Quantitative assessment of picoeukaryotes in the natural environment by using taxon-specific oligonucleotide probes in association with tyramide signal amplification-fluorescence in situ hybridization and flow cytometry

Applied and Environmental Microbiology

Volumn 69, Issue 9, 2003, Pages 5519-5529

  Biegala, Isabelle C ^a   Not, Fabrice ^a   Vaulot, Daniel ^a   Simon, Nathalie ^a  

^a STATION BIOLOGIQUE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

BIOMASS; FLUORESCENCE; SURFACE ACTIVE AGENTS;

MARINE PLANKTON BIOMASS;

MICROBIOLOGY;

SEA WATER;

FLOW CYTOMETRY; PICOPLANKTON; QUANTITATIVE ANALYSIS;

AQUATIC ENVIRONMENT; ARTICLE; BACTERIOPLANKTON; CELL COUNT; CELL LOSS; CONTROLLED STUDY; CYANOBACTERIUM; ESTUARY; EUKARYOTE; FLOW CYTOMETRY; FLUORESCENCE IN SITU HYBRIDIZATION; GEOGRAPHIC DISTRIBUTION; MICROBIAL BIOMASS; NONHUMAN; NUCLEOTIDE SEQUENCE; OLIGONUCLEOTIDE PROBE; PICOEUKARYOTE; QUANTITATIVE ANALYSIS; TAXONOMIC IDENTIFICATION; WATER TEMPERATURE;

ANIMALS; BASE SEQUENCE; BIOMASS; CHLAMYDOMONAS; ENVIRONMENT; EUKARYOTIC CELLS; FLOW CYTOMETRY; FRANCE; IN SITU HYBRIDIZATION, FLUORESCENCE; KINETICS; OLIGONUCLEOTIDE PROBES; PLANKTON; SEAWATER;

CHLOROPHYTA; CYANOBACTERIA; EUKARYOTA; MAMIELLALES; PELAGOPHYCEAE; PRASINOPHYCEAE;

EID: 0141592791     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.69.9.5519-5529.2003     Document Type: Article

References (60)

1. Amann, R. I., B. J. Binder, R. J. Olson, S. W. Chisholm, R. Devereux, and D. A. Stahl. 1990. Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analysing mixed microbial populations. Appl. Environ. Microbiol. 56:1919-1925.
2. Amann, R. I., L. Krumholz, and D. A. Stahl. 1990. Fluorescent-oligonucleotide probing of whole cells for determinative, phytogenetic, and environmental studies in microbiology. J. Bacteriol. 172:762-770.
3. Amann, R. I., B. Zarda, D. A. Stahl, and K.-H. Schleifer. 1992. Identification of individual prokaryotic cells by using enzyme-labeled, rRNA-targeted oligonucleotide probes. Appl. Environ. Microbiol. 58:3007-3011.
4. Andersen, R. A., G. W. Saunders, M. P. Paskind, and J. P. Sexton. 1993. Ultrastructure and 18S rRNA gene sequence for Pelagomonas calceolata gen. et sp. nov. and the description of a new algal class, the Pelagophyceae classis nov. J. Phycol. 29:701-715.
5. Båmstedt, U., and H. R. Skjoldal. 1976. Studies on the deep water pelagic community of Korfjorden, western Norway. Adenosine phosphate and nucleic acids in Euchaeta norvegica (Copepoda) in relation to its life cycle. Sarsia 60:63-80.
6. Biegala, I. C., G. Kennaway, E. Alverca, J.-F. Lennon, D. Vaulot, and N. Simon. 2002. Identification of bacteria associated with dinoflagellates (Dinophyceae) Alexandrium spp. using tyramide signal amplification-fluorescence in situ hybridization and confocal microscopy. J. Phycol. 38:404-411.
7. Binder, B. J., and Y. C. Liu. 1998. Growth rate regulation of rRNA content of a marine Synechococcus (Cyanobacteria) strain. Appl. Environ. Microbiol. 64:3346-3351.
8. Bobrow, M. N., T. D. Harris, K. J. Shaughnessy, and G. J. Litt. 1989. Catalyzed reporter deposition, a novel method of signal amplification. J. Immuno. Methods 125:279-285.
9. Buckley, L. J. 1984. RNA-DNA ratio: an index of larval fish growth in the sea. Mar. Biol. 80:291-298.
10. Claustre, H., and J.-C. Marty. 1995. Specific phytoplankton biomasses and their relation to primary production in the tropical North Atlantic. Deep-Sea Res. 142:1475-1493.
11. Collier, J. L. 2000. Flow cytometry and single cell in phycology. J. Phycol. 36:628-644.
12. Colobert-Le Floch, I. 2001. Absorption et régéné ration de l'azote dans les systèmes côtiers; réponse à des apports massifs de nitrate. Ph.D. thesis. Université de Bretagne Occidentale, Brest, France.
13. Courties, C., A. Vaquer, M. Troussellier, J. Lautier, M.-J. Chrétiennot-Dinet, J. Neveux, C. Machado, and H. Claustre. 1994. Smallest eukaryotic organism. Nature 370:255.
14. DeLong, E. F., G. S. Wickham, and N. R. Pace. 1989. Phylogenetic stains: ribosomal RNA-based probes for the identification of single cells. Science 243:1360-1363.
15. Díez, B., C. Pedrós-Alió, T. L. Marsh, and R. Massana. 2001. Application of denaturing gradient gel electrophoresis (DGGE) to study the diversity of marine picoeukaryotic assemblages and comparison of DGGE with other molecular techniques. Appl. Environ. Microbiol. 67:2942-2951.
16. Dortch, Q., T. L. Roberts, J. R. Clayton, and S. I. Ahmed. 1983. RNA/DNA ratios and DNA concentrations as indicators of growth rate and biomass in planktonic marine organisms. Mar. Ecol. Prog. Ser. 13:61-71.
17. Eikrem, W., and J. Throndsen. 1990. The ultrastructure of Bathycoccus gen. nov. and B. prasinos sp. nov., a non-motile picoplanktonic alga (Chlorophyta, Prasinophyceae) from the Mediterranean and Atlantic. Phycologia 29:344-350.
18. 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.
19. Giovanonni, S. J., E. F. DeLong, G. J. Olsen, and N. R. Pace. 1988. Phylogenetic group specific oligonucleotide probes for identification of single microbial cell. J. Bacteriol. 170:720-726.
20. Graham, L. E., and L. W. Wilcox. 2000. Algae. Prentice-Hall Press, London, United Kingdom.
21. Guillou, L., S.-Y. Moon-Van der Staay, H. Claustre, F. Partensky, and D. Vaulot. 1999. Diversity and abundance of Bolidophyceae (Heterokonta) in two oceanic regions. Appl. Environ. Microbiol. 65:4528-4536.
22. Johnson, P. W., and J. McN. Sieburth. 1982. In-situ morphology and occurrence of eukaryotic phototrophs of bacterial size in the picoplankton of estuarine and oceanic waters. J. Phycol. 18:318-327.
23. Keller, M. D., R. C. Selvin, W. Claus, and R. R. L. Guillard. 1987. Media for the culture of oceanic ultraphytoplankton. J. Phycol. 23:633-638.
24. Leharon, P., P. Catala, C. Fajon, F. Joux, J. Baudart, and L. Bernard. 1997. A new sensitive, whole-cell hybridization technique for detection of bacteria involving a biotinylated oligonucleotide probe targeting rRNA and tyramide signal amplification. Appl. Environ. Microbiol. 63:3274-3278.
25. Leser, T. D., M. Boye, and N. B. Hendriksen. 1995. Survival and activity of Pseudomonas sp. strain B13(FR1) in a marine microcosm determined by quantitative PCR and an rRNA-targeting probe and its effect on the indigenous bacterioplankton. Appl. Environ. Microbiol. 61:1201-1207.
26. L'Helguen, S., C. Madec, and P. Le Corre. 1996. Nitrogen uptake in permanently well-mixed temperate coastal waters. Estuarine Coast. Shelf Sci. 42:803-818.
27. Li, W. K. W. 1994. Primary production of prochlorophytes, cyanobacteria, and eucaryotic ultraphytoplankton: measurements from flow cytometric sorting. Limnol. Oceanogr. 39:169-175.
28. Li, W. K. W. 1995. Composition of ultraphytoplankton in the central North Atlantic. Mar. Ecol. Prog. Ser. 122:1-8.
29. Lim, E. L., L. A. Amaral, D. A. Caron, and E. F. DeLong. 1993. Application of rRNA-based probes for observing marine nanoplanktonic protists. Appl. Environ. Microbiol. 59:1647-1655.
30. Lim, E. L., D. A. Caron, and E. F. DeLong. 1996. Development and field application of a quantitative method for examining natural assemblages of protists with oligonucleotide probes. Appl. Environ. Microbiol. 62:1416-1423.
31. López-García, P., F. Rodríguez-Valera, C. Pedrós-Alió, and D. Moreira. 2001. Unexpected diversity of small eukaryotes in deep-sea Antarctic plankton. Nature 409:603-607.
32. Manton, I., and M. Parke. 1960. Further observations on small green flagellates with special reference to possible relatives of Chromulina pusilla Butcher. J. Mar. biol. Assoc. U.K. 39:275-298.
33. Marie, D., N. Simon, L. Guillou, F. Partensky, and D. Vaulot. 2000. DNA/RNA analysis of phytoplankton by flow cytometry. Curr. Protocols Cytometry 12(Suppl. 11):1-14.
34. Moon-van der Staay, S. Y., R. De Watchter, and D. Vaulot. 2001. Oceanic 18S rDNA sequences from picoplankton reveal unsuspected eukaryotic diversity. Nature 409:607-610.
35. Not, F., N. Simon, I. C. Biegala, and D. Vaulot. 2002. Application of fluorescence in situ hybridization with tyramide signal amplification (FISH-TSA) to assess eukaryotic picoplankton composition. Aquat. Microbiol. Ecol. 28:157-166.
36. Paul, J. H., A. Alfreider, and B. Wawrik. 2000. Micro- and macrodiversity in rbcL sequences in ambient phytoplankton populations from the southeastern Gulf of Mexico. Mar. Ecol. Prog. Ser. 198:9-18.
37. 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.
38. 2S in photosynthetic biofilms determined by oligonucleotide probes and microelectrodes. Appl. Environ. Microbiol. 59:3840-3849.
39. Rice, J., M. A. Sleigh, P. H. Burkill, G. A. Tarran, C. D. O'Connor, and M. V. Zubkov. 1997. Flow cytometric analysis of characteristics of hybridization of species-specific fluorescent oligonucleotide probes to rRNA of marine nanoflagellates. Appl. Environ. Microbiol. 63:938-944.
40. Schönuber, W., B. Fuchs, S. Juretschko, and R. Amann. 1997. Improved sensitivity of whole-cell hybridization by the combination of horseradish peroxidase-labeled oligonucleotides and tyramide signal amplification. Appl. Environ. Microbiol. 63:3268-3273.
41. Schönuber, W., B. Zarda, S. Eix., R. Rippka, M. Herdman, W. Ludwig, and R. Amann. 1999. In situ identification of cyanobacteria with horseradish peroxidase-labeled, rRNA-targeted oligonucleotide probes. Appl. Environ. Microbiol. 65:1259-1267.
42. Shapiro, L. P., and R. R. L. Guillard. 1986. Physiology and ecology of the marine eukaryotic ultraplankton. Can. Bull. Fish. Aquat. Sci. 214:371-389.
43. Sharma, V. K., K. B. Rhudy, and F. J. Millero. 2000. Diurnal variation of Texas "brown tide" (Aureoumbra lagunensis) in relation to metals. J. Environ. Sci. Health 35:1077-1088.
44. Sieburth, J. M., P. W. Johnson, and P. E. Hargraves. 1988. Ultrastructure and ecology of Aureococcus anaphageferens gen. et sp. nov. (Chrysophyceae): the dominant picoplankter during a bloom in Narragansett Bay, Rhode Island, summer 1985. J. Phycol. 24:416-425.
45. Simon, N., N. LeBot, D. Marie, F. Partensky, and D. Vaulot. 1995. Fluorescence in situ hybridization with rRNA-targeted oligonucleotide probes to identify small phytoplankton by flow cytometry. Appl. Environ. Microbiol. 61:2506-2613.
46. Simon, N., L. Campbell, E. Örnolfsdottir, R. Groben, L. Guillou, M. Lange, and L. K. Medlin. 2000. Oligonucleotide probes for the identification of three algal groups by dot blot and fluorescent whole-cell hybridization. J. Eukaryol. Microbiol. 47:76-84.
47. Stahl, D. A., and R. Amann. 1991. Development and application of nucleic acid probes, p. 205-248. In E. Stackebrandt and M. Goodfellow (ed.), Nucleic acid techniques in bacterial systematics. John Wiley & Sons Inc., New York, N.Y.
48. Stockner, J. G., and N. J. Antia. 1986. Algal picoplankton from marine and freshwater ecosystems: a multidisciplinary perspective. Can. J. Fish. Aquat. Sci. 43:2472-2503.
49. Thomas, J.-C., M. Desrosiers, Y. St-Pierre, P. Lirette, J.-G. Bisaillon, R. Beaudet, and R. Villemur. 1997. Quantitative flow cytometric detection of specific microorganisms in soil samples using rRNA targeted fluorescent probes and ethidium bromide. Cytometry 27:224-232.
50. Throndsen, J. 1976. Occurrence and productivity of small marine flagellates, Norw. J. Bot. 23:269-293.
51. Urdea, M. S., B. D. Warner, J. A. Running, M. Stempien, J. Clyne, and T. Horn. 1988. A comparison of non-radioisotopic hybridization assay methods using fluorescent, chemiluminescent and enzyme labeled synthetic oligodeoxyribonucleotide probes. Nucleic Acids Res. 16:4937-4956.
52. Van Gijlswijk, R. P. M., J. Wiegant, A. K. Raap, and H. J. Tanke. 1996. Improved localization of fluorescent tyramides for fluorescence in situ hybridization using dextran sulfate and polyvinyl alcohol. J. Histochem. Cytochem. 44:389-392.
53. van Hannen, E. J., M. P. van Agterveld, H. J. Gons, and H. J. Laanbroek. 1998. Revealing genetic diversity of eukaryotic microorganisms in aquatic environments by denaturing gradient gel electrophoresis. J. Phycol. 34:206-213.
54. Vaulot, D., and D. Marie. 1999. Diel variability of photosynthetic picoplankton in the equatorial Pacific. J. Geophys. Res. 104:3297-3310.
55. Vaulot, D., K. Romari, and F. Not. 2002. Are autotrophs less diverse than heterotrophs in marine picoplankton? Trends Microbiol. 10:266-267.
56. Veldhuis, M. J. W., and G. W. Kraay. 1990. Vertical distribution and pigment composition of a picoplanktonic prochlorophyte in the subtropical North Atlantic: a combined study of HPLC-analysis of pigments and flow cytometry. Mar. Ecol. Prog. Ser. 68:121-127.
57. Wallner, G., R. Amann, and W. Beisker. 1993. Optimizing fluorescence in situ hybridization with rRNA-targeted oligonucleotide probes for flow cytometry identification of microorganisms. Cytometry 14:136-143.
58. Wallner, G., R. Erhart, and R. Amann. 1995. Flow cytometric analysis of activated sludge with rRNA-targeted probes. Appl. Environ. Microbiol. 61:1859-1866.
59. West, N. J., W. A. Schönuber, N. J. Fuller, R. I. Amann, R. Rippka, A. F. Post, and D. J. Scanlan. 2001. Closely related Prochlorococcus genotypes show remarkably different depth distributions in two oceanic regions as revealed by in situ hybridization using 16S rRNA-targeted oligonucleotides. Microbiology 147:1731-1744.
60. Zubkov, M. V., B. M. Fuchs, P. H. Burkill, and R. Amann. 2001. Comparison of cellular and biomass specific activities of dominant bacterioplankton groups in stratified waters of the Celtic Sea. Appl. Environ. Microbiol. 67:5210-5218.