cannot be considered as microorganisms in their own right.
They are obligate intracellular parasites that have no cellular
structure and no capacity for self-multiplication.
1 Regarding
the Mimivirus (Raoult et al. 2004), the question of whether it
is a giant virus or a new domain of the living world is not
resolved (Box 5.1).
The size of microorganisms varies from a few tens to
hundreds of micrometers for the larger microorganisms
(especially eukaryotes) to a few micrometers or tenths of
micrometers for the smallest prokaryotes such as
Nanoarchaeum equitans (Fig. 5.1a). The diameter of eukaryotic cells is generally much larger than in prokaryotes: more
than 10 μm. However, the findings of eukaryotic cells less
than 2 μm in diameter (Box 5.2) have been successful; most
of the taxa of higher eukaryotes have one or more lineages of
pico-eukaryotes (Baldauf 2003). For instance, Ostreococcus
tauri (Prasinophyta, Chlorobionta, Viridiplantae; cf. Sect. 7.
5.5) measures 0.7–1.0 μm in diameter (Courties et al. 1994).
Conversely, bacteria can be large, such as Beggiatoa
(Fig. 5.1b) and Thioploca. Schulz et al. (1999) found a
“giant” bacterium, Thiomargarita namibiensis, with a cell
diameter that can reach 750 μm, which means that it is
visible to the naked eye (Fig. 5.1c).
The cells of microorganisms differ from the cells
of multicellular eukaryotic organisms by the fact that the
latter are not able to live alone in nature but as components
of an organism. In contrast, a single microbial cell is
theoretically capable of performing its own vital processes
of energy production, growth, and multiplication.
Generations of microbial cells develop in rapid succession,
usually within a few minutes to a few hours or even tens of
hours. Thus, the microbial world, under optimal development conditions, will be constantly changing, modifying
at any time the number and diversity of its cellular
components. Microorganisms, multiplying rapidly, form
sets of cells transmitting their cellular contents and their
genetic information to their offsprings with a probability
of change, genetic mutations, and thus higher evolution
than in multicellular organisms. The consequence is an
even bigger difficulty to assess their diversity and structure
their systematic.
Box 5.1: Giant Viruses (Megaviridae)
Jean-Michel Claverie and Chantal Abergel
In the collective unconscious of the general public as
well as that of biologists, the concept of “virus”
(derived from the Latin word meaning “poison”)
seems to be frozen as it was at the end of the nineteenth
century. Indeed, it is at that time that the “germ theory”
(that is to say, the “bacterial” theory) of infectious
diseases was established through the work of Robert
Koch in Germany and Louis Pasteur in France. However, as soon as 1881, Pasteur himself already knew
that the infectious agent of rabies was not a regular
microbe as it was invisible to the optical microscope
and could not be propagated on a culture medium but
only in the brain of a live rabbit. Roughly at the same
time, one of Pasteur’s assistant was developing the
porcelain filter (also called the “Chamberland” filter
after his name) able to retain all bacteria. Soon after,
it was then realized that many infectious diseases,
including the famous tobacco mosaic disease, were
caused by infectious agents capable of passing through
the Chamberland filter and thus referred to as
“ultrafiltrable.” This original notion of a virus being
too small to be contained (“contagium vivum
fluidum”) and unable to propagate without the support
of a living system (an animal, a tissue, or a cell) is the
one that durably remained in everybody’s mind.
For 20 years, however, the world of viruses and that
of cellular “microorganisms” (Bacteria and Archaea)
continuously moved closer and closer to one another
and then interpenetrated so much as to preclude
discriminations based on size, genomic complexity,
or even the recourse to an absolute parasitic lifestyle.
On the one hand, many bacteria (e.g., Rickettsia,
Buchnera, Chlamydia, etc.) were discovered that can
only survive and multiply within a host cell due to
their incomplete metabolism. On the other hand,
viruses whose size (0.4–1.2 μm) and genomic complexity (number of genes) greatly exceed those of
these parasitic bacteria are gradually discovered,
most of them in aquatic environments or sediments.
Among these giant viruses (for which we coined
the term “girus”; Claverie et al. 2006), a whole new
family is emerging which is constituted of Mimivirus
(Box Fig. 5.1) (Claverie and Abergel 2009) and its
relatives Megavirus (Arslan et al. 2011) and
Moumouvirus (Yoosuf et al. 2012). Their exceptional
J.M. Claverie (*)
Aix-Marseille University, Marseille, France
C. Abergel
CNRS, Villeurbanne Cedex, France
(continued)
1 Viruses are functionally inactive when they are outside their host.
However, a virus, as parasite of the archaea Acidianus convivator, was
discovered in hydrothermal vents of Pozzuoli (Italy) and was able to
generate outside of the host, a double tail protein (800 amino acids). It
was named ATV (Acidianus two-tailed virus) (Ha ¨ring et al. 2005).
5 Systematic and Evolution of Microorganisms: General Concepts
109
They are obligate intracellular parasites that have no cellular
structure and no capacity for self-multiplication.
1 Regarding
the Mimivirus (Raoult et al. 2004), the question of whether it
is a giant virus or a new domain of the living world is not
resolved (Box 5.1).
The size of microorganisms varies from a few tens to
hundreds of micrometers for the larger microorganisms
(especially eukaryotes) to a few micrometers or tenths of
micrometers for the smallest prokaryotes such as
Nanoarchaeum equitans (Fig. 5.1a). The diameter of eukaryotic cells is generally much larger than in prokaryotes: more
than 10 μm. However, the findings of eukaryotic cells less
than 2 μm in diameter (Box 5.2) have been successful; most
of the taxa of higher eukaryotes have one or more lineages of
pico-eukaryotes (Baldauf 2003). For instance, Ostreococcus
tauri (Prasinophyta, Chlorobionta, Viridiplantae; cf. Sect. 7.
5.5) measures 0.7–1.0 μm in diameter (Courties et al. 1994).
Conversely, bacteria can be large, such as Beggiatoa
(Fig. 5.1b) and Thioploca. Schulz et al. (1999) found a
“giant” bacterium, Thiomargarita namibiensis, with a cell
diameter that can reach 750 μm, which means that it is
visible to the naked eye (Fig. 5.1c).
The cells of microorganisms differ from the cells
of multicellular eukaryotic organisms by the fact that the
latter are not able to live alone in nature but as components
of an organism. In contrast, a single microbial cell is
theoretically capable of performing its own vital processes
of energy production, growth, and multiplication.
Generations of microbial cells develop in rapid succession,
usually within a few minutes to a few hours or even tens of
hours. Thus, the microbial world, under optimal development conditions, will be constantly changing, modifying
at any time the number and diversity of its cellular
components. Microorganisms, multiplying rapidly, form
sets of cells transmitting their cellular contents and their
genetic information to their offsprings with a probability
of change, genetic mutations, and thus higher evolution
than in multicellular organisms. The consequence is an
even bigger difficulty to assess their diversity and structure
their systematic.
Box 5.1: Giant Viruses (Megaviridae)
Jean-Michel Claverie and Chantal Abergel
In the collective unconscious of the general public as
well as that of biologists, the concept of “virus”
(derived from the Latin word meaning “poison”)
seems to be frozen as it was at the end of the nineteenth
century. Indeed, it is at that time that the “germ theory”
(that is to say, the “bacterial” theory) of infectious
diseases was established through the work of Robert
Koch in Germany and Louis Pasteur in France. However, as soon as 1881, Pasteur himself already knew
that the infectious agent of rabies was not a regular
microbe as it was invisible to the optical microscope
and could not be propagated on a culture medium but
only in the brain of a live rabbit. Roughly at the same
time, one of Pasteur’s assistant was developing the
porcelain filter (also called the “Chamberland” filter
after his name) able to retain all bacteria. Soon after,
it was then realized that many infectious diseases,
including the famous tobacco mosaic disease, were
caused by infectious agents capable of passing through
the Chamberland filter and thus referred to as
“ultrafiltrable.” This original notion of a virus being
too small to be contained (“contagium vivum
fluidum”) and unable to propagate without the support
of a living system (an animal, a tissue, or a cell) is the
one that durably remained in everybody’s mind.
For 20 years, however, the world of viruses and that
of cellular “microorganisms” (Bacteria and Archaea)
continuously moved closer and closer to one another
and then interpenetrated so much as to preclude
discriminations based on size, genomic complexity,
or even the recourse to an absolute parasitic lifestyle.
On the one hand, many bacteria (e.g., Rickettsia,
Buchnera, Chlamydia, etc.) were discovered that can
only survive and multiply within a host cell due to
their incomplete metabolism. On the other hand,
viruses whose size (0.4–1.2 μm) and genomic complexity (number of genes) greatly exceed those of
these parasitic bacteria are gradually discovered,
most of them in aquatic environments or sediments.
Among these giant viruses (for which we coined
the term “girus”; Claverie et al. 2006), a whole new
family is emerging which is constituted of Mimivirus
(Box Fig. 5.1) (Claverie and Abergel 2009) and its
relatives Megavirus (Arslan et al. 2011) and
Moumouvirus (Yoosuf et al. 2012). Their exceptional
J.M. Claverie (*)
Aix-Marseille University, Marseille, France
C. Abergel
CNRS, Villeurbanne Cedex, France
(continued)
1 Viruses are functionally inactive when they are outside their host.
However, a virus, as parasite of the archaea Acidianus convivator, was
discovered in hydrothermal vents of Pozzuoli (Italy) and was able to
generate outside of the host, a double tail protein (800 amino acids). It
was named ATV (Acidianus two-tailed virus) (Ha ¨ring et al. 2005).
5 Systematic and Evolution of Microorganisms: General Concepts
109