genus) (Table 6.3). Worth noting, halomucin is the largest
archaeal protein (9,159 amino acids) known to date. Its
amino acid composition and domain organization are similar
to mammalian mucin, which acts as a shield against dehydration of various tissues, such as the bronchial epithelium
and the eyes (Albers and Meyer 2011). Finally, a few
archaea belonging to Thermoplasmatales harbor highly
pleomorphic shapes, due to the lack of any cell wall
(Table 6.3).
At the genetic level, Archaea are a mosaic. Their informational systems (i.e., systems involved in the transmission
and expression of genetic information, namely, the
machineries of transcription, translation, replication, and
repair) are similar to eukaryotes (cf. Sect. 4.1.10), whereas
their housekeeping and metabolic genes and their general
cell organization are similar to bacteria. Since their discovery, Archaea have led to some of the most exciting
discoveries in the field of biochemistry and biotechnologies,
but archaeal genetics has been slow to get off the ground,
until recently. In fact, the last past years have witnessed
spectacular progress, and genetic tools and models are now
available for the two major archaeal phyla, the
Euryarchaeota (i.e., Halobacteriales, Methanococcales,
Methanosarcinales, and Thermococcales) and the
Crenarchaeota (i.e., Sulfolobales) (for more details on
archaeal genetics, see the excellent review of Leigh et al.
2011). This will accelerate our understanding of the biology
of Archaea.
Because the first described archaea inhabited some of the
more inhospitable places on earth (from an anthropomorphic
point of view), members of this domain have been considered for a long time as “exotic microbes” or “curiosities” by
most microbiologists. Because archaea are the only living
organisms able to grow optimally at temperatures above
100
C, the dominance of archaea over bacteria in extremely
hot environments was early recognized. In contrast, bacteria
were considered as dominant over archaea in all other
ecosystems. As a consequence, and to the exception of
methanogens, the relevance of archaea in microbial
ecosystems and in global biogeochemical cycles has been
underestimated for years (Forterre et al. 2002; Gribaldo and
Brochier-Armanet 2006). The situation has changed with the
birth of molecular ecology at the end of the 1980s. The
investigation of microbial ecosystems with molecular tools
has uncovered the incredible genetic, physiological, and
phenotypic diversity of Archaea (Schleper et al. 2005;
Lopez-Garcia and Moreira 2008). A large number of new
lineages, such as groups called I, II, III, IV, SA1, SA2,
ARMAN, ANME-1, ANME-2, “Nanohaloarchaea,” Miscellaneous Crenarchaeotal Group (MCG), etc., many of them
representing likely high-level taxonomic groups were discovered. Importantly, these uncultured archaeal lineages
could represent an important fraction of the biomass of
some ecosystems (Narasingarao et al. 2011). Despite great
advance in cultivation techniques, most of these lineages
have resisted all cultivation attempts and remain poorly
characterized. This underlines that our knowledge of
Archaea based on cultured lineages is far from being representative of the real diversity of this domain. However,
thanks to rapid progresses in DNA sequencing and
metagenomics, complete genomes of representatives of
some of these groups have been sequenced. Such cultureindependent investigations will accelerate our understanding
of these uncultured lineages and of Archaea in general.
6.6.1.3 Classification of Archaea
The Crenarchaeota
Based on 16S rRNA phylogenies, Crenarchaeota are
divided into three orders (5 families and 22 genera) with
cultured representatives: The Sulfolobales, the Desulfurococcales, and Thermoproteales, the first two being more
closely related to each other (Fig. 6.9). Recently two additional orders have been proposed, namely, the Acidilobales
and the Fervidicoccales, living in acidic hot springs. However, subsequent phylogenetic and genomic analyses
suggested that they are rather Desulfurococcales (BrochierArmanet et al. 2011). Crenarchaeota can be anaerobic,
facultative anaerobic, or aerobic extreme thermophiles or
hyperthermophiles. Their energetic metabolism is mainly
based on sulfur, even if some of them are also able to use
organic and other inorganic compounds or have lost the
ability to use sulfur. Some of them are also acidophilic,
being able to grow in pH ranging from 2 to 5.
The Sulfolobales
This order was proposed by Karl Stetter in 1989.
Sulfolobales are extreme thermophilic or hyperthermophilic
acidophiles thriving at temperatures ranging from 65 to
90
C and at pH ranging from 1 to 5. Cells are regular to
irregular cocci of about 1.0 up to 5 μm in diameter, occurring
usually singly or in pairs. Most members of the Sulfolobales
have been isolated from continental solfataric fields, from
acidic hot soils, acidic hot springs, and smoldering slag
heaps. In contrast, a few strains only have been isolated
from submarine hydrothermal systems. This order contains
a single family, the Sulfolobaceae divided into six genera:
Sulfolobus, Acidianus, Metallosphaera, Stygiolobus,
Sulfurisphaera, and Sulfurococcus. They can be aerobic,
facultative anaerobic, or anaerobic. When growing autotrophically, they gain energy by oxidizing S
0 , S 2 O 3
2À , sulfidic
ores, or H 2 and use CO 2 as a carbon source. In contrast,
organotrophic growth occurs by aerobic respiration or anaerobic sulfur respiration or by fermentation of organic
substrates. More precisely, Sulfolobus are obligate aerobes.
Some of them can grow mixotrophically or heterotrophically
by using complex organic compounds, sugar or amino acids,
164
P. Caumette et al.
archaeal protein (9,159 amino acids) known to date. Its
amino acid composition and domain organization are similar
to mammalian mucin, which acts as a shield against dehydration of various tissues, such as the bronchial epithelium
and the eyes (Albers and Meyer 2011). Finally, a few
archaea belonging to Thermoplasmatales harbor highly
pleomorphic shapes, due to the lack of any cell wall
(Table 6.3).
At the genetic level, Archaea are a mosaic. Their informational systems (i.e., systems involved in the transmission
and expression of genetic information, namely, the
machineries of transcription, translation, replication, and
repair) are similar to eukaryotes (cf. Sect. 4.1.10), whereas
their housekeeping and metabolic genes and their general
cell organization are similar to bacteria. Since their discovery, Archaea have led to some of the most exciting
discoveries in the field of biochemistry and biotechnologies,
but archaeal genetics has been slow to get off the ground,
until recently. In fact, the last past years have witnessed
spectacular progress, and genetic tools and models are now
available for the two major archaeal phyla, the
Euryarchaeota (i.e., Halobacteriales, Methanococcales,
Methanosarcinales, and Thermococcales) and the
Crenarchaeota (i.e., Sulfolobales) (for more details on
archaeal genetics, see the excellent review of Leigh et al.
2011). This will accelerate our understanding of the biology
of Archaea.
Because the first described archaea inhabited some of the
more inhospitable places on earth (from an anthropomorphic
point of view), members of this domain have been considered for a long time as “exotic microbes” or “curiosities” by
most microbiologists. Because archaea are the only living
organisms able to grow optimally at temperatures above
100
C, the dominance of archaea over bacteria in extremely
hot environments was early recognized. In contrast, bacteria
were considered as dominant over archaea in all other
ecosystems. As a consequence, and to the exception of
methanogens, the relevance of archaea in microbial
ecosystems and in global biogeochemical cycles has been
underestimated for years (Forterre et al. 2002; Gribaldo and
Brochier-Armanet 2006). The situation has changed with the
birth of molecular ecology at the end of the 1980s. The
investigation of microbial ecosystems with molecular tools
has uncovered the incredible genetic, physiological, and
phenotypic diversity of Archaea (Schleper et al. 2005;
Lopez-Garcia and Moreira 2008). A large number of new
lineages, such as groups called I, II, III, IV, SA1, SA2,
ARMAN, ANME-1, ANME-2, “Nanohaloarchaea,” Miscellaneous Crenarchaeotal Group (MCG), etc., many of them
representing likely high-level taxonomic groups were discovered. Importantly, these uncultured archaeal lineages
could represent an important fraction of the biomass of
some ecosystems (Narasingarao et al. 2011). Despite great
advance in cultivation techniques, most of these lineages
have resisted all cultivation attempts and remain poorly
characterized. This underlines that our knowledge of
Archaea based on cultured lineages is far from being representative of the real diversity of this domain. However,
thanks to rapid progresses in DNA sequencing and
metagenomics, complete genomes of representatives of
some of these groups have been sequenced. Such cultureindependent investigations will accelerate our understanding
of these uncultured lineages and of Archaea in general.
6.6.1.3 Classification of Archaea
The Crenarchaeota
Based on 16S rRNA phylogenies, Crenarchaeota are
divided into three orders (5 families and 22 genera) with
cultured representatives: The Sulfolobales, the Desulfurococcales, and Thermoproteales, the first two being more
closely related to each other (Fig. 6.9). Recently two additional orders have been proposed, namely, the Acidilobales
and the Fervidicoccales, living in acidic hot springs. However, subsequent phylogenetic and genomic analyses
suggested that they are rather Desulfurococcales (BrochierArmanet et al. 2011). Crenarchaeota can be anaerobic,
facultative anaerobic, or aerobic extreme thermophiles or
hyperthermophiles. Their energetic metabolism is mainly
based on sulfur, even if some of them are also able to use
organic and other inorganic compounds or have lost the
ability to use sulfur. Some of them are also acidophilic,
being able to grow in pH ranging from 2 to 5.
The Sulfolobales
This order was proposed by Karl Stetter in 1989.
Sulfolobales are extreme thermophilic or hyperthermophilic
acidophiles thriving at temperatures ranging from 65 to
90
C and at pH ranging from 1 to 5. Cells are regular to
irregular cocci of about 1.0 up to 5 μm in diameter, occurring
usually singly or in pairs. Most members of the Sulfolobales
have been isolated from continental solfataric fields, from
acidic hot soils, acidic hot springs, and smoldering slag
heaps. In contrast, a few strains only have been isolated
from submarine hydrothermal systems. This order contains
a single family, the Sulfolobaceae divided into six genera:
Sulfolobus, Acidianus, Metallosphaera, Stygiolobus,
Sulfurisphaera, and Sulfurococcus. They can be aerobic,
facultative anaerobic, or anaerobic. When growing autotrophically, they gain energy by oxidizing S
0 , S 2 O 3
2À , sulfidic
ores, or H 2 and use CO 2 as a carbon source. In contrast,
organotrophic growth occurs by aerobic respiration or anaerobic sulfur respiration or by fermentation of organic
substrates. More precisely, Sulfolobus are obligate aerobes.
Some of them can grow mixotrophically or heterotrophically
by using complex organic compounds, sugar or amino acids,
164
P. Caumette et al.