Automated enumeration of groups of marine picoplankton after fluorescence in situ hybridization

Applied and Environmental Microbiology

Volumn 69, Issue 5, 2003, Pages 2631-2637

  Pernthaler, Jakob ^a   Pernthaler, Annelie ^a   Amann, Rudolf ^a  

^a MAX PLANCK INSTITUTE FOR MARINE MICROBIOLOGY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

CELLS; FILTERS (FOR FLUIDS); FLUORESCENCE; MARINE BIOLOGY; MICROSCOPIC EXAMINATION;

DOUBLE-STAINED MICROBIAL CELLS;

MICROBIOLOGY;

ABUNDANCE ESTIMATION; AUTOMATION; PICOPLANKTON; QUANTITATIVE ANALYSIS;

ARTICLE; ATLANTIC OCEAN; CALIBRATION; CAMERA; CATALYSIS; CELL COUNT; CELL HYBRIDIZATION; COMPUTER PROGRAM; CONTROLLED STUDY; EPIFLUORESCENCE MICROSCOPE; IMAGE ANALYSIS; LABORATORY AUTOMATION; MICROBIAL POPULATION DYNAMICS; NONHUMAN;

AUTOMATION; BACTERIA; COLONY COUNT, MICROBIAL; ECOSYSTEM; GERMANY; IN SITU HYBRIDIZATION, FLUORESCENCE; PLANKTON; SEAWATER;

EID: 0038221073     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.69.5.2631-2637.2003     Document Type: Article

References (41)

1. Amann, R. I., L. Krumholz, and D. A. Stahl. 1990. Fluorescent-oligonucleotide probing of whole cells for determinative, phylogenetic, and environmental studies in microbiology. J. Bacteriol. 172:762-770.
2. 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.
3. Battin, T. J., A. Wille, B. Sattler, and R. Psenner. 2001. Phylogenetic and functional heterogeneity of sediment biofilms along environmental gradients in a glacial stream. Appl. Environ. Microbiol. 67:799-807.
4. Björnsen, P. K., and J. Kuparinen. 1991. Determination of bacterioplankton biomass, net production and growth efficiency in the Southern Ocean. Mar. Ecol. Prog. Ser. 71:185-194.
5. Blackburn, N., T. Fenchel, and J. Mitchell. 1998. Microscale nutrient patches in planktonic habitats shown by chemotactic bacteria. Science 282:2254-2256.
6. Blackburn, N., A. Hagstrom, J. Wikner, R. Cuadroshansson, and P. K. Bjornsen. 1998. Rapid determination of bacterial abundance, biovolume, morphology, and growth by neural network-based image analysis. Appl. Environ. Microbiol. 64:3246-3255.
7. Bloem, J., M. Veninga, and J. Shepherd. 1995. Fully automatic determination of soil bacterium numbers, cell volumes, and frequencies of dividing cells by confocal laser-scanning microscopy and image-analysis. Appl. Environ. Microbiol. 61:926-936.
8. 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.
9. Bruns, A., H. Cypionka, and J. Overmann. 2002. Cyclic AMP and acyl homoserine lactones increase the cultivation efficiency of heterotrophic bacteria from the central Baltic Sea. Appl. Environ. Microbiol. 68:3978-3987.
10. Chisholm, S. W., R. J. Olson, E. R. Zettler, R. Goericke, J. B. Waterbury, and N. A. Welschmeyer. 1988. A novel free-living prochlorophyte abundant in the oceanic euphotic zone. Nature 334:340-343.
11. 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.
12. Daims, H., N. B. Ramsing, K. H. Schleifer, and M. Wagner. 2001. Cultivation-independent, semiautomatic determination of absolute bacterial cell numbers in environmental samples by fluorescence in situ hybridization. Appl. Environ. Microbiol. 67:5810-5818.
13. Del Giorgio, P. A., D. F. Bird, Y. T. Prairie, and D. Planas. 1996. Flow cytometric determination of bacterial abundance in lake plankton with the green nucleic acid stain SYTO 13. Limnol. Oceanogr. 41:783-789.
14. Eilers, H., J. Pernthaler, and R. Amann. 2000. Succession of pelagic marine bacteria during enrichment: a close look on cultivation-induced shifts. Appl. Environ. Microbiol. 66:4634-4640.
15. 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.
16. 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.
17. Gmür, R., B. Guggenheim, E. Giertsen, and T. Thurnheer. 2000. Automated immunofluorescence for enumeration of selected taxa in supragingival dental plaque. Eur. J. Oral Sci. 108:393-402.
18. Jansen, G. J., A. C. M. Wildeboer-Veloo, R. H. J. Tonk, A. H. Franks, and G. Welling. 1999. Development and validation of an automated, microscopy-based method for enumeration of groups of intestinal bacteria. J. Microbiol. Methods 37:215-221.
19. Li, W. 1998. Annual average abundance of heterotrophic bacteria and Synechococcus in surface ocean waters. Limnol. Oceanogr. 43:1746-1753.
20. Llobet-Brossa, E., R. Rossellò-Mora, and R. Amann. 1998. Microbial community composition of Wadden Sea sediments as revealed by fluorescence in situ hybridization. Appl. Environ. Microbiol. 64:2691-2696.
21. Loferer-Krössbacher, M., J. Klima, and R. Psenner. 1998. Determination of bacterial cell dry mass by transmission electron microscopy and densitometric image analysis. Appl. Environ. Microbiol. 64:688-694.
22. Nedoma, J., J. Vrba, T. Hanzl, and L. Nedbalova. 2001. Quantification of pelagic filamentous microorganisms in aquatic environments using the lineintercept method. FEMS Microbiol. Ecol. 38:81-85.
23. Partensky, F., W. R. Hess, and D. Vaulot. 1999. Prochlorococcus, a marine photosynthetic prokaryote of global significance. Microbiol. Mol. Biol. Rev. 63:106-127.
24. 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.
25. Pernthaler, A., J. Pernthaler, H. Eilers, and R. Amann. 2001. Growth patterns of two marine isolates: adaptations to substrate patchiness? Appl. Environ. Microbiol. 67:4077-4083.
26. Pernthaler, A., J. Pernthaler, M. Schattenhofer, and R. Amann. 2002. Identification of DNA-synthesizing bacterial cells in coastal North Sea plankton. Appl. Environ. Microbiol. 68:5728-5736.
27. Pernthaler, J., A. Alfreider, T. Posch, S. Andreatta, and R. Psenner. 1997. In situ classification and image cytometry of pelagic bacteria from a high mountain lake (Gossenköllesee, Austria). Appl. Environ. Microbiol. 63:4778-4783.
28. 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.
29. 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.
30. Posch, T., M. Loferer-Krossbacher, G. Gao, A. Alfreider, J. Pernthaler, and R. Psenner. 2001. Precision of bacterioplankton biomass determination: a comparison of two fluorescent dyes, and of allometric and linear volume-tocarbon conversion factors. Aquat. Microb. Ecol. 25:55-63.
31. Posch, T., J. Pernthaler, A. Alfreider, and R. Psenner. 1997. Cell-specific respiratory activity of aquatic bacteria studied with the tetrazolium reduction method, cyto-clear slides and image analysis. Appl. Environ. Microbiol. 63:867-873.
32. Poulsen, L. K., G. Ballard, and D. A. Stahl. 1993. Use of rRNA fluorescence in situ hybridization for measuring the activity of single cells in young and established biofilms. Appl. Environ. Microbiol. 59:1354-1360.
33. Ramsing, N. B., M. J. Felris, and D. M. Ward. 2000. Highly ordered vertical structure of Synechococcus populations within the one-millimeter-thick photic zone of a hot spring cyanobacterial mat. Appl. Environ. Microbiol. 66:1038-1049.
34. Rappe, M. S., S. A. Connon, K. L. Vergin, and S. J. Giovannoni. 2002. Cultivation of the ubiquitous SAR11 marine bacterioplankton clade. Nature 418:630-633.
35. Russ, J. C. 1990. Computer-assisted microscopy. Plenum Press, Inc., New York, N.Y.
36. Schönholzer, F., D. Hahn, B. Zarda, and J. Zeyer. 2002. Automated image analysis and in situ hybridization as tools to study bacterial populations in food resources, gut and cast of Lumbricus terrestris L. J. Microbiol. Methods 48:53-68.
37. Shopov, A., S. C. Williams, and P. G. Verity. 2000. Improvements in image analysis and fluorescence microscopy to discriminate and enumerate bacteria and viruses in aquatic samples. Aquat. Microb. Ecol. 22:103-110.
38. Sieracki, M. E., P. W. Johnson, and J. M. Sieburth. 1985. Detection, enumeration, and sizing of planktonic bacteria by image-analyzed epifluorescence microscopy. Appl. Environ. Microbiol. 49:799-810.
39. Singleton, S., J. G. Cahill, G. K. Watson, C. Allison, D. Cummins, T. Thurnheer, B. Guggenheim, and R. Gmur. 2001. A fully automated microscope bacterial enumeration system for studies of oral microbial ecology. J. Immunoassay Immunochem. 22:253-274.
40. Suzuki, M. T., B. Sherr Evelyn, and F. Sherr Barry. 1993. DAPI direct counting underestimates bacterial abundances and average cell size compared to AO direct counting. Limnol. Oceanogr. 38:1566-1570.
41. Thar, R., N. Blackburn, and M. Kühl. 2000. A new system for three-dimensional tracking of motile microorganisms. Appl. Environ. Microbiol. 66:2238-2242.