

Author keywords

[No Author keywords available]

Indexed keywords

CATALYSIS; ENVIRONMENTAL IMPACT; FLUORESCENCE; LAKES;

INCUBATIONS;

BACTERIA;

ACHROMOPEPTIDASE; ENZYME; FLUOROCHROME; LYSOZYME; SURFACE WATER; UNCLASSIFIED DRUG;

BACTERIUM; FRESHWATER; QUANTITATIVE ANALYSIS;

ACTINOBACTERIA; ARTICLE; BACTERIUM CULTURE; BACTERIUM EXAMINATION; CATALYSIS; CELL ASSAY; CELL LOSS; CELL MEMBRANE PERMEABILITY; CELL WALL; CONCENTRATION (PARAMETERS); ENZYMATIC ASSAY; FLUORESCENCE IN SITU HYBRIDIZATION; FRESHWATER ENVIRONMENT; INCUBATION TIME; INTERMETHOD COMPARISON; LAKE; NONHUMAN; PLANKTON; SAMPLING;

ACTINOBACTERIA; BACTERIA; CELL MEMBRANE PERMEABILITY; COLONY COUNT, MICROBIAL; FRESH WATER; GRAM-POSITIVE BACTERIA; IN SITU HYBRIDIZATION, FLUORESCENCE; MURAMIDASE; PLANKTON; SERINE ENDOPEPTIDASES;

ACTINOBACTERIA; ACTINOBACTERIA (CLASS); ARMORACIA RUSTICANA; BACTERIA (MICROORGANISMS); POSIBACTERIA; UNCULTURED ACTINOMYCETE;

EID: 0037882329     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.69.5.2928-2935.2003     Document Type: Article

References (36)

1. Amann, R. I., W. Ludwig, and K. H. Schleifer. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59:143-169.
2. Bano, N., M. A. Moran, and R. E. Hodson. 1997. Bacterial utilization of dissolved humic substances from a freshwater swamp. Aquat. Microb. Ecol. 12:233-238.
3. Barsotti, O., J. J. Morrier, J. Freney, F. Renaud, G. Benay, D. Decoret, and J. Dumnont. 1988. Achromopeptidase for rapid lysis of oral anaerobic Gram-positive rods. Oral Microbiol. Immunol. 3:86-88.
4. Bobrow, M. N., T. D. Harris, K. J. Shaughnessy, and G. J. Litt. 1989. Catalyzed reporter deposition, a novel method of signal amplification - application to immunoassays. J. Immunol. Methods 125:279-285.
5. Bouvier, T. C., and P. A. del Giorgio. 2002. Compositional changes in free-living bacterial communities along a salinity gradient in two temperate estuaries. Limnol. Oceanogr. 47:453-470.
6. Cole, J. J. 1999. Aquatic microbiology for ecosystem scientists: new and recycled paradigms in ecological microbiology. Ecosystems 2:215-225.
7. Cottrell, M. T., and D. L. Kirchman. 2000. Community composition of marine bacterioplankton determined by 16S rRNA gene clone libraries and fluorescence in situ hybridization. Appl. Environ. Microbiol. 66:5116-5122.
8. Cottrell, M. T., and D. L. Kirchman. 2000. Natural assemblages of marine proteobacteria and members of the Cytophaga-Flavobacter cluster consuming low- and high-molecular-weight dissolved organic matter. Appl. Environ. Microbiol. 66:1692-1697.
9. Daims, H., A. Bruhl, R. Amann, K. H. Schleifer, and M. Wagner. 1999. The domain-specific probe EUB338 is insufficient for the detection of all bacteria: development and evaluation of a more comprehensive probe set. Syst. Appl. Microbiol. 22:434-444.
10. del Giorgio, P. A., and T. C. Bouvier. 2002. Linking the physiologic and phylogenetic successions in free-living bacterial communities along an estuarine salinity gradient. Limnol. Oceanogr. 47:471-486.
11. Eilers, H., J. Pernthaler, F. O. Glöckner, and R. Amann. 2000. Culturability and in situ abundance of pelagic bacteria from the North Sea. Appl. Environ. Microbiol. 66:3044-3051.
12. Eilers, H., J. Pernthaler, J. Peplies, F. O. Glöckner, G. Gerdts, and R. Amann. 2001. Isolation of novel pelagic bacteria from the German Bight and their seasonal contribution to surface picoplankton. Appl. Environ. Microbiol. 67:5134-5142.
13. Esham, E. C., W. Y. Ye, and M. A. Moran. 2000. Identification and characterization of humic substances-degrading bacterial isolates from an estuarine environment. FEMS Microbiol. Ecol. 34:103-111.
14. Fuchs, B. M., F. O. Glockner, J. Wulf, and R. Amann. 2000. Unlabeled helper oligonucleotides increase the in situ accessibility to 16S rRNA of fluorescently labeled oligonucleotide probes. Appl. Environ. Microbiol. 66:3603-3607.
15. Glöckner, F. O., B. M. Fuchs, and R. Amann. 1999. Bacterioplankton compositions of lakes and oceans: a first comparison based on fluorescence in situ hybridization. Appl. Environ. Microbiol. 65:3721-3726.
16. Glöckner, F. O., E. Zaichikov, N. Belkova, L. Denissova, J. Pernthaler, A. Pernthaler, and R. Amann. 2000. Comparative 16S rRNA analysis of lake bacterioplankton reveals globally distributed phylogenetic clusters including an abundant group of actinobacteria. Appl. Environ. Microbiol. 66:5053-5065.
17. Gray, N. D., R. Howarth, R. W. Pickup, J. G. Jones, and I. M. Head. 2000. Use of combined microautoradiography and fluorescence in situ hybridization to determine carbon metabolism in mixed natural communities of uncultured bacteria from the genus Achromatium. Appl. Environ. Microbiol. 66:4518-4522.
18. Iriberri, J., I. Azua, A. Labirua-Iturburu, I. Artolozaga, and I. Barcina. 1994. Differential elimination of enteric bacteria by protists in a freshwater system. J. Appl. Bacteriol. 77:476-483.
19. Klammer, S., T. Posch, B. Sonntag, C. Griebler, B. Mindl, and R. Psenner. Dynamics of bacterial abundance, biomass, activity, and community composition in the oligotrophic Traunsee and the Traun river (Austria). Water Air Soil Pollut., in press.
20. Kontchou, C. Y., and R. Blondeau. 1992. Biodegradation of soil humic acids by Streptomyces viridosporus. Can. J. Microbiol. 38:203-208.
21. Li, S. L., S. Norioka, and F. Sakiyama. 1998. Bacteriolytic activity and specificity of Achromobacter beta-lytic protease. J. Biochem. 124:332-339.
22. Li, S. L., S. Norioka, and F. Sakiyama. 1997. Purification, staphylolytic activity, and cleavage sites of alpha-lytic protease from Achromobacter lyticus. J. Biochem. 122:772-778.
23. Methé, B. A., W. D. Hiorns, and J. P. Zehr. 1998. Contrasts between marine and freshwater bacterial community composition: analyses of communities in Lake George and six other Adirondack lakes. Limnol. Oceanogr. 43:368-374.
24. Nürnberg, G. K., and M. Shaw. 1998. Productivity of clear and humic lakes: nutrients, phytoplankton, bacteria. Hydrobiologia 382:97-112.
25. Pechlaner, R. 1979. Response of the eutrophied Piburger See to reduced external loading and removal of monimolimnetic water. Arch. Hydrobiol. Beih. Erg. Limnol. 37:293-305.
26. Pernthaler, A., J. Pernthaler, and R. Amann. 2002. Fluorescence in situ hybridization and catalyzed reporter deposition for the identification of marine bacteria. Appl. Environ. Microbiol. 68:3094-3101.
27. Pernthaler, J., F. O. Glöckner, W. Schönhuber, and R. Amann. 2001. Fluorescence in situ hybridization (FISH) with rRNA-targeted oligonucleotide probes. Methods Microbiol. 30:207-226.
28. Pernthaler, J., F. O. Glöckner, S. Unterholzner, A. Alfreider, R. Psenner, and R. Amann. 1998. Seasonal community and population dynamics of pelagic Bacteria and Archaea in a high mountain lake. Appl. Environ. Microbiol. 64:4299-4306.
29. Pernthaler, J., T. Posch, K. Simek, J. Vrba, A. Pernthaler, F. O. Glöckner, U. Nübel, R. Psenner, and R. Amann. 2001. Predator-specific enrichment of actinobacteria from a cosmopolitan freshwater clade in mixed continuous culture. Appl. Environ. Microbiol. 67:2145-2155.
30. Posch, T., K. Simek, J. Vrba, J. Pernthaler, J. Nedoma, B. Sattler, B. Sonntag, and R. Psenner. 1999. Predator-induced changes of bacterial size-structure and productivity studied on an experimental microbial community. Aquat. Microb. Ecol. 18:235-246.
31. Rappe, M. S., D. A. Gordon, K. L. Vergin, and S. J. Giovannoni. 1999. Phylogeny of actinobacteria small subunit (SSU) rRNA gene clones recovered from marine bacterioplankton. Syst. Appl. Microbiol. 22:106-112.
32. Simek, K., D. Babenzien, T. Bittl, R. Koschel, M. Macek, J. Nedoma, and J. Vrba. 1998. Microbial food webs in an artificially divided acidic bog lake, Int. Rev. Hydrobiol. 83:3-18.
33. Tonolla, M., A. Demarta, R. Peduzzi, and D. Hahn. 1999. In situ analysis of phototrophic sulfur bacteria in the chemocline of meromictic Lake Cadagno (Switzerland). Appl. Environ. Microbiol. 65:1325-1330.
34. Tranvik, L. J. 1988. Availability of dissolved organic-carbon for planktonic bacteria in oligotrophic lakes of differing humic content. Microb. Ecol. 16:311-322.
35. Tsunasawa, S., T. Masaki, M. Hirose, M. Soejima, and F. Sakiyama. 1989. The primary structure and structural characteristics of Achromobacter lyticus protease-1, a lysine-specific serine protease. J. Biol. Chem. 264:3832-3839.
36. Zwart, G., B. C. Crump, M. Agterveld, F. Hagen, and S. K. Han. 2002. Typical freshwater bacteria: an analysis of available 16S rRNA gene sequences from plankton of lakes and rivers. Aquat. Microb. Ecol. 28:141-155.