Well-developed genetic tools are now available for
Methanococcus and Methanosarcina (Leigh et al. 2011). It
has been suggested that methanogenesis was ancestral in
Archaea, meaning that the last common ancestor to all
present-day archaea was a methanogen. However, recent
analyzes suggest rather that this metabolism appeared secondarily during the diversification of Euryarchaeota,
namely, in the last common ancestor of all present-day
methanogens (Bapteste et al. 2005). This implies that
methanogenesis would have been secondarily lost in their
non-methanogen relatives (e.g., Archaeoglobales, Halobacteriales, “Nanohaloarchaea,” Thermoplasmatales and
relatives, Fig. 6.9). Supporting this hypothesis, all the
genes involved in methanogenesis are present in Archaeaoglobales, excepted those involved in the last step of this
pathway, preventing the biosynthesis of CH 4 in these
archaea (see below). A seventh order tentatively called
“Methanoplasmatales,” which likely correspond to the RCIII (Rice cluster III), has been recently proposed (Paul et al.
2012). These archaea have been detected in various habitats
including marine environments, and soils, but also in the
intestinal tracts of termites and mammals. This lineage is
closely related to Thermoplasmatales, marine group II, and
DHVE groups.
The order Methanomicrobiales has been proposed by
William E. Balch and Ralph S. Wolfe in 1981. Members of
this order are strictly anaerobic. They present very diverse
morphologies: short rods, curved rods, plates, irregular
cocci, filaments, etc., ranging from 0.4 to 2.6 μm in diameter
and from 0.1 to 1 in width  1.5–10 μm in length. Some of
them are flagellated. All Methanomicrobiales are able to use
H 2 and CO 2 as a substrate for methanogenesis, many of them
can utilize formate, and some can also use alcohols. In
contrast to their close relatives Methanosarcinales, they
can use neither acetate nor methylated C-1 compounds
(such as methanol, methylamines, or methyl sulfides) for
methanogenesis, even if acetate can be used as a carbon
source by some species. In contrast to Methanobacteriales
and Methanopyrales, Methanomicrobiales cell wall does not
contain pseudomurein. Some of them (Methanospirillum
hungatei) are surrounded by proteinaceous sheaths
(Table 6.3). Most Methanobacteriales are mesophilic, but
psychrophilic (e.g., Methanogenium frigidum) and thermophilic (e.g., Methanoculleus thermophilus) are known. They
have been reported in various anaerobic habitats (e.g., marine
and freshwater sediments, swamps, anaerobic digesters,
rumens of various animals, oil fields, underground waters,
etc.). Methanomicrobiales are generally free-living, but
some species (e.g., Methanoplanus endosymbiosus) are
endosymbionts of anaerobic H 2 producer protists, such as
ciliates living in freshwater sediments (e.g., Metopus
contortus). Methanomicrobiales has been divided into four
families. Methanocorpusculaceae and Methanospirillaceae
each contain a single genus Methanocorpusculum and
Methanospirillum. Both genera use H 2 with CO 2 and formate
for methanogenesis, whereas some representatives can also
use 2-propanol (or 2-butanol) with CO 2 . Methanoregulaceae
group three genera (Methanolinea, Methanoregula, and
Methanosphaerula), whereas Methanomicrobiaceae gather
six genera (Methanoculleus, Methanofollis, Methanogenium,
Methanolacinia, Methanomicrobium, and Methanoplanus).
Members of both families use H 2 with CO 2 , but some are
also able to use formate for CH 4 production. In addition
Methanomicrobiaceae can produce CH 4 from 2-propanol
and CO 2 , from 2-butanol and CO 2 , or from cyclopentanol
and CO 2 . From an evolutionary point of view, Methanomicrobiales belong to class II methanogens and are closely
related to Methanocellales and Methanosarcinales and to
Halobacteriales (Fig. 6.9). For additional information on
Methanomicrobiales, see Dworkin and collaborators (2006).
The order Methanosarcinales has been proposed by David
R. Boone and collaborators in 2002. Members of this order are
strictly anaerobic. They present very diverse morphologies:
coccoid, flat, polygonal, irregular cocci, spheroids, rods,
pseudosarcinae, or sheathed rods, etc., ranging in size from
0.5 to 100 μm in diameter and from 0.8 wide  7 μm long.
They can form filaments and aggregates (that can be massive).
Some of them are flagellated. Like Methanomicrobiales,
Methanosarcinales cell wall does not contain pseudomurein,
and some are surrounded by a proteinaceous sheath
(Methanosaeta
concilii)
or
methanochondroitin
(Methanosarcina mazei and Methanosarcina acetivorans,
Table 6.3). Most of them are mesophiles, even if some species
are thermophilic (e.g., Methanosaeta thermophila). They live
at pH neutral to weakly alkaline. Some Methanosarcinales are
also halotolerant and halophilic (e.g., Methanohalobium
evestigatum). They are able to use numerous substrates for
methanogenesis. Contrarily to Methanomicrobiales, Methanosarcinales can grow by splitting acetate to CH 4 and CO 2 .
They can also dismutate methyl compounds (methanol,
methyl amines, methyl sulfides, etc.) producing CO 2 and
CH 4 , or use H 2 to reduce methyl compounds. They are important components of ecosystems due to their capacity to achieve
the terminal steps of the degradation of organic matter in
anoxic environments where light and terminal electron
acceptors other than CO 2 are limiting. Representatives of the
Methanosarcinales are widespread and are found in very
diverse anaerobic environments (e.g., freshwater, ocean,
muds, sediments (even in extremely halophilic ones), gas
industry pipelines, underground waters, sludge from anaerobic
sewages, rumen and gastrointestinal tracts of metazoa, deep
terrestrial subsurface, etc.). This order comprises three
families: Methanosaetaceae, Methanosarcinaceae, and
Methermicoccaceae. Methanosaetaceae are represented by a
single genus (Methanosaeta). They are able to use acetate as
sole energy source leading to production of CH 4 and CO 2 , and
6 Taxonomy and Phylogeny of Prokaryotes
169
Methanococcus and Methanosarcina (Leigh et al. 2011). It
has been suggested that methanogenesis was ancestral in
Archaea, meaning that the last common ancestor to all
present-day archaea was a methanogen. However, recent
analyzes suggest rather that this metabolism appeared secondarily during the diversification of Euryarchaeota,
namely, in the last common ancestor of all present-day
methanogens (Bapteste et al. 2005). This implies that
methanogenesis would have been secondarily lost in their
non-methanogen relatives (e.g., Archaeoglobales, Halobacteriales, “Nanohaloarchaea,” Thermoplasmatales and
relatives, Fig. 6.9). Supporting this hypothesis, all the
genes involved in methanogenesis are present in Archaeaoglobales, excepted those involved in the last step of this
pathway, preventing the biosynthesis of CH 4 in these
archaea (see below). A seventh order tentatively called
“Methanoplasmatales,” which likely correspond to the RCIII (Rice cluster III), has been recently proposed (Paul et al.
2012). These archaea have been detected in various habitats
including marine environments, and soils, but also in the
intestinal tracts of termites and mammals. This lineage is
closely related to Thermoplasmatales, marine group II, and
DHVE groups.
The order Methanomicrobiales has been proposed by
William E. Balch and Ralph S. Wolfe in 1981. Members of
this order are strictly anaerobic. They present very diverse
morphologies: short rods, curved rods, plates, irregular
cocci, filaments, etc., ranging from 0.4 to 2.6 μm in diameter
and from 0.1 to 1 in width  1.5–10 μm in length. Some of
them are flagellated. All Methanomicrobiales are able to use
H 2 and CO 2 as a substrate for methanogenesis, many of them
can utilize formate, and some can also use alcohols. In
contrast to their close relatives Methanosarcinales, they
can use neither acetate nor methylated C-1 compounds
(such as methanol, methylamines, or methyl sulfides) for
methanogenesis, even if acetate can be used as a carbon
source by some species. In contrast to Methanobacteriales
and Methanopyrales, Methanomicrobiales cell wall does not
contain pseudomurein. Some of them (Methanospirillum
hungatei) are surrounded by proteinaceous sheaths
(Table 6.3). Most Methanobacteriales are mesophilic, but
psychrophilic (e.g., Methanogenium frigidum) and thermophilic (e.g., Methanoculleus thermophilus) are known. They
have been reported in various anaerobic habitats (e.g., marine
and freshwater sediments, swamps, anaerobic digesters,
rumens of various animals, oil fields, underground waters,
etc.). Methanomicrobiales are generally free-living, but
some species (e.g., Methanoplanus endosymbiosus) are
endosymbionts of anaerobic H 2 producer protists, such as
ciliates living in freshwater sediments (e.g., Metopus
contortus). Methanomicrobiales has been divided into four
families. Methanocorpusculaceae and Methanospirillaceae
each contain a single genus Methanocorpusculum and
Methanospirillum. Both genera use H 2 with CO 2 and formate
for methanogenesis, whereas some representatives can also
use 2-propanol (or 2-butanol) with CO 2 . Methanoregulaceae
group three genera (Methanolinea, Methanoregula, and
Methanosphaerula), whereas Methanomicrobiaceae gather
six genera (Methanoculleus, Methanofollis, Methanogenium,
Methanolacinia, Methanomicrobium, and Methanoplanus).
Members of both families use H 2 with CO 2 , but some are
also able to use formate for CH 4 production. In addition
Methanomicrobiaceae can produce CH 4 from 2-propanol
and CO 2 , from 2-butanol and CO 2 , or from cyclopentanol
and CO 2 . From an evolutionary point of view, Methanomicrobiales belong to class II methanogens and are closely
related to Methanocellales and Methanosarcinales and to
Halobacteriales (Fig. 6.9). For additional information on
Methanomicrobiales, see Dworkin and collaborators (2006).
The order Methanosarcinales has been proposed by David
R. Boone and collaborators in 2002. Members of this order are
strictly anaerobic. They present very diverse morphologies:
coccoid, flat, polygonal, irregular cocci, spheroids, rods,
pseudosarcinae, or sheathed rods, etc., ranging in size from
0.5 to 100 μm in diameter and from 0.8 wide  7 μm long.
They can form filaments and aggregates (that can be massive).
Some of them are flagellated. Like Methanomicrobiales,
Methanosarcinales cell wall does not contain pseudomurein,
and some are surrounded by a proteinaceous sheath
(Methanosaeta
concilii)
or
methanochondroitin
(Methanosarcina mazei and Methanosarcina acetivorans,
Table 6.3). Most of them are mesophiles, even if some species
are thermophilic (e.g., Methanosaeta thermophila). They live
at pH neutral to weakly alkaline. Some Methanosarcinales are
also halotolerant and halophilic (e.g., Methanohalobium
evestigatum). They are able to use numerous substrates for
methanogenesis. Contrarily to Methanomicrobiales, Methanosarcinales can grow by splitting acetate to CH 4 and CO 2 .
They can also dismutate methyl compounds (methanol,
methyl amines, methyl sulfides, etc.) producing CO 2 and
CH 4 , or use H 2 to reduce methyl compounds. They are important components of ecosystems due to their capacity to achieve
the terminal steps of the degradation of organic matter in
anoxic environments where light and terminal electron
acceptors other than CO 2 are limiting. Representatives of the
Methanosarcinales are widespread and are found in very
diverse anaerobic environments (e.g., freshwater, ocean,
muds, sediments (even in extremely halophilic ones), gas
industry pipelines, underground waters, sludge from anaerobic
sewages, rumen and gastrointestinal tracts of metazoa, deep
terrestrial subsurface, etc.). This order comprises three
families: Methanosaetaceae, Methanosarcinaceae, and
Methermicoccaceae. Methanosaetaceae are represented by a
single genus (Methanosaeta). They are able to use acetate as
sole energy source leading to production of CH 4 and CO 2 , and
6 Taxonomy and Phylogeny of Prokaryotes
169