various lineages of hyperthermophiles with optimal growth
temperatures greater than 80
C such as the Thermococcales.
A few years later, Carl Woese proposed to rename
Eubacteria and Archaebacteria as Bacteria and Archaea,
respectively, to remove the “bacteria” suffix which implies
that Archaea are somehow bacteria and that both prokaryotic
domains share a closer evolutionary link compared to
Eucarya. In fact, the tree of life based on 16S/18S rRNA
being unrooted (cf. Sect. 4.1.10), it is impossible to determine the relationships between the three domains.
6.6.1.2 Diversity of Archaea
While more than 10 bacterial phyla were described in the
seminal works of Carl Woese, Archaea were divided into two
phyla, Crenarchaeota and Euryarchaeota, corresponding
to only three and nine cultivated orders (Woese 1987).
Euryarchaeota (also referred to as euryotes or euryarchaeotes,
from Greek “Euryos” meaning varied/diverse) bring together
various lineages presenting very different lifestyle, such
as
hyperthermophilic
or
mesophilic
methanogens
(Methanococcales, Methanobacteriales, Methanocellales,
Methanomicrobiales, Methanosarcinales, Methanopyrales,
and the recently proposed “Methanoplasmatales”), extreme
halophiles (Halobacteriales and the recently discovered
“Nanohaloarchaea”), sulfate reducers (Archaeoglobales),
thermoacidophiles (Thermoplasmatales), and some
hyperthermophiles (Thermococcales). In contrast, the
second phylum gathers exclusively thermophiles or
hyperthermophiles. It was named Crenarchaeota (also
referred to as crenotes or crenarchaeotes) from the Greek
“Krenos” meaning source/origin because Carl Woese
thought that the ancestor of Archaea was hyperthermophile,
a feature retained by Crenarchaeota. For a long time, only
two archaeal phyla were recognized, but new phyla (i.e.,
Korarchaeota, “Nanoarchaeota”, Thaumarchaeota, and
more recently the Aigarchaeota) have been proposed in the
last few years.
Most archaea and bacteria look alike. They are similar in
size, shape, and cellular organization. However a few atypical cell morphologies are found in archaea as polygonal,
triangular, or ultrathin square cells or very irregular cells.
As bacteria, archaea exhibit a variety of phenotypes and
physiologies. In fact, except for methanogenesis, all
metabolisms described in archaea exist also in bacteria.
Conversely no photosynthesis involving chlorophyll, spore
production*, or pathogens have been reported in archaea so
far. Archaea can be heterotrophic or autotrophic, can use
various electron acceptors and electron donors, be aerobic,
or anaerobic, etc. The main feature distinguishing bacteria
from archaea is the nature of their cell envelope. In
contrast to bacteria, the archaeal membranes contain lipids
made of isoprene (and not fatty acid) chains, ether (and not
ester) linkages, and L-glycerol (and not D-glycerol) moiety,
in addition to the phosphate group. Moreover, archaeal
envelope does not contain peptidoglycan or murein,
resulting in insensitivity to the most common antibiotics
targeting the bacterial cell wall (for a recent and complete
review on the archaeal envelope, see Albers and Meyer
2011). Worth noting, the archaeal cell envelope is highly
variable even among closely related lineages (Table 6.3),
highlighting an unexpectedly very dynamic structure.
To the exception of Ignicoccus hospitalis (the host of
Nanoarchaeum equitans), which harbors two membranes,
the archaeal cell envelope is composed of a single membrane. In nearly all archaea characterized to date, this membrane is surrounded by a proteinaceous protein layer called
the S-layer, which form a crystalline array (Table 6.3). Slayers are also found in bacteria. S-layer contributes to the
shape, osmoprotection, and permeability of the cell. In most
cases, the S-layer is composed of a single protein (or glycoprotein) aligned in lattices with oblique (p1 or p2), tetragonal
(p4), or hexagonal (p3 or p6) symmetry. S-layer proteins
have sizes ranging from 40 to 200 kDa and are also found in
many bacteria. The composition and structure of the S-layer
varies among archaea. While the hexagonal symmetry is
predominant in archaeal S-layers, oblique or tetragonal
lattices exist (Albers and Meyer 2011). In addition to Slayer, very atypical and stable proteinaceous structures
have been reported in two unrelated species, namely,
Methanospirillum hungatei (Methanomicrobiales) and
Methanosaeta concilii (Methanosarcinales) (Table 6.3). It
consists in tubular sheaths enclosing linear chains of cells,
the individual cells within the chains being themselves
surrounded either by an S-layer (M. hungatei) or by an
amorphous granular protein layer (M. concilli) (Albers and
Meyer 2011).
In many archaea, the S-layer is the only component of the
cell wall, whereas in others various additional components
can be found in the cell envelope. For instance, some
methanogens (e.g., Methanobacteriales or Methanopyrales)
harbor a cell wall composed of pseudopeptidoglycan (also
called pseudomurein), which superficially resemble bacterial peptidoglycan. The comparison of the proteins
involved in the biosynthesis of archaeal pseudomurein and
bacterial murein showed no homology, suggesting that the
two pathways emerged twice independently during evolution. A fibrillar polymer, called methanochondroitin, is
found in the cell wall of members of the Methanosarcina
genus when they form aggregates, but not in single cells.
Strikingly a very similar polymer, the chondroitin, is part of
the connective tissue matrix of vertebrates (Albers and
Meyer 2011). Other polymers can be encountered in the
cell envelope of some extreme halophiles belonging to
Halobacteriales such as glutaminylglycan (Natronococcus
occultus),
highly
sulfated
heteropolysaccharides
(Halococcus morrhuae), or halomucin (Haloquadratum
162
P. Caumette et al.
temperatures greater than 80
C such as the Thermococcales.
A few years later, Carl Woese proposed to rename
Eubacteria and Archaebacteria as Bacteria and Archaea,
respectively, to remove the “bacteria” suffix which implies
that Archaea are somehow bacteria and that both prokaryotic
domains share a closer evolutionary link compared to
Eucarya. In fact, the tree of life based on 16S/18S rRNA
being unrooted (cf. Sect. 4.1.10), it is impossible to determine the relationships between the three domains.
6.6.1.2 Diversity of Archaea
While more than 10 bacterial phyla were described in the
seminal works of Carl Woese, Archaea were divided into two
phyla, Crenarchaeota and Euryarchaeota, corresponding
to only three and nine cultivated orders (Woese 1987).
Euryarchaeota (also referred to as euryotes or euryarchaeotes,
from Greek “Euryos” meaning varied/diverse) bring together
various lineages presenting very different lifestyle, such
as
hyperthermophilic
or
mesophilic
methanogens
(Methanococcales, Methanobacteriales, Methanocellales,
Methanomicrobiales, Methanosarcinales, Methanopyrales,
and the recently proposed “Methanoplasmatales”), extreme
halophiles (Halobacteriales and the recently discovered
“Nanohaloarchaea”), sulfate reducers (Archaeoglobales),
thermoacidophiles (Thermoplasmatales), and some
hyperthermophiles (Thermococcales). In contrast, the
second phylum gathers exclusively thermophiles or
hyperthermophiles. It was named Crenarchaeota (also
referred to as crenotes or crenarchaeotes) from the Greek
“Krenos” meaning source/origin because Carl Woese
thought that the ancestor of Archaea was hyperthermophile,
a feature retained by Crenarchaeota. For a long time, only
two archaeal phyla were recognized, but new phyla (i.e.,
Korarchaeota, “Nanoarchaeota”, Thaumarchaeota, and
more recently the Aigarchaeota) have been proposed in the
last few years.
Most archaea and bacteria look alike. They are similar in
size, shape, and cellular organization. However a few atypical cell morphologies are found in archaea as polygonal,
triangular, or ultrathin square cells or very irregular cells.
As bacteria, archaea exhibit a variety of phenotypes and
physiologies. In fact, except for methanogenesis, all
metabolisms described in archaea exist also in bacteria.
Conversely no photosynthesis involving chlorophyll, spore
production*, or pathogens have been reported in archaea so
far. Archaea can be heterotrophic or autotrophic, can use
various electron acceptors and electron donors, be aerobic,
or anaerobic, etc. The main feature distinguishing bacteria
from archaea is the nature of their cell envelope. In
contrast to bacteria, the archaeal membranes contain lipids
made of isoprene (and not fatty acid) chains, ether (and not
ester) linkages, and L-glycerol (and not D-glycerol) moiety,
in addition to the phosphate group. Moreover, archaeal
envelope does not contain peptidoglycan or murein,
resulting in insensitivity to the most common antibiotics
targeting the bacterial cell wall (for a recent and complete
review on the archaeal envelope, see Albers and Meyer
2011). Worth noting, the archaeal cell envelope is highly
variable even among closely related lineages (Table 6.3),
highlighting an unexpectedly very dynamic structure.
To the exception of Ignicoccus hospitalis (the host of
Nanoarchaeum equitans), which harbors two membranes,
the archaeal cell envelope is composed of a single membrane. In nearly all archaea characterized to date, this membrane is surrounded by a proteinaceous protein layer called
the S-layer, which form a crystalline array (Table 6.3). Slayers are also found in bacteria. S-layer contributes to the
shape, osmoprotection, and permeability of the cell. In most
cases, the S-layer is composed of a single protein (or glycoprotein) aligned in lattices with oblique (p1 or p2), tetragonal
(p4), or hexagonal (p3 or p6) symmetry. S-layer proteins
have sizes ranging from 40 to 200 kDa and are also found in
many bacteria. The composition and structure of the S-layer
varies among archaea. While the hexagonal symmetry is
predominant in archaeal S-layers, oblique or tetragonal
lattices exist (Albers and Meyer 2011). In addition to Slayer, very atypical and stable proteinaceous structures
have been reported in two unrelated species, namely,
Methanospirillum hungatei (Methanomicrobiales) and
Methanosaeta concilii (Methanosarcinales) (Table 6.3). It
consists in tubular sheaths enclosing linear chains of cells,
the individual cells within the chains being themselves
surrounded either by an S-layer (M. hungatei) or by an
amorphous granular protein layer (M. concilli) (Albers and
Meyer 2011).
In many archaea, the S-layer is the only component of the
cell wall, whereas in others various additional components
can be found in the cell envelope. For instance, some
methanogens (e.g., Methanobacteriales or Methanopyrales)
harbor a cell wall composed of pseudopeptidoglycan (also
called pseudomurein), which superficially resemble bacterial peptidoglycan. The comparison of the proteins
involved in the biosynthesis of archaeal pseudomurein and
bacterial murein showed no homology, suggesting that the
two pathways emerged twice independently during evolution. A fibrillar polymer, called methanochondroitin, is
found in the cell wall of members of the Methanosarcina
genus when they form aggregates, but not in single cells.
Strikingly a very similar polymer, the chondroitin, is part of
the connective tissue matrix of vertebrates (Albers and
Meyer 2011). Other polymers can be encountered in the
cell envelope of some extreme halophiles belonging to
Halobacteriales such as glutaminylglycan (Natronococcus
occultus),
highly
sulfated
heteropolysaccharides
(Halococcus morrhuae), or halomucin (Haloquadratum
162
P. Caumette et al.