Protist Systematics


Protist systematics is concerned with the classification of the typically microscopic organisms found in abundance nearly everywhere in the Earth's biosphere. Such organisms include the algae, the protozoa and certain lower fungi. Protists were assigned to the taxon Protista by Haeckel. However, it wasn't until the technological innovation of the electron microscope and the repopularisation by Margulis of the theory of serial endosymbiosis to explain the origin of eukaryotes that the discipline of protistology achieved a critical mass. By the end of the twentieth century, protistologists agreed that the Protista was not a natural assemblage. Data from both the ultrastructure of the flagellar/ciliary apparatuses of diverse lineages and later gene/genome sequences confirmed this. Currently, a consensus is emerging that there are possibly three major assemblages of eukaryotes into which the majority of protists can be assigned: Adl et al. (2012) have named these the Amorphea, Excavata and Diaphoretickes.

Key Concepts:

  • Protists are typically microscopic organisms, commonly called algae, protozoa and lower fungi.

  • The taxon Protista was established by Haeckel (1866, 1878) to include these organisms and some others, but it was not enthusiastically embraced by botanists and zoologists in the 19th Century.

  • Up until the mid‐twentieth century, protists were classified using significant features of their cell structure, such as plastids and storage products, their body form and their modes of locomotion. One popular classification grouped them into amoebae (i.e. Sarcodina), flagellates (i.e. Mastigophora), ciliates (i.e. Ciliophora) and spore‐formers (i.e. Sporozoa) (e.g. Manwell, 1961).

  • The technological innovation of the transmission electron microscope and the repopularisation by Margulis (1970, 1981) of the theory of serial endosymbiosis to explain the origin of eukaryotes refocussed attention on protists.

  • In the mid‐twentieth century, even though the Kingdom Protista was gaining popularity, experts recognised that it was likely not a monophyletic group.

  • By the late twentieth century, gene sequences of the ribosomal RNA gene and in this century, sequences of hundreds of genes confirm that the protists must be split into several different lineages, which include the animals, plants and fungi.

  • While there is not total agreement, an emerging consensus recognises these major groups: Archaeplastida, Sar, Excavata, Amoebozoa, Opisthokonta and a number of smaller lineages whose affinities are not yet determined.

Keywords: protists; protozoa; algae; lower fungi; eukaryotic microorganisms; animals; plants; classification; taxonomy; megasystematics

Figure 1.

A model of eukaryogenesis through serial endosymbioses. A prokaryote ancestor (a) evolves as a nucleated (n) proeukaryote (d) that becomes ciliated/flagellated (fl) and ingests (e) an α‐proteobacterium (b), which evolves as the first mitochondrion (mi). Later this ancestral eukaryote (e) ingests a cyanobacterium (c), which evolves as the first plastid (pl), and in some forms loses the flagellum to become an immotile phototrophic form, like a red alga (h). The heterotrophic ancestral eukaryote gave rise to a variety of lineages, such as ciliates with their micronucleus and macronucleus (f) and cryptomonad‐like flagellates (g). Some cryptomonads ingested a red algal cell (i), and this is a secondary endosymbiosis. The ciliate Mesodinium rubrum (k) ingested a cryptomonad, making this a tertiary endosymbiosis that has six compartments containing DNA (1–6). Reproduced with permission of Hausmann, Hülsmann and Radek. © Schweizerbar'sche Verlag.

Figure 2.

The chlorophycean Chlamydomonas reinhardtii, at one time classified in the Phytoflagellata of the Sarcomastigophora. Reproduced with permission of Wolfgang Bettighofer. © Wolfgang Bettighofer.

Figure 3.

The euglenophycean Euglena viridis, at one time classified in the Phytoflagellata of the Sarcomastigophora. Reproduced with permission of William Bourland. © William Bourland.

Figure 4.

The amoebozoan Planoprotostelium aurantium, at one time classified in the Sarcodina of the Sarcomastigophora. Reproduced with permission of Frederick W. Spiegel. © Frederick W Spiegel.

Figure 5.

An undescribed rhizarian amoeboflagellate, probably a Cercomonas species, showing a flagellated (a) and amoeboid stage with a single pseudopodium (b). At one time it would have been classified in the Sarcodina of the Sarcomastigophora. Reproduced with permission of Francisco Amaro Torres. © Francisco Amaro Torres.

Figure 6.

The kinetoplastean Trypanoplasma borreli, at one time classified in the Zooflagellata of the Sarcomastigophora. Reproduced with permission of David J. Patterson, Linda Amaral‐Zettler, M. Pegler and Thomas Nerad. © David J. Patterson, Linda Amaral‐Zettler, M. Pegler, and Thomas Nerad.

Figure 7.

The parabasalian Metadevescovina sp. from the termite Neotermes jouteli, at one time classified in the Zooflagellata of the Sarcomastigophora. This protist has three flagella extending from the anterior end on the lower left, whereas the other ‘filaments' are actually ectosymbiotic bacteria. Reproduced with permission of Patrick Keeling and Erick James. © Patrick Keeling and Erick James.

Figure 8.

The oligohymenophorean ciliate Paramecium caudatum. Reproduced with permission of William Bourland. © William Bourland.

Figure 9.

The spirotrich ciliate Euplotes eurystomus. Reproduced with permission of William Bourland. © William Bourland.

Figure 10.

The spores, actually oocysts, of three apicomplexans – Eimeria (top left) from the intestinal tract of a chicken, Cytoisospora (bottom left) from the intestinal tract of a dog and Monocystis agilis (right) from the seminiferous vesicles of the earthworm Lumbricis terrestris. At one time these would have been classified in the Sporozoa. Reproduced with permission of Jan Slapeta. © Jan Slapeta.

Figure 11.

The spores of the microsporidian Antonospora locustae, a parasite of the locust, showing in (a) ungerminated spores (U) and germinated ones (G), and in (b) a germinated spore with its everted polar tube (PT). At one time it might have been classified in the Sporozoa. Reproduced with permission of Keeling (2009). © PLoS.

Figure 12.

Flagellar apparatus of Chlamydomonas reinhardtii at a level below the cruciate microtubular rootlets. This flagellate has two ciliated basal bodies or kinetosomes (1, 2), and associated with them are two probasal bodies. This arrangement is quite different from its former ‘phytoflagellate’ relative Euglena (cf. Figure ). Reproduced and adapted with permission from Geimer and Melkonian (). © The Company of Biologists Ltd.

Figure 13.

Flagellar rootlets and cytoskeletal apparatus of Euglena gracilis showing the origin of the microtubular rootlets near the dorsal (DB) and ventral (VB) basal bodies or kinetosomes. This arrangement is quite different from its former ‘phytoflagellate’ relative Chlamydomonas (cf. Figure ). Reproduced with permission from Yubuki and Leander (). © Springer.

Figure 14.

Global phylogeny of eukaryotes based on an alignment of 258 genes and inferred using the CAT+Γ4 model. The numbers at the nodes are support values if the branch was not supported in all analyses. Reproduced and adapted with permission of Fabien Burki. © Fabien Burki.

Figure 15.

Schematic representation of the eukaryote ‘Tree of Life’ outlining the major groups in the revised classification of eukaryotes proposed by Adl et al. (). See also Table for further detail. Revised tree provided with permission by Sina Adl. © Sina Adl.



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Further Reading

Burki F , Inagaki Y , Bråte J et al. (2009) Large‐scale phylogenomic analyses reveal that two enigmatic protist lineages, Telonemia and Centroheliozoa, are related to photosynthetic chromalveolates. Genome Biology and Evolution 9: 231–238.

Burki F , Shalchian‐Tabrizi K and Pawlowski J (2008) Phylogenomics reveals a new “megagroup” including most photosynthetic eukaryotes. Biology Letters 4: 366–369.

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Lynn, Denis H(Jan 2014) Protist Systematics. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1002/9780470015902.a0003153.pub2]