The extent of protist diversity: Insights from molecular ecology of freshwater eukaryotes

Proceedings of the Royal Society B: Biological Sciences

Volumn 272, Issue 1576, 2005, Pages 2073-2081

  Šlapeta, Jan ^a   Moreira, David ^a   López García, Purificación ^a  

^a UNIVERSITÉ PARIS SUD   (France)

Author keywords

Environmental PCR; Eukaryotes; Molecular ecology; Protist diversity

Indexed keywords

RIBOSOME RNA;

EUKARYOTE; FRESHWATER ECOSYSTEM; MOLECULAR ECOLOGY; PROTIST; SPECIES DIVERSITY;

ARTICLE; CONTROLLED STUDY; EUKARYOTE; FRESHWATER ENVIRONMENT; GENETIC VARIABILITY; MOLECULAR ECOLOGY; NONHUMAN; NUCLEOTIDE SEQUENCE; POND; PRIORITY JOURNAL; RNA GENE; SEDIMENT; TAXONOMY; UNINDEXED SEQUENCE;

ALVEOLATA; CENTROHELIOZOA; CERCOZOA; CILIOPHORA; CRYPTOPHYTA; EUKARYOTA; HAPTOPHYCEAE; PROTISTA; STRAMENOPILES;

EID: 26244431747     PISSN: 09628452     EISSN: 14712970     Source Type: Journal    
DOI: 10.1098/rspb.2005.3195     Document Type: Article

References (53)

1. Amaral Zettler, L. A., Gomez, F., Zettler, E., Keenan, B. G., Amils, R. & Sogin, M. L. 2002 Microbiology: eukaryotic diversity in Spain's River of Fire. Nature 417, 137.
2. Andersen, R. A., Van de Peer, Y., Potter, D., Sexton, J. P., Kawachi, M. & Lajeunesse, T. 1999 Phylogenetic analysis of the SSU rRNA from members of the Chrysophyceae. Protist 150, 71-84.
3. Arndt, H., Dietrich, D., Auer, B., Cleven, E.-J., Grafenhan, T., Weitere, M. & Mylnikov, A. P. 2000 Functional diversity of heterotrophic flagellates in aquatic ecosystems. In The flagellates: unity, diversity and evolution (ed. B. S. C. Leadbeater & J. C. Green), pp. 240-268. London: Taylor & Francis.
4. Baldauf, S. L. 2003 The deep roots of eukaryotes. Science 300, 1703-1706.
5. Bass, D. & Cavalier-Smith, T. 2004 Phylum-specific environmental DNA analysis reveals remarkably high global biodiversity of Cercozoa (Protozoa). Int. J. Syst. Evol. Microbiol. 54, 2393-2404.
6. Berney, C., Fahrni, J. & Pawlowski, J. 2004 How many novel eukaryotic 'kingdoms'? Pitfalls and limitations of environmental DNA surveys. BMC Biol. 2, 13.
7. Bowman, B. H., Taylor, J. W., Brownlee, A. G., Lee, J., Lu, S. D. & White, T. J. 1992 Molecular evolution of the fungi: relationship of the Basidiomycetes, Ascomycetes, and Chytridiomycetes. Mol. Biol. Evol. 9, 285-296.
8. Cavalier-Smith, T. 2004 Only six kingdoms of life. Proc. R. Soc. B 271, 1251-1262. (doi:10.1098/rspb.2004.2705.)
9. Cavalier-Smith, T. & Chao, E. E. 2003a Phylogeny and classification of phylum Cercozoa (Protozoa). Protist 154, 341-358.
10. Cavalier-Smith, T. & Chao, E. E. 2003b Phylogeny of Choanozoa, Apusozoa, and other Protozoa and early eukaryote megaevolution. J. Mol. Evol. 56, 540-563.
11. Clay, B. & Kugrens, P. 1999 Systematics of the enigmatic kathablepharids, including EM characterization of the type species, Kathablepharis phoenikoston, and new observations on K. remigera comb. nov. Protist 150, 43-59.
12. Cole, J. R. et al. 2003 The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy. Nucleic Acids Res. 31, 442-423.
13. Dawson, S. C. & Pace, N. R. 2002 Novel kingdom-level eukaryotic diversity in anoxic environments. Proc. Natl Acad. Sci. USA 99, 8324-8329.
14. Deane, J. A., Strachan, I. M., Saunders, G. W., Hill, D. R. A. & McFadden, G. I. 2002 Cryptomonad evolution: nuclear 18S rDNA phylogeny versus cell morphology and pigmentation. J. Phycol. 38, 1236-1244.
15. de Vargas, C., Norris, R., Zaninetti, L., Gibb, S. W. & Pawlowski, J. 1999 Molecular evidence of cryptic speciation in planktonic foraminifers and their relation to oceanic provinces. Proc. Natl Acad. Sci. USA 96, 2864-2868.
16. Diez, B., Pedros-Alio, C. & Massana, R. 2001 Study of genetic diversity of eukaryotic picoplankton in different oceanic regions by small-subunit rRNA gene cloning and sequencing. Appl. Environ. Microbiol. 67, 2932-2941.
17. Edgcomb, V. P., Kysela, D. T., Teske, A., de Vera Gomez, A. & Sogin, M. L. 2002 Benthic eukaryotic diversity in the Guaymas Basin hydrothermal vent environment. Proc. Natl Acad. Sci. USA 99, 7658-7662.
18. Edvardsen, B., Eikrem, W., Green, J. C., Andersen, R. A., Moon-van der Staay, S. Y. & Medlin, L. K. 2000 Phylogenetic reconstructions of the Haptophyta inferred from 18S ribosomal DNA sequences and available morphological data. Phycologia 39, 19-35.
19. Fenchel, T. & Finlay, B. J. 1995 Ecology and evolution in anoxic worlds. Oxford series in ecology and evolution. Oxford University Press.
20. Finlay, B. J. 1998 The global diversity of Protozoa and other small species. Int. J. Parasitol. 28, 29-48.
21. Finlay, B. J. 2002 Global dispersal of free-living microbial eukaryote species. Science 296, 1061-1063.
22. Finlay, B. J. 2004 Protist taxonomy: an ecological perspective. Phil. Trans. R. Soc. B 359, 599-610. (doi:10.1098/rstb.2003.1450.)
23. Finlay, B. J. & Esteban, G. F. 2001 Exploring Leeuwenhoek's legacy: the abundance and diversity of protozoa. Int. Microbiol. 4, 125-133.
24. Finlay, B. J. & Fenchel, T. 1999 Divergent perspectives on protist species richness. Protist 150, 229-233.
25. Finlay, B. J., Esteban, G. F. & Fenchel, T. 1998 Protozoan diversity: converging estimates of the global number of free-living ciliate species. Protist 149, 29-37.
26. Fleedale, G. & Vickerman, K. 2000 Phylum Euglenozoa. In An illustrated guide to the Protozoa (ed. J. J. Lee, G. F. Leedale & P. Bradbury), vol. 2, pp. 1135-1185. Lawrence, KS: Allen Press.
27. Foissner, W. 1999 Protist diversity: estimates of the near-imponderable. Protist 150, 363-368.
28. Green, J. C., Perch-Nielsen, K. & Westbroek, P. 1990 Phylum Prymnesiophyta. In Handbook of Protoctista (ed. L. Margulis, J. O. Corliss, M. Melkonian & D. J. Chapman), pp. 293-317. Boston: Jones and Bartlett Publishers.
29. Guindon, S. & Gascuel, O. 2003 A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52, 696-704.
30. Hoef-Emden, K. & Melkonian, M. 2003 Revision of the genus Cryptomonas (Cryptophyceae): a combination of molecular phylogeny and morphology provides insights into a long-hidden dimorphism. Protist 154, 371-409.
31. Huber, T., Faulkner, G. & Hugenholtz, P. 2004 Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics 20, 2317-2319.
32. Johnson, M. D., Tengs, T., Oldach, D. W., Delwiche, C. F. & Stoecker, D. K. 2004 Highly divergent SSU rRNA genes found in the marine ciliates Myrionecta rubra and Mesodinium pulex. Protist 155, 347-359.
33. King, N. & Carroll, S. B. 2001 A receptor tyrosine kinase from choanoflagellates: molecular insights into early animal evolution. Proc. Natl Acad. Sci. USA 98, 15032-15037.
34. López-García, P., Rodríguez-Valera, F., Pedrós-Alió, C. & Moreira, D. 2001 Unexpected diversity of small eukaryotes in deep-sea Antarctic plankton. Nature 409, 603-607.
35. López-García, P., Philippe, H., Gail, F. & Moreira, D. 2003 Autochthonous eukaryotic diversity in hydrothermal sediment and experimental microcolonizers at the Mid-Atlantic Ridge. Proc. Natl Acad. Sci. USA 100, 697-702.
36. Lynn, D. H. & Small, E. B. 2000 Phylum Ciliophora. In An illustrated guide to the Protozoa (ed. J. J. Lee, G. F. Leedale & P. Bradbury), vol. 1, pp. 371-656. Lawrence, KS: Allen Press.
37. Margulis, L. & Schwanz, K. V. 1998 Five kingdoms: an illustrated guide to the phyla of life on Earth, 3rd edn. New York: W. H. Freeman. 520pp.
38. Marin, B., Klingberg, M. & Melkonian, M. 1998 Phylogenetic relationships among the cryptophyta: analyses of nuclear-encoded SSU rRNA sequences support the monophyly of extant plastid-containing lineages. Protist 149, 265-276.
39. Massana, R., Castresana, J., Balague, V. V., Guillou, L., Romari, K., Groisillier, A., Valentin, K. & Pedros-Alio, C. 2004 Phylogenetic and ecological analysis of novel marine stramenopiles. Appl. Environ. Microbiol. 70, 3528-3534.
40. Moon-van der Staay, S. Y., De Wachter, R. & Vaulot, D. 2001 Oceanic 18S rDNA sequences from picoplankton reveal unsuspected eukaryotic diversity. Nature 409, 607-610.
41. Moreira, D. & López-García, P. 2002 The molecular ecology of microbial eukaryotes unveils a hidden world. Trends Microbiol. 10, 31-38.
42. Nanney, D. L., Park, C., Preparata, R. & Simon, E. M. 1998 Comparison of sequence differences in a variable 23S rRNA domain among sets of cryptic species of ciliated protozoa. J. Eukaryot. Microbiol. 45, 91-100.
43. Patterson, D. J., Vors, N., Simpson, A. G. B. & O'Kelly, C. 2000 Residual free-living and predatory heterotrophic flagellates. In An illustrated guide to the Protozoa (ed. J. J. Lee, G. F. Leedale & P. Bradbury), vol. 2, pp. 1302-1328. Lawrence, KS: Allen Press.
44. Romari, K. & Vaulot, D. 2004 Composition and temporal variability of picoeukaryote communities at a coastal site of the English Channel from 18S rDNA sequences. Limnol. Oceanogr. 49, 784-798.
45. Ronquist, F. & Huelsenbeck, J. P. 2003 MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19, 1572-1574.
46. Saez, A. G., Probert, I., Geisen, M., Quinn, P., Young, J. R. & Medlin, L. K. 2003 Pseudo-cryptic speciation in coccolithophores. Proc. Natl Acad. Sci. USA 100, 7163-7168.
47. Snell, E. A., Furlong, R. F. & Holland, P. W. 2001 Hsp70 sequences indicate that choanoflagellates are closely related to animals. Curr. Biol. 11, 967-970.
48. Stoeck, T. & Epstein, S. 2003 Novel eukaryotic lineages inferred from small-subunit rRNA analyses of oxygen-depleted marine environments. Appl. Environ. Microbiol. 69, 2657-2663.
49. Stoeck, T., Taylor, G. T. & Epstein, S. S. 2003 Novel eukaryotes from the permanently anoxic Cariaco Basin (Caribbean Sea). Appl. Environ. Microbiol. 69, 5656-5663.
50. Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F. & Higgins, D. G. 1997 The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25, 4876-4882.
51. van Hannen, E. J., Mooij, W., van Agterveld, M. P., Gons, H. J. & Laanbroek, H. J. 1999 Detritus-dependent development of the microbial community in an experimental system: qualitative analysis by denaturing gradient gel electrophoresis. Appl. Environ. Microbiol. 65, 2478-2484.
52. von der Heyden, S., Chao, E. E., Vickerman, K. & Cavalier-Smith, T. 2004 Ribosomal RNA phylogeny of bodonid and diplonemid flagellates and the evolution of Euglenozoa. J. Eukaryot. Microbiol. 51, 402-416.
53. Weisse, T. 2002 The significance of inter- and intraspecific variation in bacterivorous and herbivorous protists. Antonie Van Leeuwenhoek 81, 327-341.