based phototrophy, photosynthesis requires additional
pigments known as “antennas” and is coupled to carbon
fixation. In 2001, homologues of bacteriorhodopsins were
discovered in uncultured planktonic marine SAR86
gammaproteobacteria (Beja et al. 2000). Accordingly, these
were referred as proteorhodopsins. Since then, homologues of
proteorhodopsin were shown to be widespread in the oceans
and in many prokaryotic lineages including the ubiquitous
and abundant SAR11 alphaproteobacteria, archaea from
group II, etc. This suggests that proteorhodopsin-based
phototrophy is a significant oceanic microbial process, and
therefore could represent a significant source of energy for
microbial communities living in the ocean photic zone.
To thrive in environments rich in salts, Halobacteriales
must cope with high osmotic pressures. Most halophilic or
halotolerant microorganisms use a “salt-out” strategy
consisting in the expulsion of salt from the cytoplasm to
maintain low intracellular ionic concentrations and the use
of organic solutes (e.g., glycerol or glycine betaine) to maintain an osmotic balance with the extracellular medium. In
contrast, Halobacteriales, a few anaerobic halophilic bacteria
(Haloanaerobiales), and Salinibacter ruber (Bacteroidetes)
have adopted a radically different strategy referred as to
“salt-in,” which consists in the molar accumulation of ions,
especially K
+ and Cl
À ions (and often Na
+
) in their cytoplasm.
The import of K
+ allows balancing the high osmotic pressure
generated by high environmental Na
+ levels. This equilibrium
between intracellular K
+ and extracellular Na
+ is essential to
prevent cells from dehydration. Some haloalkaliphilic archaea
use organic osmotic solutes (e.g., 2-sulfotrehalose) in addition
to high intracellular salt levels. The salt-out strategy is energetically costly due to the importance of organic-compatible
solutes and less suitable at saturating salt levels, which probably explain why organisms using the salt-in strategy predominate under extreme hypersaline conditions. Due to the salt-in
strategy, halobacteriales proteins must be adapted to function
at molar salt levels. The side effect is that these proteins
commonly denature in low-salt solutions. In addition, the
cell wall of many Halobacteriales is composed of
glycoproteins enriched in acidic amino acids (i.e., aspartate
and glutamate). The negative charges provided by the carboxyl groups of these amino acids are surrounded by the Na
+
ions which stabilize these glycoproteins, ensuring the integrity of the wall. If Na
+ concentration becomes too low, the
negatively charged glycoproteins repel each other, leading to
destabilization of the cell wall and cell lysis. It has been early
noticed that cytoplasmic proteins are also enriched in acidic
amino acids. In addition they are depleted in hydrophobic
amino acids, compared with their homologues found in
nonhalophilic species. The replacement of large hydrophobic
residues by small hydrophilic residues on cytoplasmic protein
surface increases their overall polarity, preventing their aggregation and allowing them to remain functional. In parallel
their increase in acidic residues creates a high density of
negative charges coordinating a network of hydrated cations,
which help to maintain the proteins in solution.
Halobacteriales have been developed as genetic model
because they are efficiently transformable. Moreover, they
are simple to manipulate, in particular they are easy to culture,
fast growing, and resistant to contamination by nonhalophilic
microorganisms. They have been exploited to uncover genes
involved in osmotic stress. Furthermore, they are also good
models for structural biology because their proteins function
under conditions of low water availability and biotechnology
(Leigh et al. 2011). From an evolutionary point of view,
Halobacteriales represent a relatively late diverging order
within Euryarchaeota. They are related to “Nanohaloarchaea,”
a lineage of uncultured nanometric archaea (0.6 μm in diameter), which are prevalent in worldwide distributed hypersaline
environments (Narasingarao et al. 2011). Halobacteriales are
grouping with methanogens class II (i.e., Methanocellales,
Methanomicrobiales, and Methanosarcinales) (Fig. 6.9). For
additional information on Halobacteriales, see Dworkin and
collaborators (2006).
The Thermococcales
This order has been proposed by Wolfram Zillig and
collaborators in 1987. It gathers anaerobic heterotrophic
hyperthermophiles which grow optimally at neutral pH
(6.0–7.0), even if a few alkaliphilic strains able to grow at
pH 9 have been reported. Thermococcales cells are spherical
and some of them are flagellated. Their metabolism is based
on fermentation. They use polymeric organic substrates like
peptides and carbohydrates as energy and carbon sources.
The fermentation process produces H 2 which in turn can be
used to reduce S
0 to H 2 S. Depending of the considered strains,
S
0 can either be required for growth or to stimulate growth. In
some strains (e.g., Palaeococcus), S
0 can be replaced by Fe
2+
.
From an evolutionary point of view, Thermococcales have
diverged early within Euryarchaeota (Fig. 6.9). Members of
this group are very abundant and commonly found within
marine hot water environments. They represent therefore a
major constituent of the biomass in these ecosystems.
Thermococcales contain a single family Thermococcaceae,
represented by three genera: Pyrococcus, Thermococcus, and
Paleococcus, the two first being more closely related to each
other. Pyrococcus live in marine hydrothermal vents, whereas
Thermococcus are also found in terrestrial freshwater, marine
solfataric ecosystems, deep-sea hydrothermal vents, and offshore oil wells. Thermococcales have been developed as
genetic models for studying DNA replication and repair, transcription and its regulation, carbon and energy metabolism,
CRISPR systems, and cellular responses to stress, such as
oxidative, osmotic, temperature, and pressure (Leigh et al.
2011). Thermococcales are also used as models in various
fields of biotechnology due to their capacity to efficiently
172
P. Caumette et al.
pigments known as “antennas” and is coupled to carbon
fixation. In 2001, homologues of bacteriorhodopsins were
discovered in uncultured planktonic marine SAR86
gammaproteobacteria (Beja et al. 2000). Accordingly, these
were referred as proteorhodopsins. Since then, homologues of
proteorhodopsin were shown to be widespread in the oceans
and in many prokaryotic lineages including the ubiquitous
and abundant SAR11 alphaproteobacteria, archaea from
group II, etc. This suggests that proteorhodopsin-based
phototrophy is a significant oceanic microbial process, and
therefore could represent a significant source of energy for
microbial communities living in the ocean photic zone.
To thrive in environments rich in salts, Halobacteriales
must cope with high osmotic pressures. Most halophilic or
halotolerant microorganisms use a “salt-out” strategy
consisting in the expulsion of salt from the cytoplasm to
maintain low intracellular ionic concentrations and the use
of organic solutes (e.g., glycerol or glycine betaine) to maintain an osmotic balance with the extracellular medium. In
contrast, Halobacteriales, a few anaerobic halophilic bacteria
(Haloanaerobiales), and Salinibacter ruber (Bacteroidetes)
have adopted a radically different strategy referred as to
“salt-in,” which consists in the molar accumulation of ions,
especially K
+ and Cl
À ions (and often Na
+
) in their cytoplasm.
The import of K
+ allows balancing the high osmotic pressure
generated by high environmental Na
+ levels. This equilibrium
between intracellular K
+ and extracellular Na
+ is essential to
prevent cells from dehydration. Some haloalkaliphilic archaea
use organic osmotic solutes (e.g., 2-sulfotrehalose) in addition
to high intracellular salt levels. The salt-out strategy is energetically costly due to the importance of organic-compatible
solutes and less suitable at saturating salt levels, which probably explain why organisms using the salt-in strategy predominate under extreme hypersaline conditions. Due to the salt-in
strategy, halobacteriales proteins must be adapted to function
at molar salt levels. The side effect is that these proteins
commonly denature in low-salt solutions. In addition, the
cell wall of many Halobacteriales is composed of
glycoproteins enriched in acidic amino acids (i.e., aspartate
and glutamate). The negative charges provided by the carboxyl groups of these amino acids are surrounded by the Na
+
ions which stabilize these glycoproteins, ensuring the integrity of the wall. If Na
+ concentration becomes too low, the
negatively charged glycoproteins repel each other, leading to
destabilization of the cell wall and cell lysis. It has been early
noticed that cytoplasmic proteins are also enriched in acidic
amino acids. In addition they are depleted in hydrophobic
amino acids, compared with their homologues found in
nonhalophilic species. The replacement of large hydrophobic
residues by small hydrophilic residues on cytoplasmic protein
surface increases their overall polarity, preventing their aggregation and allowing them to remain functional. In parallel
their increase in acidic residues creates a high density of
negative charges coordinating a network of hydrated cations,
which help to maintain the proteins in solution.
Halobacteriales have been developed as genetic model
because they are efficiently transformable. Moreover, they
are simple to manipulate, in particular they are easy to culture,
fast growing, and resistant to contamination by nonhalophilic
microorganisms. They have been exploited to uncover genes
involved in osmotic stress. Furthermore, they are also good
models for structural biology because their proteins function
under conditions of low water availability and biotechnology
(Leigh et al. 2011). From an evolutionary point of view,
Halobacteriales represent a relatively late diverging order
within Euryarchaeota. They are related to “Nanohaloarchaea,”
a lineage of uncultured nanometric archaea (0.6 μm in diameter), which are prevalent in worldwide distributed hypersaline
environments (Narasingarao et al. 2011). Halobacteriales are
grouping with methanogens class II (i.e., Methanocellales,
Methanomicrobiales, and Methanosarcinales) (Fig. 6.9). For
additional information on Halobacteriales, see Dworkin and
collaborators (2006).
The Thermococcales
This order has been proposed by Wolfram Zillig and
collaborators in 1987. It gathers anaerobic heterotrophic
hyperthermophiles which grow optimally at neutral pH
(6.0–7.0), even if a few alkaliphilic strains able to grow at
pH 9 have been reported. Thermococcales cells are spherical
and some of them are flagellated. Their metabolism is based
on fermentation. They use polymeric organic substrates like
peptides and carbohydrates as energy and carbon sources.
The fermentation process produces H 2 which in turn can be
used to reduce S
0 to H 2 S. Depending of the considered strains,
S
0 can either be required for growth or to stimulate growth. In
some strains (e.g., Palaeococcus), S
0 can be replaced by Fe
2+
.
From an evolutionary point of view, Thermococcales have
diverged early within Euryarchaeota (Fig. 6.9). Members of
this group are very abundant and commonly found within
marine hot water environments. They represent therefore a
major constituent of the biomass in these ecosystems.
Thermococcales contain a single family Thermococcaceae,
represented by three genera: Pyrococcus, Thermococcus, and
Paleococcus, the two first being more closely related to each
other. Pyrococcus live in marine hydrothermal vents, whereas
Thermococcus are also found in terrestrial freshwater, marine
solfataric ecosystems, deep-sea hydrothermal vents, and offshore oil wells. Thermococcales have been developed as
genetic models for studying DNA replication and repair, transcription and its regulation, carbon and energy metabolism,
CRISPR systems, and cellular responses to stress, such as
oxidative, osmotic, temperature, and pressure (Leigh et al.
2011). Thermococcales are also used as models in various
fields of biotechnology due to their capacity to efficiently
172
P. Caumette et al.