In situ hybridization of phytoplankton using fluorescently labeled rRNA probes

Methods in Enzymology

Volumn 395, Issue , 2005, Pages 299-310

  Groben, René ^a   Medlin, Linda ^a  

^a NONE

Author keywords

[No Author keywords available]

Indexed keywords

FLUORESCENT DYE; FLUOROCHROME; MICROSATELLITE DNA; RIBOSOME RNA;

ALGA; ALGAL CELL CULTURE; AMPLIFIED FRAGMENT LENGTH POLYMORPHISM; CELL TYPE; DNA FINGERPRINTING; DNA SEQUENCE; FLUORESCENCE MICROSCOPY; IN SITU HYBRIDIZATION; MOLECULAR PROBE; NONHUMAN; OLIGONUCLEOTIDE PROBE; PHYTOPLANKTON; PRIORITY JOURNAL; RANDOM AMPLIFIED POLYMORPHIC DNA; REVIEW; RNA PROBE; SEQUENCE ANALYSIS; SIMPLE SEQUENCE REPEAT; TAXONOMY; WHOLE CELL;

ALGAE;

EID: 19944399735     PISSN: 00766879     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0076-6879(05)95018-0     Document Type: Article

References (34)

1. Amann R.I. In situ identification of micro-organisms by whole cell hybridization with rRNA-targeted nucleic acid probes. Akkermans A.D.L., van Elsas J.D., de Bruijn F.J. "Molecular Microbial Ecology Manual 3.3.6" 1995;1-15 Kluwer Academic Publishers, Dordrecht, NL
2. Amann R., Fuchs B.M., Behrens S. The identification of microorganisms by fluorescence in situ hybridization. Curr. Opin. Biotechnol. 12:2001;231-236
3. Anderson R.A., Saunders G.W., Paskind M.P., Sexton J.P. The ultrastructure and 18S rRNA gene sequence for Pelagomonas calceolata gen. & sp. nov., and the description of a new algal class, the Pelagophyceae classis nov. J. Phycol. 29:1993;701-715
4. Baillie B.K., Belda-Baille C.A., Silvestre V., Sison M., Gomez A.V., Monje V. Genetic variation in Symbiodinium isolates from giant clams based on random-amplified-polymorphic DNA (RAPD) patterns. Mar. Biol. 136:2000;829-836
5. Barker G.L.A., Green J.C., Hayes P.K., Medlin L.K. Preliminary results using the RAPD analysis to screen bloom populations of Emiliania huxleyi (Haptophyta). Sarsia. 79:1994;301-306
6. Brand L.E. Review of genetic variation in marine phytoplankton species and the ecological implications. Biol. Oceanogr. 6:1989;397-409
7. Guillou L., Chretiennot-Dinet M.-J., Medlin L.K., Claustre H., Goeer S.L.-D., Vaulot D. Bolidomonas: A new genus with two species belonging to a new algal class, the Bolidophyceae (Heterokonta). J. Phycol. 35:1999a;368-381
8. Guillou L., Moon-van-der-Staay S.Y., Claustre H., Partensky F., Vaulot D. Diversity and abundance of Bolidophyceae (Heterokonta) in two oceanic regions. Appl. Environ. Microbiol. 65:1999b;4528-4536
9. Iglesias-Rodriguez M.D., Garcia Sáez A., Groben R., Edwards K.J., Batley J., Medlin L.K., Hayes P.K. Polymorphic microsatellite loci in global populations of the marine coccolithophorid. Emiliania huxleyi. Mol. Ecol. Notes. 2:2002;495-497
10. John U., Cembella A., Hummert C., Elbrächter M., Groben R., Medlin L.K. Discrimination of the toxigenic dinoflagellate species Alexandrium tamarense and Alexandrium ostenfeldii in co-occurring natural populations from Scottish coastal waters. Eur. J. Phycol. 38:2003;25-40
11. John U., Groben R., Beszteri B., Medlin L.K. Utility of amplified fragment length polymorphisms (AFLP) to analyse genetic structures within the Alexandrium tamarense species complex. Protist. 155:2004;169-179
12. Karp A., Isaac P.G., Ingram D.S. "Molecular Tools for Screening Biodiversity." 1998;Chapman & Hall, London, UK
13. Kawachi M., Inouye I., Honda D., O'Kelly C.J., Bailey J.C., Bidigare R.R., Andersen R.A. The Pinguiophyceae classis nova, a new class of photosynthetic strameophiles whose member produce large amounts of omega-3 fatty acid. Phycol. Res. 50:2002;31-47
14. Kristiansen J. Biogeography of silica-scaled chrysophytes. Nova Hedwigia Beih. 132:2001;23-39
15. Lange M., Guillou L., Vaulot D., Simon N., Amann R.I., Ludwig W., Medlin L.K. Identification of the class Prymnesiophyceae and the genus Phaeocystis with ribosomal RNA-targeted nucleic acid probes detected by flow cytometry. J. Phycol. 32:1996;858-868
16. Medlin L.K., Lange M., Edvardsen B., Larsen A. Cosmopolitan flagellates and their genetic links. Green J.C., Leadbeater B.S.C. "The Flagellate Algae" 2000a;288-308 Francis and Taylor, London
17. Medlin L.K., Lange M., Noethig E.V. Genetic diversity of marine phytoplankton: A review and a look to Antarctic phytoplankton. Antarctic. Sci. 12:2000b;325-331
18. Miller P.E., Scholin C.A. Identification and enumeration of cultures and wild Pseudo-Nitzschia (Bacillariophyceae) using species-specific LSU rRNA-targeted fluorescent probes and filter-based whole cell hybridization. J. Phycol. 34:1998;371-382
19. Moon-van der Staay S.Y., van der Staay G.W.M., Guillou L., Claustre H., Vaulot D. Abundance and diversity of Prymnesiophyceae in picoplankton communities from the equatorial Pacific Ocean inferred from 18S rDNA sequences. Limnol. Oceanogr. 45:2000;98-109
20. Ormond R.F., Gage J.D., Angel M.V. "Marine Biodiversity: Patterns and Processes." 1998;Cambridge University Press, Cambridge
21. Parsons M.L., Scholin C.A., Miller P.E., Doucette G.J., Powell C.L., Fryxell G.A., Dortch Q., Soniat T.M. Pseudo-nitzschia species (Bacillariophyceae) in Louisiana coastal waters: Molecular probe field trials, genetic variability, and domoic acid analyses. J. Phycol. 35:(Suppl):1999;1368- 1378
22. Partensky F., Hoepffner N., Li W.K.W., Ulloa O., Vaulot D. Photoacclimation of Prochlorococcus sp. (Prochlorophyta) strains isolated from the North Atlantic and the Mediterranean Sea. Plant Physiol. 101:1993;285-296
23. Posada D., Crandall K.A. Modeltest: Testing the model of DNA substitution. Bioinformatics. 14:1998;817-818
24. Rynearson T.A., Armbrust E.V. DNA fingerprinting reveals extensive genetic diversity in a field population of the centric diatom. Ditylum brightwellii. Limnol. Oceanogr. 45:2000;1329-1340
25. Scholin C.A., Buck K.R., Britschgi T., Cangelosi G., Chavez F.P. Identification of Pseudo-nitzschia australis (Bacillariophyceae) using rRNA-targeted probes in whole cell and sandwich hybridization formats. Phycologia. 35:1996;190-197
26. Scholin C., Miller P., Buck K., Chavez F., Harris P., Haydock P., Howard J., Cangelosi G. Detection and quantification of Pseudo-nitzschia australis in cultured and natural populations using LSU rRNA-targeted probes. Limnol. Oceanogr. 42:1997;1265-1272
27. Simon N., Brenner J., Edvardsen B., Medlin L.K. The identification of Chrysochromulina and Prymnesium species (Haptophyta, Prymnesiophyceae) using fluorescent or chemiluminescent oligonucleotide probes: A means for improving studies on toxic algae. Eur. J. Phycol. 32:1997;393-401
28. Simon N., Campbell L., Ornolfsdottir E., Groben R., Guillou L., Lange M., Medlin L.K. Oligonucleotide probes for the identification of three algal groups by dot blot and fluorescent whole-cell hybridization. J. Euk. Microbiol. 47:2000;76-84
29. Simon N., LeBot N., Marie D., Partensky F., Vaulot D. Fluorescent in situ hybridization with rRNA-targeted oligonucleotide probes to identify small phytoplankton by flow cytometry. Appl. Environ. Microbiol. 61:1995;2506-2513
30. Stahl D.A., Amann R. Development and application of nucleic acid probes. Stackebrandt E., Goodfellow M. "Nucleic Acids Techniques in Bacterial Systematics" 1991;205-248 John Wiley & Sons, Chichester, UK
31. Swofford D.L. PAUP*, Phylogenetic Analysis Using Parsimony. Version 4.0 Beta version 8, program and documentation. 2002;Illinois Natural History Survey, University of Illinois, Champaign, IL
32. Waterbury J.B., Watson S.W., Guillard R.R.L., Brand L.E. Widespread occurrence of a unicellular, marine planktonic cyanobacterium. Nature. 277:1979;293-294
33. Woese C.R. Bacterial evolution. Microbiol. Rev. 51:1987;221-271
34. Wood A.M., Leatham T. The species concept in phytoplankton ecology. J. Phycol. 28:1992;723-729