Keywords
Eukaryotes Unicellular Phylogeny Archaeplastida Rhizaria Alveolata
Stramenopiles Haptobionta Discicristates Excavates Opisthokonta Metazoa Fungi
Amoebobionta Cryptobionta
7.1
Introduction
In the vernacular language, the term “microbe” is usually
regarded as a synonym of “bacteria,” in fact both Bacteria
and Archaea (prokaryotes), according to modern taxonomy.
The notion of “microbes” in fact encompasses Bacteria
(unicellular and multicellular)
1 and Archaea, together with
unicellular eukaryotes, which constitute the bulk of the eukaryote domain. 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 coenocyte*, a giant multinucleate
cell. The frontier between clearly unicellular and clearly multicellular organisms is often somewhat vague: between them,
there is a continuum of intermediate situations (cf. Sect. 5.2).
The number of eukaryote species actually described,
according to the criteria of the botanical and the zoological
nomenclature codes, is not accurately known. This is due to the
fact that many anciently described taxa are only known
through very rough diagnoses, so that their taxonomic value
is under debate. Some of them are taken into consideration in
the lists, while they may just represent synonyms of better
described taxa. Others were prematurely considered as possible synonyms of accepted taxa, while further studies could
lead to reestablishing them as valid taxa. Overall, the number
of eukaryote species currently recognized lies between
1,740,000 (Bouchet 2000; Lecointre and Le Guyader 2006)
and 2,000,000 (Rokas 2006). The species diversity of
eukaryotes would appear to be considerably higher than that
of prokaryotes, with only 11,000 species or so (Lecointre
and Le Guyader 2006). However, it is worth noting that the
species concept is very different in eukaryotes and
prokaryotes, so that the comparison is meaningless (cf. Sect.
6.1). The species that are definitely described represent a small
part of the actual species diversity of the Earth. Estimates of
this diversity lie between 3 and 50 million species (May 1997;
Pedro ´s-Alio ´ 2003); a statistical approach predicts ~8.7 million
(Æ1.3 million SE), of which 2.2 million (Æ0.2 million SE) are
marine (Mora et al. 2011).
The vast majority of known eukaryote species belong to the
Metazoa (kingdom Opisthokonta; ~73 %) and Embryophyta
(kingdom Archaeplastida; ~16 %), taxa which only encompass
multicellular organisms. Unicellular eukaryotes only represent
~10 % of all eukaryotic species, even if coenocytic species,
such as Oobionta (kingdom Stramenopiles) and species which
are unicellular in only one phase of their life cycle, such as
social amoeba, are taken into consideration. In contrast, if only
taxa of high phylogenetic level, e.g. kingdoms, sub-kingdoms,
and phyla (hereafter the “phyletic diversity”), are taken into
consideration, most eukaryotes are unicellular (Fig. 7.1) or,
though not sensu stricto unicellular, such as Phytomyxea,
Oobionta, and Fungi (hereafter “affiliate taxa”), fall within
the field of the microbiology. Moreover, because of the thorough exploration of the biosphere and molecular tools, new
taxa of high phylogenetic level are continually being discovered; all of them are unicellular, which contributes to further
enhancing the overwhelming importance of unicellular taxa
within eukaryotes (Box 7.1).
Taking into consideration the huge phyletic diversity
of unicellular eukaryotes and of affiliate taxa, which
corresponds to nearly the whole diversity of eukaryotes
(Fig. 7.1), it is impossible to present here a comprehensive
description of the whole of these high-level taxa. Even a
whole work would not be enough for such a purpose. In addition, some of these taxa are constituted by a single or a couple of
poorly known species whose position within the eukaryote tree
is uncertain. The choice was therefore to select one part, indeed
a small part of these high-level taxa, but a part likely to illustrate
the amazing diversity of eukaryotes. For each selected taxon,
some traits will be recurrently tackled topics, e.g. the chloroplast structure and the photosynthetic pigments (photosynthetic
species), the kinetic apparatus, and the cell wall. Some derived
characters, more or less specific to a taxon and suitable to
constitute a biomarker* (genetic, biochemical, cytological,
and biological) will also be emphasized. The biological life
cycle of at least one species belonging to the taxon will be
analyzed and illustrated in a standardized way. Finally, the
role of the taxon in the functioning of the biosphere will be
described. Unfortunately, for some of the selected taxa, these
aims were only partially achieved, due to the lack of knowledge.
The nomenclature of eukaryotes is ruled by two distinct
codes: the International Code of Nomenclature for algae,
fungi, and plants (ICN; “Botanical Code”) and the International
Code of Zoological Nomenclature (ICZN) (cf. Sect. 5.1.3).
These codes are based upon the Linnean eighteenth century
concept of a living world divided into two sharply differentiated
kingdoms, namely the vegetable (or plant) kingdom and the
animal kingdom. From the 1960s onward, this dualistic concept
of Life was progressively demolished, though data challenging
1 Many Bacteria are multicellular, such as. Cyanobacteria,
Actinobacteria and Firmicutes (e.g. Candidatus Arthromitus).
192
C.-F. Boudouresque
Eukaryotes Unicellular Phylogeny Archaeplastida Rhizaria Alveolata
Stramenopiles Haptobionta Discicristates Excavates Opisthokonta Metazoa Fungi
Amoebobionta Cryptobionta
7.1
Introduction
In the vernacular language, the term “microbe” is usually
regarded as a synonym of “bacteria,” in fact both Bacteria
and Archaea (prokaryotes), according to modern taxonomy.
The notion of “microbes” in fact encompasses Bacteria
(unicellular and multicellular)
1 and Archaea, together with
unicellular eukaryotes, which constitute the bulk of the eukaryote domain. 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 coenocyte*, a giant multinucleate
cell. The frontier between clearly unicellular and clearly multicellular organisms is often somewhat vague: between them,
there is a continuum of intermediate situations (cf. Sect. 5.2).
The number of eukaryote species actually described,
according to the criteria of the botanical and the zoological
nomenclature codes, is not accurately known. This is due to the
fact that many anciently described taxa are only known
through very rough diagnoses, so that their taxonomic value
is under debate. Some of them are taken into consideration in
the lists, while they may just represent synonyms of better
described taxa. Others were prematurely considered as possible synonyms of accepted taxa, while further studies could
lead to reestablishing them as valid taxa. Overall, the number
of eukaryote species currently recognized lies between
1,740,000 (Bouchet 2000; Lecointre and Le Guyader 2006)
and 2,000,000 (Rokas 2006). The species diversity of
eukaryotes would appear to be considerably higher than that
of prokaryotes, with only 11,000 species or so (Lecointre
and Le Guyader 2006). However, it is worth noting that the
species concept is very different in eukaryotes and
prokaryotes, so that the comparison is meaningless (cf. Sect.
6.1). The species that are definitely described represent a small
part of the actual species diversity of the Earth. Estimates of
this diversity lie between 3 and 50 million species (May 1997;
Pedro ´s-Alio ´ 2003); a statistical approach predicts ~8.7 million
(Æ1.3 million SE), of which 2.2 million (Æ0.2 million SE) are
marine (Mora et al. 2011).
The vast majority of known eukaryote species belong to the
Metazoa (kingdom Opisthokonta; ~73 %) and Embryophyta
(kingdom Archaeplastida; ~16 %), taxa which only encompass
multicellular organisms. Unicellular eukaryotes only represent
~10 % of all eukaryotic species, even if coenocytic species,
such as Oobionta (kingdom Stramenopiles) and species which
are unicellular in only one phase of their life cycle, such as
social amoeba, are taken into consideration. In contrast, if only
taxa of high phylogenetic level, e.g. kingdoms, sub-kingdoms,
and phyla (hereafter the “phyletic diversity”), are taken into
consideration, most eukaryotes are unicellular (Fig. 7.1) or,
though not sensu stricto unicellular, such as Phytomyxea,
Oobionta, and Fungi (hereafter “affiliate taxa”), fall within
the field of the microbiology. Moreover, because of the thorough exploration of the biosphere and molecular tools, new
taxa of high phylogenetic level are continually being discovered; all of them are unicellular, which contributes to further
enhancing the overwhelming importance of unicellular taxa
within eukaryotes (Box 7.1).
Taking into consideration the huge phyletic diversity
of unicellular eukaryotes and of affiliate taxa, which
corresponds to nearly the whole diversity of eukaryotes
(Fig. 7.1), it is impossible to present here a comprehensive
description of the whole of these high-level taxa. Even a
whole work would not be enough for such a purpose. In addition, some of these taxa are constituted by a single or a couple of
poorly known species whose position within the eukaryote tree
is uncertain. The choice was therefore to select one part, indeed
a small part of these high-level taxa, but a part likely to illustrate
the amazing diversity of eukaryotes. For each selected taxon,
some traits will be recurrently tackled topics, e.g. the chloroplast structure and the photosynthetic pigments (photosynthetic
species), the kinetic apparatus, and the cell wall. Some derived
characters, more or less specific to a taxon and suitable to
constitute a biomarker* (genetic, biochemical, cytological,
and biological) will also be emphasized. The biological life
cycle of at least one species belonging to the taxon will be
analyzed and illustrated in a standardized way. Finally, the
role of the taxon in the functioning of the biosphere will be
described. Unfortunately, for some of the selected taxa, these
aims were only partially achieved, due to the lack of knowledge.
The nomenclature of eukaryotes is ruled by two distinct
codes: the International Code of Nomenclature for algae,
fungi, and plants (ICN; “Botanical Code”) and the International
Code of Zoological Nomenclature (ICZN) (cf. Sect. 5.1.3).
These codes are based upon the Linnean eighteenth century
concept of a living world divided into two sharply differentiated
kingdoms, namely the vegetable (or plant) kingdom and the
animal kingdom. From the 1960s onward, this dualistic concept
of Life was progressively demolished, though data challenging
1 Many Bacteria are multicellular, such as. Cyanobacteria,
Actinobacteria and Firmicutes (e.g. Candidatus Arthromitus).
192
C.-F. Boudouresque