Taxonomy and Phylogeny
of Unicellular Eukaryotes
7
Charles-Franc ¸ois Boudouresque
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.
C.-F. Boudouresque* (*)
Institut Me ´diterrane ´en d’Oce ´anologie (MIO), UM 110, CNRS 7294
IRD 235, Universite ´ de Toulon, Aix-Marseille Universite ´,
Campus de Luminy, 13288 Marseille Cedex 9, France
e-mail: charles.boudouresque@mio.osupytheas.fr
* Chapter Coordinator
J.-C. Bertrand et al. (eds.), Environmental Microbiology: Fundamentals and Applications: Microbial Ecology,
DOI 10.1007/978-94-017-9118-2_7, # Springer Science+Business Media Dordrecht 2015
191
of Unicellular Eukaryotes
7
Charles-Franc ¸ois Boudouresque
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.
C.-F. Boudouresque* (*)
Institut Me ´diterrane ´en d’Oce ´anologie (MIO), UM 110, CNRS 7294
IRD 235, Universite ´ de Toulon, Aix-Marseille Universite ´,
Campus de Luminy, 13288 Marseille Cedex 9, France
e-mail: charles.boudouresque@mio.osupytheas.fr
* Chapter Coordinator
J.-C. Bertrand et al. (eds.), Environmental Microbiology: Fundamentals and Applications: Microbial Ecology,
DOI 10.1007/978-94-017-9118-2_7, # Springer Science+Business Media Dordrecht 2015
191