Fluorescent oligonucleotide rDNA probes that specifically bind to a common nanoflagellate, Paraphysomonas vestita

Microbiology

Volumn 143, Issue 5, 1997, Pages 1717-1727

  Rice, Jason ^a   O'Connor, C David ^a   Sleigh, Michael A ^a   Burkill, Peter H ^b   Giles, Ian G ^a   Zubkov, Mikhail V ^a  

^a UNIVERSITY OF SOUTHAMPTON   (United Kingdom)

^b PLYMOUTH MARINE LABORATORY   (United Kingdom)

Author keywords

Flagellate recognition; Fluorescent oligonucleotide probes; Nanoflagellates; Ribosomal RNA

Indexed keywords

RIBOSOME DNA; RIBOSOME RNA;

ARTICLE; DNA RNA HYBRIDIZATION; FLAGELLATE; FLUORESCENCE; NONHUMAN; NUCLEOTIDE SEQUENCE; OLIGONUCLEOTIDE PROBE; PRIORITY JOURNAL; SPECIES DIFFERENTIATION;

CILIOPHORA; EUKARYOTA; MASTIGOPHORA (FLAGELLATES); PARAPHYSOMONAS VESTITA; PROTISTA;

EID: 0030943793     PISSN: 13500872     EISSN: None     Source Type: Journal    
DOI: 10.1099/00221287-143-5-1717     Document Type: Article

References (39)

1. Amann, R. I., Krumholz, L. & Stahl, D. A. (1990). Fluorescent oligonucleotide probing of whole cells for determinative, phylogenetic and environmental studies in microbiology. J Bacteriol 172, 762-770.
2. Amann, R. I., Ludwig, W. & Schleifer, K.-H. (1992). Identification and in situ detection of individual bacterial cells. FEMS Microbiol Lett 100, 45-50.
3. Amann, R. I., Ludwig, W. & Schleifer, K.-H. (1995). Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59, 143-169.
4. Azam F., Fenchel, T., Field, J. G., Meyer-Reil, L. A. & Thingstad, F. (1983). The ecological role of water column microbes in the sea. Mar Ecol Prog Ser 10, 257-263.
5. Bertin, B., Broux, O. & Van Hoegaerden, M. (1990). Flow cytometric detection of yeast by in situ hybridisation with a fluorescent ribosomal RNA probe. J Microbiol Methods 12, 1-12.
6. Bohlool B. B. & Schmidt, E. L. (1980). The immunofluorescence approach in microbial ecology. Adv Microb Ecol 4, 203-241.
7. Breslauer, K. J.. Frank, R., Blocker, H. & Nlarkey, L. A. (1986). Predicting DNA duplex stability from the base sequence. Proc Natl Acad Sci USA 83, 3746-3750.
8. Bresser, J. & Evinger-Hodges, M. (1987). Comparison and optimisation of in situ hybridisation procedures yielding rapid, sensitive mRNA detections. Gene Anal Tech 4, 89-104.
9. Burkill, P. H., Edwards, E. S., Landry, M., Paranjape, M., Reckermann, M., Sieracki, M., Sleigh, M. A., Stoecker, D. K. & Verity, P. (1994). Microzooplankton biomass: JGOFS protocols. In Protocols for the Joint Global Ocean Flux Study (JGOFS) Core Measurements, Intergovernmental Oceanographic Commission Manual and Guide, vol. 29, pp.147-151. Edited by A. H. Knap. Paris: UNESCO.
10. Campbell, L., Shapiro, L. P. & Haugen, E. (1994). Immunochemical characterization of eukaryotic ultraplankton from the Atlantic and Pacific oceans. J Plankton Res 16, 35-51.
11. Clarholm, M. (1984). Microbes as predators or prey. Heterotrophic, free-living protozoa: neglected microorganisms with an important task in regulating bacterial populations. In Current Perspectives in Microbial Ecology, pp. 321-326. Edited by M. J. Klug & C. A. Reddy. Washington, DC: American Society for Microbiology.
12. Dale, R. M. K. & Ward, D. C. (1975). Mercurated polynucleotides: new probes for hybridisation and selective polymer fractionation. Biochemistry 14, 2458-2469.
13. DeLong, E. F., Wickam, G. S. & Pace, N. R. (1989). Phylogenetic stains: ribosomal RNA-based probes for the identification of single cells. Science 243, 1360-1363.
14. DeLong, E. F., Wu, K. Y., Prézelin, B. B. & Jovine, R. V. M. (1994). High abundance of Archaea in Antarctic marine picoplankton. Nature 371, 695-697.
15. Devereux, R., Kane, M. D., Winfrey, J. & Stahl, D. A. (1992). Genus- and group-specific hybridisation probes for determination and environmental studies of sulphate reducing bacteria. Syst Appl Microbiol 15, 601-609.
16. Felsenstein, J. (1995). Phylip Manual (version 3.5c). Seattle: University of Washington.
17. Fenchel, T. (1982). Ecology of heterotrophic microflagellates. IV. Quantitative occurrence and importance as bacterial consumers. Mar Ecol Prog Ser 9, 35-42.
18. Fenchel, T. (1988). Marine plankton food chains. Annu Rev Ecol Syst 19, 19-38.
19. Giovannoni, S. J., De Long, E. F., Olsen, G. J. & Pace, N. R. (1988). Phylogenetic group-specific oligodeoxynucleotide probes for the identification of single microbial cells. J Bacteriol 170, 720-726.
20. Giovannoni, S. J., Britschgi, T. B., Moyer, C. L. & Field, K. G. (1990). Genetic diversity in Sargasso Sea bacterioplankton. Nature 345, 60-63.
21. Göbel, U. B., Geiser, A. & Stanbridge, E. J. (1987). Oligonucleotide probes complementary to variable regions of ribosomal RNA discriminate between Mycoplasma species. J Gen Microbiol 133, 1969-1974.
22. Hicks, R. E., Amann, R. I. & Stahl, D. A. (1992). Dual staining of natural bacterioplankton with 4′,6-diamidino-2-phenylindole and fluorescent oligonucleotide probes targeting Kingdom-level 16S rRNA sequences. Appl Environ Microbiol 58, 2158-2163.
23. Katz, S. (1963). The reversible reaction of Hg(II) and double-stranded polynucleotides. A step function theory and its significance. Biochim Biophys Acta 68, 240-253.
24. Lee, S. & Kemp, P. F. (1994). Single-cell RNA content of natural marine planktonic bacteria measured by hybridization with multiple 16S rRNA-targeted fluorescent probes. Limnol Oceanogr 39, 869-879.
25. Lee, S., Malone, C. & Kemp, P. F. (1993). Use of multiple 16S rRNA-targeted fluorescent probes to increase signal strength and measure cellular RNA from natural planktonic bacteria. Mar Ecol Prog Ser 101, 193-201.
26. Lim, E. L., Amaral, L. A., Caron, D. A. & DeLong, E. F. (1993). Applicant of rRNA-based probes for observing marine nanoplanktonic protists. Appl Environ Microbiol 59, 1647-1655.
27. Lim, E. L., Caron, D. A. & DeLong, E. F. (1996). Development and field application of a quantitative method for examining natural assemblages of protists with oligonucleotide probes. Appl Environ Microbiol 62, 1416-1423.
28. Manz, W., Szewzyk, U., Ericsson, P., Amann, R., Schleifer, K.-H. & Stenström, T.-A. (1993). In situ identification of bacteria in drinking water and adjoining biofilms by hybridisation with 16S and 23S rRNA-directed fluorescent oligonucleotide probes. Appl Environ Microbiol 59, 2293-2298.
29. Neefs, J.-M., Van de Peer, Y., Hendricks, L. & De Wachter, R. (1990). Compilation of small ribosomal subunit RNA sequences. Nucleic Acids Res 18 (suppl.), 2237-2317.
30. Neefs, J.-M., Van de Peer, Y., De Rijk, P., Goris, A. & De Wachter, R. (1991). Compilation of small ribosomal subunit RNA sequences. Nucleic Acids Res 19 (suppl.), 1987-2018.
31. Nickrent, D. L. & Sargent, M. L. (1991). An overview of the secondary structure of the V4 region of Eukaryotic small-subunit ribosomal RNA. Nucleic Acids Res 19, 227-235.
32. Olsen, G. J. (1994). Archaea, Archaea, everywhere. Nature 371, 657-658.
33. Schildkraut, C. & Lifson, S. (1965). Dependence of the melting temperature of DNA on salt concentration. Biopolymers 3, 195-208.
34. Sherr, E. B. & Sherr, B. F. (1994). Bacterivory and herbivory: key roles of phagotrophic protists in pelagic food webs. Microb Ecol 28, 223-235.
35. Stahl, D. A. & Amann, R. (1991). Development and application of nucleic acid probes. In Nucleic Acid Techniques in Bacterial Systematics, pp. 205-244. Edited by E. Stackebrandt & M. Goodfellow. Chichester: Wiley.
36. Stahl, D. A., Flesher, B., Mansfield, H. R. & Montgomery, L. (1988). Use of phylogenetically based hybridisation probes for studies of ruminai microbial ecology. Appl Environ Microbiol 54, 1079-1084.
37. Thompson, J. D., Higgins, D. G. & Gibson, T. J. (1994). Clustal W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22, 4673-4680.
38. Trebesius, K., Amann, R., Ludwig, W., Mühlegger, K. & Schleifer, K.-H. (1994). Identification of whole fixed bacterial cells with nonradioactive 23S rRNA-targeted polynucleotide probes. Appl Environ Microbiol 60, 3228-3235.
39. Ward, D. M., Weller, R. & Bateson, M. M. (1990). 16S rRNA sequences reveal numerous uncultured microorganisms in a natural community. Nature 345, 63-65.