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Taxonomy and Phylogeny of Unicellular Eukaryotes

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Environmental Microbiology: Fundamentals and Applications

Abstract

The notion of ‘microbes’ encompasses Bacteria (unicellular and multicellular) and Archaea, together with unicellular eukaryotes. In addition, microbiologists have traditionally included within their study field a number of eukaryotes named ‘fungi’ (customary meaning), e.g. Fungi (modern meaning), which are generally multicellular, and Oobionta, which are constituted by a giant multinucleate cell. Unicellular eukaryotes only represent ~10 % of all eukaryotic species; however, if only kingdoms, sub-kingdoms and phyla (‘phyletic diversity’) are taken into consideration, most eukaryotes are unicellular. Taking into consideration the huge phyletic diversity of unicellular eukaryotes and of affiliate taxa, which nearly fits the whole diversity of eukaryotes, it is impossible to present here a comprehensive description of the whole of these taxa. The choice was therefore to select a part of high-level taxa, likely to illustrate the amazing diversity of eukaryotes. For each selected taxon, some traits are recurrently tackled topics, e.g. the chloroplast structure and the photosynthetic pigments, the kinetic apparatus and the cell wall. Some derived characters, more or less specific to a taxon and prone to constitute a biomarker (genetic, biochemical, cytological and/or biological), are also emphasized. The biological life cycle of at least one species belonging to the taxon is illustrated in a standardized way. Finally, the role of the taxon in the functioning of the biosphere is described. Eukaryotes, one of the three domains of Life (together with Bacteria and Archaea), encompass a dozen or so high-level taxa (here kingdoms). Most of these kingdoms include taxa traditionally considered as belonging to the former polyphyletic plant kingdom together with taxa belonging to the former animal kingdom. Similarly, most of these kingdoms encompass ensembles formerly referred to as ‘algae’, ‘fungi’ (customary meaning) and protozoa, which modern phylogenies proved to be highly polyphyletic and therefore artificial. Here, eukaryotic taxa are placed within putatively monophyletic ensembles (kingdoms): Archaeplastida (=Plantae), Rhizaria, Alveolata, Stramenopiles (=Heterokonta), Haptobionta (=Haptophytes), Discicristates, Excavates, Opisthokonta (including Metazoa and Fungi, modern meaning), Amoebobionta (=Amoebozoa) and Cryptobionta.

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Notes

  1. 1.

    Many Bacteria are multicellular, such as. Cyanobacteria, Actinobacteria and Firmicutes (e.g. Candidatus Arthromitus).

  2. 2.

    Within prokaryotes, the highest taxonomic rank is that of the phylum. In contrast, within eukaryotes, the highest taxonomic rank is constituted by kingdoms, though their use and definition are not ruled by the traditional nomenclature codes, constrained ‘by nature’ by the Linnean dichotomy plant-animals.

  3. 3.

    Spore, from the ancient Greek word spora (meaning ‘seed’, ‘sowing’).

  4. 4.

    In prokaryotes, the term ‘spore’ is used with a different meaning from the one defined here for eukaryotes.

  5. 5.

    For the use of undulipodium rather than flagellum, in eukaryotes, see Sect. 5.4.2. Flagella are structures that characterize prokaryotes. Undulipodiums are much more complex structures, completely different from a biochemical and functioning point of view, which are specific to eukaryotes.

  6. 6.

    The gametogenous, sporogenous, and carpoconidiogenous generations (gametogen, sporogen, and carpoconidiogen) are traditionally named ‘gametophyte’, ‘sporophyte’, and ‘carposporophyte’, respectively, by most botanists. This terminology, stemming from the Linnean traditional dichotomy between a botanical and a zoological kingdoms, is particularly inappropriate in that similar generations and life cycles can be found within both these customary kingdoms. ‘-phyte’ comes from the ancient Greek ‘phuton’ and means ‘plant’.

  7. 7.

    Incertae sedis (Latin for ‘of uncertain placement’) is the term used to define a taxonomic group whose relationships are unknown or undefined.

  8. 8.

    Rhodobionta: from the ancient Greek words ‘rhodon’ (pink) and ‘biont’ (living thing).

  9. 9.

    Uronic acids (e.g. the galacturonic acid) are a class of sugar acids (hexoses) with both carbonyl and carboxylic acid functional groups. In the case of pectin, the hexose is galactose.

  10. 10.

    Apart from Streptobionta, lignin is also present in a species of Rhodobionta living in the intertidal zone. According to Martone et al. (2009), the lignin biosynthetic pathways may have been present in the common unicellular ancestor of Viridiplantae and Rhodobionta.

  11. 11.

    MPOs = Multicellular Photosynthetic Organisms.

  12. 12.

    Chlorarachniobionta: from the Greek ‘chloros’ (green) and ‘arachne’ (spider).

  13. 13.

    The nucleomorph of Chlorarachniobionta has lost most of its genes: it has only 380 kb.

  14. 14.

    Foraminifera: from the Latin ‘foramen’, an opening and ‘ferre’, to bear. For short, ‘hole bearers’.

  15. 15.

    A crista is a fold in the inner membrane of a mitochondrion.

  16. 16.

    The customary notion of ‘invertebrates’ does not correspond to a monophyletic taxon (modern meaning), but encompasses a paraphyletic group of taxa.

  17. 17.

    Dinobionta: from the Ancient Greek ‘dinô’, meaning spinning top, vortex. This name refers to the fact that cells frequently turn on themselves like tops. A similar but different Greek root, ‘deinos’, meaning terrible, awesome, is the origin of the name of the dinosaurs (=terrible lizards).

  18. 18.

    The unipartite mastigoneme of Dinobionta corresponds to the terminal part of the tripartite mastigoneme of Chromobionta (cf. Sect. 7.9.3).

  19. 19.

    The name Apicomplexa is derived from le Latin apex (top) and complexus (infolds).

  20. 20.

    Stramenopiles: from the Latin stramen (straw) and pilus (hair), in reference to the undulipodiums covered by mastigonemes.

  21. 21.

    The suffix ‘phyceae’ is used to designate taxa (taxonomic rank: class) belonging to ‘algae’ (traditional sense). ‘Phyceae’ comes from the ancient Greek ‘phykos’ which means ‘seaweed’.

  22. 22.

    Actinophryda: from the ancient Greek aktina (ray) and ophrys (eyebrow).

  23. 23.

    The name of Opalinida is derived from their opalescent appearance when illuminated with sunlight.

  24. 24.

    The name of Labyrinthulobionta is derived from Labyrinthula, a diminutive of the Latin Labyrinthus (labyrinth) and the ancient Greek biont (living thing).

  25. 25.

    Oobionta: From the Greek “oon”, egg. The name refers to the female gametes, that are rounded, large, and non motile, that ancient writers named ‘eggs’.

  26. 26.

    The name of Chromobionta is derived from the ancient Greek khrôma (color) and biont (living thing). The name refers to the fact that the green color of chlorophyll, when present, is usually masked by the abundance of pigments in a different color (brown, yellow, gold, etc.).

  27. 27.

    Some authors (e.g. Andersen 2004) refer to the Chromobionta as ‘Heterokonta’, which causes confusion. For most authors, Heterokonta are what we refer to here as the stramenopiles.

  28. 28.

    The term ‘pico-eukaryote’ refers to the small size of these organisms; ‘pico’ is a Spanish expression (‘y pico’) meaning ‘and some’. It should be noted that the size of these organisms (up to 3 μm) is much greater than the picometer.

  29. 29.

    This undulipodium is often referred to in the literature as the ‘posterior’ undulipodium, which is incorrect. Rather, as in all bikonts, both undulipodiums are anterior.

  30. 30.

    Haptobionta, from the ancient Greek hapsis (binding) and biont (living thing). The name refers to the possible role of the haptonema.

  31. 31.

    In fact, coccolithophorids (=coccolithophores, Coccolithophorida) only correspond to a class of Haptobionta, namely the Prymnesiophyceae (de Reviers 2003; Andersen 2004), although sometimes incorrectly used with a wider meaning.

  32. 32.

    Cryptobionta, from the ancient Greek kruptos (hidden) and biont (living thing). This name is not based on a general characteristic of the taxon, but the name of one of the genera belonging to it, Cryptomonas.

  33. 33.

    Discicritates, from the Latin discus (disk) and crista (crest). This name refers to the mitochondrial cristae which resemble ping-pong rackets.

  34. 34.

    Opisthokonta: from the ancient Greek opistho (hind) and kontos (pole, in reference to the undulipodium).

  35. 35.

    Fungi is the plural of the Latin word ‘Fungus’, which means ‘mushroom’. By convention, the term ‘Fungi’ is used here even when used in the singular.

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Authors and Affiliations

  1. Institut Méditerranéen d’Océanologie (MIO), UM 110, CNRS 7294 IRD 235, Université de Toulon, Aix-Marseille Université, Campus de Luminy, 13288, Marseille Cedex 9, France

    Charles-François Boudouresque

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  1. Charles-François Boudouresque
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Correspondence to Charles-François Boudouresque .

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Editors and Affiliations

  1. Université de Toulon, Aix-Marseille Université, Institut Méditerranéen d’Océanologie (MIO), UM 110, CNRS 7294 IRD 235, Cedex 9, Marseille, France

    Jean-Claude Bertrand

  2. Université de Pau et des Pays de l’Adour, Institut des Sciences Analytiques et de Physico-chimie pour l’Environnement et les Matériaux (IPREM), UM 110, CNRS 5254, Pau Cedex, France

    Pierre Caumette

  3. Observatoire Océanologique de Banyuls, Laboratoire de Biodiversité et Biotechnologie Microbiennes (LBBM), Sorbonne Universités, UPMC Univ, Paris 06, USR CNRS 3579, Banyuls-sur-Mer, France

    Philippe Lebaron

  4. Institut Méditerranéen de Biodiversité et d’Ecologie marine et continentale (IMBE), UMR-CNRS-IRD 7263, Aix-Marseille Université, Cedex 20, Marseille, France

    Robert Matheron

  5. Microbial Ecology Center, UMR CNRS 5557/USC INRA 1364, Villeubanne, France

    Philippe Normand

  6. Laboratoire Microorganismes: Génome et Environnement (LMGE), UMR CNRS 6023, Université Blaise Pascal, Clermont Université, Aubère Cedex, France

    Télesphore Sime-Ngando

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Boudouresque, CF. (2015). Taxonomy and Phylogeny of Unicellular Eukaryotes. In: Bertrand, JC., Caumette, P., Lebaron, P., Matheron, R., Normand, P., Sime-Ngando, T. (eds) Environmental Microbiology: Fundamentals and Applications. Springer, Dordrecht. https://doi.org/10.1007/978-94-017-9118-2_7

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