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. 2004 Apr 29;359(1444):599–610. doi: 10.1098/rstb.2003.1450

Protist taxonomy: an ecological perspective.

Bland J Finlay 1
PMCID: PMC1693346  PMID: 15253347

Abstract

This is an exploration of contemporary protist taxonomy within an ecological perspective. As it currently stands, the 'morphospecies' does not accommodate the information that might support a truly ecological species concept for the protists. But the 'morphospecies' is merely a first step in erecting a taxonomy of the protists, and it is expected to become more meaningful in the light of genetic, physiological and ecological research in the near future. One possible way forward lies in the recognition that sexual and asexual protists may all be subject to forces of cohesion that result in (DNA) sequence-similarity clusters. A starting point would then be the detection of 'ecotypes'--where genotypic and phenotypic clusters correspond; but for that we need better information regarding the extent of clonality in protists, and better characterization of ecological niches and their boundaries. There is some progress with respect to the latter. Using the example of a community of ciliated protozoa living in the stratified water column of a freshwater pond, it is shown to be possible to gauge the potential of protists to partition their local environment into ecological niches. Around 40 morphospecies can coexist in the superimposed water layers, which presumably represent different ecological niches, but we have yet to discover if these are discrete or continuously variable. It is a myth that taxonomic problems are more severe for protists than for animals and plants. Most of the fundamental problems associated with species concepts (e.g. asexuals, sibling species, phenotypic variation) are distributed across biota in general. The recent history of the status of Pfiesteria provides a model example of an integrated approach to solving what are essentially taxonomic problems.

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Selected References

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  1. ATWOOD K. C., SCHNEIDER L. K., RYAN F. J. Periodic selection in Escherichia coli. Proc Natl Acad Sci U S A. 1951 Mar;37(3):146–155. doi: 10.1073/pnas.37.3.146. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Bapteste Eric, Brinkmann Henner, Lee Jennifer A., Moore Dorothy V., Sensen Christoph W., Gordon Paul, Duruflé Laure, Gaasterland Terry, Lopez Philippe, Müller Miklós. The analysis of 100 genes supports the grouping of three highly divergent amoebae: Dictyostelium, Entamoeba, and Mastigamoeba. Proc Natl Acad Sci U S A. 2002 Feb 5;99(3):1414–1419. doi: 10.1073/pnas.032662799. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Burkholder J. M., Noga E. J., Hobbs C. H., Glasgow H. B., Jr, Smith S. A. New 'phantom' dinoflagellate is the causative agent of major estuarine fish kills. Nature. 1992 Jul 30;358(6385):407–410. doi: 10.1038/358407a0. [DOI] [PubMed] [Google Scholar]
  4. Cavalier-Smith T. Kingdom protozoa and its 18 phyla. Microbiol Rev. 1993 Dec;57(4):953–994. doi: 10.1128/mr.57.4.953-994.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Cohan F. M. Bacterial species and speciation. Syst Biol. 2001 Aug;50(4):513–524. doi: 10.1080/10635150118398. [DOI] [PubMed] [Google Scholar]
  6. Cohan Frederick M. What are bacterial species? Annu Rev Microbiol. 2002 Jan 30;56:457–487. doi: 10.1146/annurev.micro.56.012302.160634. [DOI] [PubMed] [Google Scholar]
  7. Corliss J. O. Nuclear characteristics and phylogeny in the protistan phylum Ciliophora. Biosystems. 1975 Nov;7(3-4):338–349. doi: 10.1016/0303-2647(75)90012-x. [DOI] [PubMed] [Google Scholar]
  8. Darling K. F., Wade C. M., Stewart I. A., Kroon D., Dingle R., Brown A. J. Molecular evidence for genetic mixing of Arctic and Antarctic subpolar populations of planktonic foraminifers. Nature. 2000 May 4;405(6782):43–47. doi: 10.1038/35011002. [DOI] [PubMed] [Google Scholar]
  9. Finlay B. J., Embley T. M., Fenchel T. A new polymorphic methanogen, closely related to Methanocorpusculum parvum, living in stable symbiosis within the anaerobic ciliate Trimyema sp. J Gen Microbiol. 1993 Feb;139(2):371–378. doi: 10.1099/00221287-139-2-371. [DOI] [PubMed] [Google Scholar]
  10. Finlay B. J., Fenchel T. Protozoan community structure in a fractal soil environment. Protist. 2001 Sep;152(3):203–218. doi: 10.1078/1434-4610-00060. [DOI] [PubMed] [Google Scholar]
  11. Finlay Bland J. Global dispersal of free-living microbial eukaryote species. Science. 2002 May 10;296(5570):1061–1063. doi: 10.1126/science.1070710. [DOI] [PubMed] [Google Scholar]
  12. Forey Peter L., Fortey Richard A., Kenrick Paul, Smith Andrew B. Taxonomy and fossils: a critical appraisal. Philos Trans R Soc Lond B Biol Sci. 2004 Apr 29;359(1444):639–653. doi: 10.1098/rstb.2003.1453. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Foster Kenneth W. Making a robust biomolecular time scale for phylogenetic studies. Protist. 2003 Apr;154(1):43–55. doi: 10.1078/143446103764928486. [DOI] [PubMed] [Google Scholar]
  14. Godfray H. Charles J. Challenges for taxonomy. Nature. 2002 May 2;417(6884):17–19. doi: 10.1038/417017a. [DOI] [PubMed] [Google Scholar]
  15. Kaiser Jocelyn. Microbiology. The science of Pfiesteria: elusive, subtle, and toxic. Science. 2002 Oct 11;298(5592):346–349. doi: 10.1126/science.298.5592.346. [DOI] [PubMed] [Google Scholar]
  16. Keeling P. J., McFadden G. I. Origins of microsporidia. Trends Microbiol. 1998 Jan;6(1):19–23. doi: 10.1016/S0966-842X(97)01185-2. [DOI] [PubMed] [Google Scholar]
  17. Marin Birger, Palm Anne, Klingberg Max, Melkonian Michael. Phylogeny and taxonomic revision of plastid-containing euglenophytes based on SSU rDNA sequence comparisons and synapomorphic signatures in the SSU rRNA secondary structure. Protist. 2003 Apr;154(1):99–145. doi: 10.1078/143446103764928521. [DOI] [PubMed] [Google Scholar]
  18. Moore L. R., Rocap G., Chisholm S. W. Physiology and molecular phylogeny of coexisting Prochlorococcus ecotypes. Nature. 1998 Jun 4;393(6684):464–467. doi: 10.1038/30965. [DOI] [PubMed] [Google Scholar]
  19. Oren Aharon. Prokaryote diversity and taxonomy: current status and future challenges. Philos Trans R Soc Lond B Biol Sci. 2004 Apr 29;359(1444):623–638. doi: 10.1098/rstb.2003.1458. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Overmann Jörg, Schubert Karin. Phototrophic consortia: model systems for symbiotic interrelations between prokaryotes. Arch Microbiol. 2002 Jan 22;177(3):201–208. doi: 10.1007/s00203-001-0377-z. [DOI] [PubMed] [Google Scholar]
  21. Palys T., Nakamura L. K., Cohan F. M. Discovery and classification of ecological diversity in the bacterial world: the role of DNA sequence data. Int J Syst Bacteriol. 1997 Oct;47(4):1145–1156. doi: 10.1099/00207713-47-4-1145. [DOI] [PubMed] [Google Scholar]
  22. Patterson DJ. The Diversity of Eukaryotes. Am Nat. 1999 Oct;154(S4):S96–S124. doi: 10.1086/303287. [DOI] [PubMed] [Google Scholar]
  23. Patterson David J. Progressing towards a biological names register. Nature. 2003 Apr 17;422(6933):661–661. doi: 10.1038/422661a. [DOI] [PubMed] [Google Scholar]
  24. Pröschold T., Marin B., Schlösser U. G., Melkonian M. Molecular phylogeny and taxonomic revision of Chlamydomonas (Chlorophyta). I. Emendation of Chlamydomonas Ehrenberg and Chloromonas Gobi, and description of Oogamochlamys gen. nov. and Lobochlamys gen. nov. Protist. 2001 Dec;152(4):265–300. doi: 10.1078/1434-4610-00068. [DOI] [PubMed] [Google Scholar]
  25. Roger AJ. Reconstructing Early Events in Eukaryotic Evolution. Am Nat. 1999 Oct;154(S4):S146–S163. doi: 10.1086/303290. [DOI] [PubMed] [Google Scholar]
  26. Rublee P. A., Kempton J. W., Schaefer E. F., Allen C., Harris J., Oldach D. W., Bowers H., Tengs T., Burkholder J. M., Glasgow H. B. Use of molecular probes to assess geographic distribution of Pfiesteria species. Environ Health Perspect. 2001 Oct;109 (Suppl 5):765–767. doi: 10.1289/ehp.01109s5765. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Saito Keiko, Drgon Tomás, Robledo José A. F., Krupatkina Danara N., Vasta Gerardo R. Characterization of the rRNA locus of Pfiesteria piscicida and development of standard and quantitative PCR-based detection assays targeted to the nontranscribed spacer. Appl Environ Microbiol. 2002 Nov;68(11):5394–5407. doi: 10.1128/AEM.68.11.5394-5407.2002. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Steidinger K., Landsberg J., Richardson R. W., Truby E., Blakesley B., Scott P., Tester P., Tengs T., Mason P., Morton S. Classification and identification of Pfiesteria and Pfiesteria-like species. Environ Health Perspect. 2001 Oct;109 (Suppl 5):661–665. doi: 10.1289/ehp.01109s5661. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Taylor FJ. Ultrastructure as a Control for Protistan Molecular Phylogeny. Am Nat. 1999 Oct;154(S4):S125–S136. doi: 10.1086/303288. [DOI] [PubMed] [Google Scholar]
  30. Vogelbein Wolfgang K., Lovko Vincent J., Shields Jeffrey D., Reece Kimberly S., Mason Patrice L., Haas Leonard W., Walker Calvin C. Pfiesteria shumwayae kills fish by micropredation not exotoxin secretion. Nature. 2002 Aug 5;418(6901):967–970. doi: 10.1038/nature01008. [DOI] [PubMed] [Google Scholar]
  31. Ward D. M., Ferris M. J., Nold S. C., Bateson M. M. A natural view of microbial biodiversity within hot spring cyanobacterial mat communities. Microbiol Mol Biol Rev. 1998 Dec;62(4):1353–1370. doi: 10.1128/mmbr.62.4.1353-1370.1998. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. de Vargas C., Norris R., Zaninetti L., Gibb S. W., Pawlowski J. Molecular evidence of cryptic speciation in planktonic foraminifers and their relation to oceanic provinces. Proc Natl Acad Sci U S A. 1999 Mar 16;96(6):2864–2868. doi: 10.1073/pnas.96.6.2864. [DOI] [PMC free article] [PubMed] [Google Scholar]

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