Box 5.1 (continued)
subdomain that diverged very early on from the branch
leading to the modern eukaryotes (Box Fig. 5.2).
The controversy remains strong: did the emergence
of DNA viruses predate that of eukaryotes? Were
these two phenomena related? Is it absurd to imagine
that viruses might have emerged before their hosts? Or
are these viruses the last representative of a 4th cellular domain now extinct and that only managed to
survive as parasites within the extant eukaryotic
domain?
In the latter case, these giant viruses might be the
result of reductive evolution from ancestral
microorganisms (somewhat like the one followed by
Rickettsia). All these questions can only be answered
by identifying more giant viruses whose genomes
should have kept other traces (e.g., ribosomal proteins)
of reductive evolution. In the present state of our
knowledge, the presence/absence of functional protein
of the translation system remains the most fundamental criterion for discriminating viruses from the most
reduced parasitic bacteria. In the context of reductive
evolution, the loss of one key component of the translation apparatus would constitute the initiating event
irreversibly committing a cellular parasite to a
viruslike evolutionary pathway, rather than becoming
an organelle as it is the normal fate for obligate intracellular bacteria (Claverie 2006; Claverie and Abergel
2010).
Although Mimivirus was discovered fortuitously
only recently, environmental DNA sequencing
(“metagenomics”) hinted soon afterward that many
other members of the Megaviridae existed in the
marine environment where they constitute a significant fraction of large DNA viruses (Monier et al.
2008). Ironically, this is probably because of their
size and nonfilterability which delayed the discovery
of these abundant viruses (as well as the fact that they
do not produce a visible disease in humans or
animals).
A handful of large DNA viruses related to the
Acanthamoeba-infecting Megaviridae have been found
to infect different species of unicellular eukaryotes such
as Cafeteria roenbergensis (Fischer et al. 2010) and
Phaeocystis globosa (Santini et al. 2013). These marine
giruses are often isolated in the context of blooms of their
host species, the population of which they regulate.
Ironically, the latest discovered viruses are the largest,
the most abundant, and possibly those whose geoclimatic influence is the most significant on our planet.
Box 5.2: Pico-eukaryotes: Highly Diversified Small Cells
Herve Moreau
Pico-eukaryotes are eukaryotic microorganisms that
have a size below 2–3 μm. This definition based on
the size of the cells has no phylogenetic significance
but corresponds to operational considerations enabling
to divide marine plankton in subcategories like pico-,
nano-, and microplankton.
Probably because they are small and their morphology
is very simple, the diversity of pico-eukaryotes is often
underestimated. It is only in 2001 that several studies
based on sequencing of the 18S ribosomal gene revealed
this diversity in the sea (Moon-van der Staay et al. 2001;
Lo ´pez-Garcı ´a et al. 2001). For practical reasons
(easy detection of pigments), diversity of autotrophic
pico-eukaryotes is the best known. In the sea, they belong
essentially to the phylogenetic groups Prasinophyceae
(Chlorobionta),
Dinophyceae,
Bacillariophyceae
(Diatoms), Cryptophyceae, Prymnesiophyceae, and
Bolidophyceae (Vaulot et al. 2008). In marine picoplankton, the respective contribution of prokaryotes
(Cyanobacteria) and pico-eukaryotes to primary production remains difficult to determine. Prokaryotes are
clearly more numerous in terms of cell number (around
80 %), but the bigger size of eukaryotes and their higher
productivity allow these organisms, at least in coastal
areas, to be responsible for the major part of biomass
production in this cell size compartment (Worden et al.
2004).
Heterotrophic pico-eukaryotes are less known,
although most of the ribosomal sequences found in
metagenomic studies correspond to organisms belonging to heterotrophic lineages. It is, however, now clear
that partial amplification of the 18S ribosomal gene
(the most used gene marker) by “universal primers”
introduces a bias towards detection of heterotrophs.
Few of these organisms are cultivated, and it is sometimes impossible to determine the autotrophic or
heterotrophic nature of the organisms corresponding
to these 18S sequences. Cultivation of microorganisms
of which only the sequence of one marker gene is
known remains challenging, and a combination of
techniques like in situ hybridization, cell sorting, and
single-cell whole-genome amplification is more and
more used to obtain functional information.
H. Moreau (*)
UMR 7232 LOBB, Observatoire Oce ´anographique de Banyuls,
66650 Banyuls-sur-Mer, France
(continued)
5 Systematic and Evolution of Microorganisms: General Concepts
111
subdomain that diverged very early on from the branch
leading to the modern eukaryotes (Box Fig. 5.2).
The controversy remains strong: did the emergence
of DNA viruses predate that of eukaryotes? Were
these two phenomena related? Is it absurd to imagine
that viruses might have emerged before their hosts? Or
are these viruses the last representative of a 4th cellular domain now extinct and that only managed to
survive as parasites within the extant eukaryotic
domain?
In the latter case, these giant viruses might be the
result of reductive evolution from ancestral
microorganisms (somewhat like the one followed by
Rickettsia). All these questions can only be answered
by identifying more giant viruses whose genomes
should have kept other traces (e.g., ribosomal proteins)
of reductive evolution. In the present state of our
knowledge, the presence/absence of functional protein
of the translation system remains the most fundamental criterion for discriminating viruses from the most
reduced parasitic bacteria. In the context of reductive
evolution, the loss of one key component of the translation apparatus would constitute the initiating event
irreversibly committing a cellular parasite to a
viruslike evolutionary pathway, rather than becoming
an organelle as it is the normal fate for obligate intracellular bacteria (Claverie 2006; Claverie and Abergel
2010).
Although Mimivirus was discovered fortuitously
only recently, environmental DNA sequencing
(“metagenomics”) hinted soon afterward that many
other members of the Megaviridae existed in the
marine environment where they constitute a significant fraction of large DNA viruses (Monier et al.
2008). Ironically, this is probably because of their
size and nonfilterability which delayed the discovery
of these abundant viruses (as well as the fact that they
do not produce a visible disease in humans or
animals).
A handful of large DNA viruses related to the
Acanthamoeba-infecting Megaviridae have been found
to infect different species of unicellular eukaryotes such
as Cafeteria roenbergensis (Fischer et al. 2010) and
Phaeocystis globosa (Santini et al. 2013). These marine
giruses are often isolated in the context of blooms of their
host species, the population of which they regulate.
Ironically, the latest discovered viruses are the largest,
the most abundant, and possibly those whose geoclimatic influence is the most significant on our planet.
Box 5.2: Pico-eukaryotes: Highly Diversified Small Cells
Herve Moreau
Pico-eukaryotes are eukaryotic microorganisms that
have a size below 2–3 μm. This definition based on
the size of the cells has no phylogenetic significance
but corresponds to operational considerations enabling
to divide marine plankton in subcategories like pico-,
nano-, and microplankton.
Probably because they are small and their morphology
is very simple, the diversity of pico-eukaryotes is often
underestimated. It is only in 2001 that several studies
based on sequencing of the 18S ribosomal gene revealed
this diversity in the sea (Moon-van der Staay et al. 2001;
Lo ´pez-Garcı ´a et al. 2001). For practical reasons
(easy detection of pigments), diversity of autotrophic
pico-eukaryotes is the best known. In the sea, they belong
essentially to the phylogenetic groups Prasinophyceae
(Chlorobionta),
Dinophyceae,
Bacillariophyceae
(Diatoms), Cryptophyceae, Prymnesiophyceae, and
Bolidophyceae (Vaulot et al. 2008). In marine picoplankton, the respective contribution of prokaryotes
(Cyanobacteria) and pico-eukaryotes to primary production remains difficult to determine. Prokaryotes are
clearly more numerous in terms of cell number (around
80 %), but the bigger size of eukaryotes and their higher
productivity allow these organisms, at least in coastal
areas, to be responsible for the major part of biomass
production in this cell size compartment (Worden et al.
2004).
Heterotrophic pico-eukaryotes are less known,
although most of the ribosomal sequences found in
metagenomic studies correspond to organisms belonging to heterotrophic lineages. It is, however, now clear
that partial amplification of the 18S ribosomal gene
(the most used gene marker) by “universal primers”
introduces a bias towards detection of heterotrophs.
Few of these organisms are cultivated, and it is sometimes impossible to determine the autotrophic or
heterotrophic nature of the organisms corresponding
to these 18S sequences. Cultivation of microorganisms
of which only the sequence of one marker gene is
known remains challenging, and a combination of
techniques like in situ hybridization, cell sorting, and
single-cell whole-genome amplification is more and
more used to obtain functional information.
H. Moreau (*)
UMR 7232 LOBB, Observatoire Oce ´anographique de Banyuls,
66650 Banyuls-sur-Mer, France
(continued)
5 Systematic and Evolution of Microorganisms: General Concepts
111