short chains or aggregates of cocci. They are anaerobic continental obligate heterotrophs which ferment complex organic
compounds. Their growth is inhibited by elemental sulfur and
also by H 2 . Finally, Desulfurococcales include additional
genera, namely, the Acidilobus, Caldisphaera, and
Fervidicoccus. The former and the latter were recently proposed to represent new crenarchaeotal orders (Acidilobales
and Fervidicoccales), whereas more recent analyses have
confirmed that their membership of Desulfurococcales (see
Brochier-Armanet et al. 2011), Acidilobus are acidophiles
which grow optimally at pH close to 4 in terrestrial acidic
hot springs. They are obligate heterotrophs growing via the
fermentation of complex organic compounds. For additional
information on Desulfurococcales, see Dworkin and
collaborators (2006).
The Thermoproteales
This order was defined by Wolfram Zillig and collaborators in
1981. Thermoproteales are extreme thermophiles or
hyperthermophiles with optimal growth temperatures ranging
from 75 to 100
C and from neutral to slightly acidic pH (from
3.7 to 7). Currently, the order is represented by two families:
the Thermoproteaceae and the Thermofilaceae, which contain
a single genus (Thermofilum) and five genera (Caldivirga,
Pyrobaculum,
Thermocladium,
Thermoproteus,
and
Vulcanisaeta), respectively. The former are rods of at least
0.4 μm in diameter, whereas the latter are ultrathin filaments of
only 0.15–0.35 μm in diameter and 1–100 μm in length. Some
Thermoproteales bear spherical bodies (“golf clubs”) at their
terminals (e.g., Vulcanisaeta) and are flagellated
(Pyrobaculum) or not (Thermofilum). Thermofilaceae and
some Thermoproteus are obligate heterotrophic anaerobes
that use peptides and S
0 as donor and accepter of electrons,
respectively. Other Thermoproteus are facultative
lithoautotrophic anaerobes that use H 2 , simple or complex
compounds as electron donors, and S
0 or malate as electron
acceptors. In contrast, most Pyrobaculum are anaerobes, but
some are also aerobes. They can be either obligate
heterotrophs or facultative lithoautotrophs. They can use a
wide range of substrates as electron donors (e.g., H2,
S 2 O 3
2À , and complex organic compounds) and electron
acceptors (e.g., S
0
, S 2 O 3
2À , SO 3
À , O 2 , NO 3
À , NO 2
À , Fe
3+
,
selenate, selenite, arsenate, L-cysteine, and oxidized glutathione). Caldivirga grows heterotrophically under anaerobic or
microaerobic conditions at weakly acidic pH (3.7–4.2) by using
complex organic compounds as electron donors and S
0
,
S 2 O 3
2À , and SO 4
2À as electron acceptors. Thermocladium are
obligate heterotrophs that use S
0
, S 2 O 3
2
, SO 4
2À , and
L-cystine as electron acceptor under anaerobic or microaerobic
conditions. Finally, Vulcanisaeta grows optimally at
pH 4.0–4.5 on proteinaceous substrates as carbon sources and
use S
0
or S 2 O 3
2À as electron acceptor. To the exception of
Pyrobaculum aerophilum, which was isolated from a marine
hydrothermal system, all Thermoproteales have been obtained
from terrestrial volcanic habitats (e.g., springs, water holes,
mud holes, and soils of continental solfataric fields, etc.) with
low salinity and acidity to neutral pH. In their ecosystem,
Thermoproteales are important component of food webs.
They can function as primary producers and/or as consumers
of organic material. For additional information on
Thermoproteales, see Dworkin and collaborators (2006).
The Euryarchaeota
Based on phylogenies of 16S rRNA, the Euryarchaeota have
been divided initially into nine orders: Methanobacteriales,
Methanococcales, Methanopyrales, Methanomicrobiales,
Methanosarcinales, Halobacteriales, Thermoplasmatales,
Thermococcales, and Archaeoglobales. Recently additional
orders have been proposed: Methanocellales, Methanoplasmatales, etc. Euryarchaeota are much more diverse
than Crenarchaeota. They present very different physiologies, live all types of environments: from temperate
environments to the coldest or the hottest, from most alkaline
to most acidic, and to most hypersaline ones. Large-scale
phylogenetic analyses indicate that Thermococcales represent
the earliest diverging lineage within Euryarchaeota;
methanogens class I (Methanobacteriales, Methanococcales,
Methanopyrales) and the large cluster containing Thermoplasmatales, “Methanoplasmatales,” DHEV2, and group II,
occupy an intermediate position, whereas Archaeoglobales
and the large group gathering Halobacteriales and
methanogens class II (i.e., Methanosarcinales, Methanomicrobiales, and Methanocellales) branch apically in the
Euryarchaeota tree (Fig. 6.9).
The Methanogens (Fig. 6.10a–d)
Methanogens represent a large and highly diversified group
of unrelated strictly anaerobic archaea, which produce large
amount of methane (CH 4 ) as the major end product of their
energy metabolism. Methanogens are key components of
most anaerobic ecosystems due to their capacity to achieve
the final step in the decomposition of organic matter. However, many methanogens are also autotrophs, being able to
use CO 2 as sole source of carbon. Different types of
reactions can lead to CH 4 production. The former ones
are based on CO 2 reduction to CH 4 . In this case, CO 2 is
reduced by electrons provided by H 2 (hydrogenotrophic
methanogens), formate, CO, or certain alcohols (e.g.,
2-propanol, ethanol, etc.). Nearly all methanogens can use
H 2 as electron donor, but many are also able to utilize
formate, whereas very few use alcohols. The second type
of reaction is based on methyl compounds. Indeed, some
methanogens are able to use methyl-containing C-1
compounds (e.g., methanol, methylamine, dimethylamine,
trimethylamine, dimethylsulfide, formate, etc.) as substrate
6 Taxonomy and Phylogeny of Prokaryotes
167
compounds. Their growth is inhibited by elemental sulfur and
also by H 2 . Finally, Desulfurococcales include additional
genera, namely, the Acidilobus, Caldisphaera, and
Fervidicoccus. The former and the latter were recently proposed to represent new crenarchaeotal orders (Acidilobales
and Fervidicoccales), whereas more recent analyses have
confirmed that their membership of Desulfurococcales (see
Brochier-Armanet et al. 2011), Acidilobus are acidophiles
which grow optimally at pH close to 4 in terrestrial acidic
hot springs. They are obligate heterotrophs growing via the
fermentation of complex organic compounds. For additional
information on Desulfurococcales, see Dworkin and
collaborators (2006).
The Thermoproteales
This order was defined by Wolfram Zillig and collaborators in
1981. Thermoproteales are extreme thermophiles or
hyperthermophiles with optimal growth temperatures ranging
from 75 to 100
C and from neutral to slightly acidic pH (from
3.7 to 7). Currently, the order is represented by two families:
the Thermoproteaceae and the Thermofilaceae, which contain
a single genus (Thermofilum) and five genera (Caldivirga,
Pyrobaculum,
Thermocladium,
Thermoproteus,
and
Vulcanisaeta), respectively. The former are rods of at least
0.4 μm in diameter, whereas the latter are ultrathin filaments of
only 0.15–0.35 μm in diameter and 1–100 μm in length. Some
Thermoproteales bear spherical bodies (“golf clubs”) at their
terminals (e.g., Vulcanisaeta) and are flagellated
(Pyrobaculum) or not (Thermofilum). Thermofilaceae and
some Thermoproteus are obligate heterotrophic anaerobes
that use peptides and S
0 as donor and accepter of electrons,
respectively. Other Thermoproteus are facultative
lithoautotrophic anaerobes that use H 2 , simple or complex
compounds as electron donors, and S
0 or malate as electron
acceptors. In contrast, most Pyrobaculum are anaerobes, but
some are also aerobes. They can be either obligate
heterotrophs or facultative lithoautotrophs. They can use a
wide range of substrates as electron donors (e.g., H2,
S 2 O 3
2À , and complex organic compounds) and electron
acceptors (e.g., S
0
, S 2 O 3
2À , SO 3
À , O 2 , NO 3
À , NO 2
À , Fe
3+
,
selenate, selenite, arsenate, L-cysteine, and oxidized glutathione). Caldivirga grows heterotrophically under anaerobic or
microaerobic conditions at weakly acidic pH (3.7–4.2) by using
complex organic compounds as electron donors and S
0
,
S 2 O 3
2À , and SO 4
2À as electron acceptors. Thermocladium are
obligate heterotrophs that use S
0
, S 2 O 3
2
, SO 4
2À , and
L-cystine as electron acceptor under anaerobic or microaerobic
conditions. Finally, Vulcanisaeta grows optimally at
pH 4.0–4.5 on proteinaceous substrates as carbon sources and
use S
0
or S 2 O 3
2À as electron acceptor. To the exception of
Pyrobaculum aerophilum, which was isolated from a marine
hydrothermal system, all Thermoproteales have been obtained
from terrestrial volcanic habitats (e.g., springs, water holes,
mud holes, and soils of continental solfataric fields, etc.) with
low salinity and acidity to neutral pH. In their ecosystem,
Thermoproteales are important component of food webs.
They can function as primary producers and/or as consumers
of organic material. For additional information on
Thermoproteales, see Dworkin and collaborators (2006).
The Euryarchaeota
Based on phylogenies of 16S rRNA, the Euryarchaeota have
been divided initially into nine orders: Methanobacteriales,
Methanococcales, Methanopyrales, Methanomicrobiales,
Methanosarcinales, Halobacteriales, Thermoplasmatales,
Thermococcales, and Archaeoglobales. Recently additional
orders have been proposed: Methanocellales, Methanoplasmatales, etc. Euryarchaeota are much more diverse
than Crenarchaeota. They present very different physiologies, live all types of environments: from temperate
environments to the coldest or the hottest, from most alkaline
to most acidic, and to most hypersaline ones. Large-scale
phylogenetic analyses indicate that Thermococcales represent
the earliest diverging lineage within Euryarchaeota;
methanogens class I (Methanobacteriales, Methanococcales,
Methanopyrales) and the large cluster containing Thermoplasmatales, “Methanoplasmatales,” DHEV2, and group II,
occupy an intermediate position, whereas Archaeoglobales
and the large group gathering Halobacteriales and
methanogens class II (i.e., Methanosarcinales, Methanomicrobiales, and Methanocellales) branch apically in the
Euryarchaeota tree (Fig. 6.9).
The Methanogens (Fig. 6.10a–d)
Methanogens represent a large and highly diversified group
of unrelated strictly anaerobic archaea, which produce large
amount of methane (CH 4 ) as the major end product of their
energy metabolism. Methanogens are key components of
most anaerobic ecosystems due to their capacity to achieve
the final step in the decomposition of organic matter. However, many methanogens are also autotrophs, being able to
use CO 2 as sole source of carbon. Different types of
reactions can lead to CH 4 production. The former ones
are based on CO 2 reduction to CH 4 . In this case, CO 2 is
reduced by electrons provided by H 2 (hydrogenotrophic
methanogens), formate, CO, or certain alcohols (e.g.,
2-propanol, ethanol, etc.). Nearly all methanogens can use
H 2 as electron donor, but many are also able to utilize
formate, whereas very few use alcohols. The second type
of reaction is based on methyl compounds. Indeed, some
methanogens are able to use methyl-containing C-1
compounds (e.g., methanol, methylamine, dimethylamine,
trimethylamine, dimethylsulfide, formate, etc.) as substrate
6 Taxonomy and Phylogeny of Prokaryotes
167