the Linnean system and announcing the phylogenetic revolution
can be found as early as the late nineteenth century. Nowadays,
eukaryotes, one of the three domains of Life (together with
Bacteria and Archaea), encompass a dozen kingdoms.
2 Most
of these kingdoms include taxa traditionally considered as
belonging to the former plant kingdom and taxa belonging to
the former animal kingdom (cf. Sects. 5.5.2 and 5.5.3). From the
level of the species to that of the class, sometimes to phylum
level, there is no major difficulty in applying the rules of either
the botanical or the zoological code. However, beyond these
levels, for high-level taxa, there is no reason for choosing one
code, since the taxa include both former “plants” and “animals.”
For high-level taxa, the “rule” is therefore common practice or
logic. This practice is very different from one author to another.
Here, the practice of Lecointre and Le Guyader (2006) and/or
of Boudouresque (2011) was adopted. The suffixes “phytes”
(¼plants), “mycota” (¼fungi, in the customary meaning) and
“zoa” (¼animals, in the customary meaning) were therefore
often changed into “bionta” (¼living organism). This is especially necessary when e.g. Dinobionta are considered, a taxon
claimed by both “botanists” (as Dinophyta or Dinophyceae)
and “zoologists” (as Dinozoa and Dinoflagellates), though
the situation is a bit more complicated than this rather facile
shortcut would suggest. Within Dinobionta, some species are
photosynthetic, some others are mixotrophic, while some others
are heterotrophic, including formidable predators such as
Karlodinium armiger. Classifying Dinobionta within a traditional Linnean kingdom, namely plants or animals, is therefore
meaningless. Altogether, for every high-level taxon, the different names recently used in the literature (though they are not
always exact synonyms) will be given.
7.2
General Characteristics of Eukaryotes
Eukaryotes differ from prokaryotes by a large number of
characters. Overall, this set of differences is very robust and
no organism appears to be intermediate between eukaryotes
Box 7.1 (continued)
Group-specific PCR amplifications prior to
sequencing are particularly suited for the characterization of highly diverse, albeit rare micro-eukaryotic
taxa thriving in low abundance and low biomasscarrying capacity in some environments. In fact,
targeted approaches are often the only way to detect
taxa harboring highly divergent 18S rDNA sequences
compared to those used for the design of so-called
“universal” PCR primers. Using highly specific
primers, foraminiferal SSU rDNA sequences could
be enriched from degraded, ancient DNA preserved
in subsurface deep-sea sediments as well as from soilsextracted DNA although foraminiferans are traditionally considered as strictly marine protists (Lejzerowicz
et al. 2010, 2013).
Life in Extreme Environments
“Extreme environments” are usually defined as
environments in which the values of one or several
physicochemical parameters (e.g. temperature, pH,
pressure, or salinity) are such that specific adaptations
are required for the organisms to survive and multiply
there. Life in extreme environments is not limited to
prokaryotes and according to descriptive metagenetic
analyses, is not limited to few taxonomic groups of
eukaryotes. Indeed, diverse taxa were detected in extreme
environments ranging from hyperacid (pH Æ1) to hypersaline (6 M) waters, from anoxic basins to the deep-sea
abysses (À3,000 m) including hydrothermal sediments
(continued)
Box 7.1 (continued)
(À2,200 m) as well as in polar areas. For example,
eukaryotic microbial communities present in diverse
micro-habitats of an hydrothermal vent system were
dominated by 18S rDNA sequences belonging to
kinetoplastids and ciliates although other sequences
could be assigned to diverse groups of Alveolata, Radiolaria, or Opisthokonta (Lo ´pez-Garcı ´a et al. 2003).
Conversely, the acid mine drainage waters surveyed
by Baker et al. (2009) were found to host numerous
sequences with no close relative in reference
databases. These phylotypes might be the first
representatives of a new phylum of high taxonomic
rank named APC (Acidophilic Protist Clade). Given
the high level of sequence divergence, specific probes
designed for FISH experiments were successful at
identifying the largest cells of the APC in environmental samples.
The metagenetic exploration of micro-eukaryotic
diversity is still in its infancy and whether the entire
phyla are endemic to extreme environments or include
cosmopolitan species remains to be tested. High
throughput sequencing technologies are increasingly
popular and rapidly satisfying the need for additional
sequence data and the processing of numerous
samples. However, although environmental sequences
are informative for phylogenetic placement and taxonomic diversity description based on known,
sequenced organisms, they constitute poor indicators
of species physiology and ecological traits.
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.
196
C.-F. Boudouresque
can be found as early as the late nineteenth century. Nowadays,
eukaryotes, one of the three domains of Life (together with
Bacteria and Archaea), encompass a dozen kingdoms.
2 Most
of these kingdoms include taxa traditionally considered as
belonging to the former plant kingdom and taxa belonging to
the former animal kingdom (cf. Sects. 5.5.2 and 5.5.3). From the
level of the species to that of the class, sometimes to phylum
level, there is no major difficulty in applying the rules of either
the botanical or the zoological code. However, beyond these
levels, for high-level taxa, there is no reason for choosing one
code, since the taxa include both former “plants” and “animals.”
For high-level taxa, the “rule” is therefore common practice or
logic. This practice is very different from one author to another.
Here, the practice of Lecointre and Le Guyader (2006) and/or
of Boudouresque (2011) was adopted. The suffixes “phytes”
(¼plants), “mycota” (¼fungi, in the customary meaning) and
“zoa” (¼animals, in the customary meaning) were therefore
often changed into “bionta” (¼living organism). This is especially necessary when e.g. Dinobionta are considered, a taxon
claimed by both “botanists” (as Dinophyta or Dinophyceae)
and “zoologists” (as Dinozoa and Dinoflagellates), though
the situation is a bit more complicated than this rather facile
shortcut would suggest. Within Dinobionta, some species are
photosynthetic, some others are mixotrophic, while some others
are heterotrophic, including formidable predators such as
Karlodinium armiger. Classifying Dinobionta within a traditional Linnean kingdom, namely plants or animals, is therefore
meaningless. Altogether, for every high-level taxon, the different names recently used in the literature (though they are not
always exact synonyms) will be given.
7.2
General Characteristics of Eukaryotes
Eukaryotes differ from prokaryotes by a large number of
characters. Overall, this set of differences is very robust and
no organism appears to be intermediate between eukaryotes
Box 7.1 (continued)
Group-specific PCR amplifications prior to
sequencing are particularly suited for the characterization of highly diverse, albeit rare micro-eukaryotic
taxa thriving in low abundance and low biomasscarrying capacity in some environments. In fact,
targeted approaches are often the only way to detect
taxa harboring highly divergent 18S rDNA sequences
compared to those used for the design of so-called
“universal” PCR primers. Using highly specific
primers, foraminiferal SSU rDNA sequences could
be enriched from degraded, ancient DNA preserved
in subsurface deep-sea sediments as well as from soilsextracted DNA although foraminiferans are traditionally considered as strictly marine protists (Lejzerowicz
et al. 2010, 2013).
Life in Extreme Environments
“Extreme environments” are usually defined as
environments in which the values of one or several
physicochemical parameters (e.g. temperature, pH,
pressure, or salinity) are such that specific adaptations
are required for the organisms to survive and multiply
there. Life in extreme environments is not limited to
prokaryotes and according to descriptive metagenetic
analyses, is not limited to few taxonomic groups of
eukaryotes. Indeed, diverse taxa were detected in extreme
environments ranging from hyperacid (pH Æ1) to hypersaline (6 M) waters, from anoxic basins to the deep-sea
abysses (À3,000 m) including hydrothermal sediments
(continued)
Box 7.1 (continued)
(À2,200 m) as well as in polar areas. For example,
eukaryotic microbial communities present in diverse
micro-habitats of an hydrothermal vent system were
dominated by 18S rDNA sequences belonging to
kinetoplastids and ciliates although other sequences
could be assigned to diverse groups of Alveolata, Radiolaria, or Opisthokonta (Lo ´pez-Garcı ´a et al. 2003).
Conversely, the acid mine drainage waters surveyed
by Baker et al. (2009) were found to host numerous
sequences with no close relative in reference
databases. These phylotypes might be the first
representatives of a new phylum of high taxonomic
rank named APC (Acidophilic Protist Clade). Given
the high level of sequence divergence, specific probes
designed for FISH experiments were successful at
identifying the largest cells of the APC in environmental samples.
The metagenetic exploration of micro-eukaryotic
diversity is still in its infancy and whether the entire
phyla are endemic to extreme environments or include
cosmopolitan species remains to be tested. High
throughput sequencing technologies are increasingly
popular and rapidly satisfying the need for additional
sequence data and the processing of numerous
samples. However, although environmental sequences
are informative for phylogenetic placement and taxonomic diversity description based on known,
sequenced organisms, they constitute poor indicators
of species physiology and ecological traits.
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.
196
C.-F. Boudouresque