utilize polymeric substrates and their capacity to produce a
vast array of stable, polymer-degrading hydrolases. For additional information on Thermococcales, see Dworkin and
collaborators (2006).
The Thermoplasmatales
This order was proposed by Reysenbach in 2001. It gathers
aerobic and facultative anaerobic acidophiles which can be
autotrophic or heterotrophic. The most acidophilic
organisms known to date belong to this order. Most
representatives of this order maintain their intracellular pH
near neutrality, thanks to sophisticated mechanisms such as
very effective H
+ pumps that expel H
+ outside of the cell and
membranes that are highly impermeable to H
+
. Some
Thermoplasmatales are flagellated. The name is a reminder
that the first described representatives of this order were
thermophilic acidophiles, although currently mesophilic
representatives are known. Thermoplasmatales are divided
into three families: Ferroplasmaceae, Picrophilaceae, and
Thermoplasmataceae, each containing a single genus,
namely, Ferroplasma, Picrophilus, and Thermoplasma.
Thermoplasma cells are of 0.2–5 μm in size. As they are
devoid of cell wall or envelope (see above), the cells are
pleomorphic, a feature shared with bacterial Mycoplasma.
Because of this lack of cell wall and because the colonies of
Thermoplasma resemble those of bacterial Mycoplasma,
both were initially classified in the same taxonomic group.
Molecular phylogeny studies have proven later that these
features resulted from independent evolutionary processes
(i.e., convergence) and that Mycoplasma and Thermoplasma
are in fact unrelated. Thermoplasma are facultative aerobes
growing at temperatures ranging from 33 to 67
C (optimal
near 60
C) at pH 1–2. They are not able to survive at neutral
pH. They are chemoorganotrophs. They can grow anaerobically through S
0 respiration which leads to the release of
large amounts of H 2 S. They are also able to grow anaerobically without S
0 , suggesting that additional unidentified
molecules can be used as electron acceptors. Thermoplasma
can also grow aerobically. Hot springs, solfataric fields,
warm acidic tropical swamps, marine hydrothermal systems,
as well as aerobic and anaerobic zones of continental volcanic areas constitute natural habitats of Thermoplasma. They
are also found in anthropized environments as coal refuse
piles and associated water samples. Ferroplasma (as
Thermoplasma) are pleomorphic. They are mesophilic
chemolithoautotrophs. They are able to use CO 2 as a carbon
source and Fe
2+
, pyrite, or Mn
2+ as energy source. Some of
them are also able to grow heterotrophically. They occur in
many sulfidic ore-containing mines and heaps on earth, as well
as in acidic geothermal pool. Picrophilus are hyperacidophilic
obligate aerobic heterotrophic irregular cocci of 1–1.5 μm.
They grow optimally at temperatures near 60
C and pH 0.7,
but can still divide at pH 0. No growth occurs below 47
C and
above 65
C, or at pH higher than 3.5. Unlike other
Thermoplasmatales, intracellar pH of Picrophilus is low
(approximately 4.6), suggesting specific adaptations allowing
enzymatic activity in acidic medium. However, the nature of
these modifications remains to be determined. They thrive in
geothermal solfataric soils and springs, and terrestrial geothermal environments. Thermoplasmatales group with DHEV2,
the recently proposed “Methanoplasmatales,” and the uncultured group II (Fig. 6.9). For additional information on
Thermoplasmatales, see Dworkin and collaborators (2006).
The Archaeoglobales
This order was proposed by Karl Stetter in 1989. It gathers
regular to irregular lobe-shaped cocci of 0.3–1.3 μm in diameter occurring singly or in pairs that may be flagellated.
Archaeoglobales grow anaerobically at temperatures ranging
from 65 to 95
C, at neutral or weakly acidic pH. This order
contains a single family Archaeoglobaceae, which is divided
into three genera Archaeoglobus, Ferroglobus, and
Geoglobus. Most of them live in anoxic shallow and abyssal
submarine hydrothermal vents, hot oil field waters but some
have been identified in terrestrial environments including hot
springs and terrestrial oil wells where SO 4
2À are abundant.
Archaeoglobus are chemoorganotrophic sulfate reducers that
oxidize H 2 or organic compounds (e.g., lactate, glucose, pyruvate, acetate, or formate) and reduce SO 4
2À , SO 3
2À
, or S 2 O 3
2À
(but not S
0
) leading to H 2 S formation. Some of them are also
chemolithoautotrophic, being also able to use CO 2 as carbon
source. In contrast, Ferroglobus are chemolithotrophic which
grow anaerobically by using aromatic compounds such as
benzoate as electron donors and Fe
3+ as electron acceptor.
They are also able to use H 2 and H 2 S as energy sources and
NO 3
À as a terminal electron acceptor leading to the formation
of NO 2
À . S 2 O 3
2À can also be used as a terminal electron
acceptor. Geoglobus are anaerobic chemoorganotrophs that
grow by oxidizing acetate, pyruvate, palmitate, and stearate
coupled to reduction of Fe
3+
. They can also grow autotrophically with H 2 as electron donor and poorly crystalline Fe
3+
oxide as electron acceptor. From an evolutionary point of
view, Archaeoglobales branch after the methanogens class I
(Methanopyrales, Methanococcales, Methanobacteriales)
and Thermoplasmatales, but before the diversification of the
large group containing Halobacteriales, Methanomicrobiales,
Methanosarcinales, and Methanocellales (Fig. 6.9). Evolutionary and genomic studies have shown that Archaeoglobales
are descendants of methanogens that have secondarily lost the
capacity to produce methane. This hypothesis was strongly
reinforced by the discovery in the genome of Archaeoglobus
fulgidus of almost all genes encoding enzymes and cofactors
involved in methanogenesis. The only missing genes are those
encoding methyl CoM reductase (the enzyme involved in the
6 Taxonomy and Phylogeny of Prokaryotes
173
vast array of stable, polymer-degrading hydrolases. For additional information on Thermococcales, see Dworkin and
collaborators (2006).
The Thermoplasmatales
This order was proposed by Reysenbach in 2001. It gathers
aerobic and facultative anaerobic acidophiles which can be
autotrophic or heterotrophic. The most acidophilic
organisms known to date belong to this order. Most
representatives of this order maintain their intracellular pH
near neutrality, thanks to sophisticated mechanisms such as
very effective H
+ pumps that expel H
+ outside of the cell and
membranes that are highly impermeable to H
+
. Some
Thermoplasmatales are flagellated. The name is a reminder
that the first described representatives of this order were
thermophilic acidophiles, although currently mesophilic
representatives are known. Thermoplasmatales are divided
into three families: Ferroplasmaceae, Picrophilaceae, and
Thermoplasmataceae, each containing a single genus,
namely, Ferroplasma, Picrophilus, and Thermoplasma.
Thermoplasma cells are of 0.2–5 μm in size. As they are
devoid of cell wall or envelope (see above), the cells are
pleomorphic, a feature shared with bacterial Mycoplasma.
Because of this lack of cell wall and because the colonies of
Thermoplasma resemble those of bacterial Mycoplasma,
both were initially classified in the same taxonomic group.
Molecular phylogeny studies have proven later that these
features resulted from independent evolutionary processes
(i.e., convergence) and that Mycoplasma and Thermoplasma
are in fact unrelated. Thermoplasma are facultative aerobes
growing at temperatures ranging from 33 to 67
C (optimal
near 60
C) at pH 1–2. They are not able to survive at neutral
pH. They are chemoorganotrophs. They can grow anaerobically through S
0 respiration which leads to the release of
large amounts of H 2 S. They are also able to grow anaerobically without S
0 , suggesting that additional unidentified
molecules can be used as electron acceptors. Thermoplasma
can also grow aerobically. Hot springs, solfataric fields,
warm acidic tropical swamps, marine hydrothermal systems,
as well as aerobic and anaerobic zones of continental volcanic areas constitute natural habitats of Thermoplasma. They
are also found in anthropized environments as coal refuse
piles and associated water samples. Ferroplasma (as
Thermoplasma) are pleomorphic. They are mesophilic
chemolithoautotrophs. They are able to use CO 2 as a carbon
source and Fe
2+
, pyrite, or Mn
2+ as energy source. Some of
them are also able to grow heterotrophically. They occur in
many sulfidic ore-containing mines and heaps on earth, as well
as in acidic geothermal pool. Picrophilus are hyperacidophilic
obligate aerobic heterotrophic irregular cocci of 1–1.5 μm.
They grow optimally at temperatures near 60
C and pH 0.7,
but can still divide at pH 0. No growth occurs below 47
C and
above 65
C, or at pH higher than 3.5. Unlike other
Thermoplasmatales, intracellar pH of Picrophilus is low
(approximately 4.6), suggesting specific adaptations allowing
enzymatic activity in acidic medium. However, the nature of
these modifications remains to be determined. They thrive in
geothermal solfataric soils and springs, and terrestrial geothermal environments. Thermoplasmatales group with DHEV2,
the recently proposed “Methanoplasmatales,” and the uncultured group II (Fig. 6.9). For additional information on
Thermoplasmatales, see Dworkin and collaborators (2006).
The Archaeoglobales
This order was proposed by Karl Stetter in 1989. It gathers
regular to irregular lobe-shaped cocci of 0.3–1.3 μm in diameter occurring singly or in pairs that may be flagellated.
Archaeoglobales grow anaerobically at temperatures ranging
from 65 to 95
C, at neutral or weakly acidic pH. This order
contains a single family Archaeoglobaceae, which is divided
into three genera Archaeoglobus, Ferroglobus, and
Geoglobus. Most of them live in anoxic shallow and abyssal
submarine hydrothermal vents, hot oil field waters but some
have been identified in terrestrial environments including hot
springs and terrestrial oil wells where SO 4
2À are abundant.
Archaeoglobus are chemoorganotrophic sulfate reducers that
oxidize H 2 or organic compounds (e.g., lactate, glucose, pyruvate, acetate, or formate) and reduce SO 4
2À , SO 3
2À
, or S 2 O 3
2À
(but not S
0
) leading to H 2 S formation. Some of them are also
chemolithoautotrophic, being also able to use CO 2 as carbon
source. In contrast, Ferroglobus are chemolithotrophic which
grow anaerobically by using aromatic compounds such as
benzoate as electron donors and Fe
3+ as electron acceptor.
They are also able to use H 2 and H 2 S as energy sources and
NO 3
À as a terminal electron acceptor leading to the formation
of NO 2
À . S 2 O 3
2À can also be used as a terminal electron
acceptor. Geoglobus are anaerobic chemoorganotrophs that
grow by oxidizing acetate, pyruvate, palmitate, and stearate
coupled to reduction of Fe
3+
. They can also grow autotrophically with H 2 as electron donor and poorly crystalline Fe
3+
oxide as electron acceptor. From an evolutionary point of
view, Archaeoglobales branch after the methanogens class I
(Methanopyrales, Methanococcales, Methanobacteriales)
and Thermoplasmatales, but before the diversification of the
large group containing Halobacteriales, Methanomicrobiales,
Methanosarcinales, and Methanocellales (Fig. 6.9). Evolutionary and genomic studies have shown that Archaeoglobales
are descendants of methanogens that have secondarily lost the
capacity to produce methane. This hypothesis was strongly
reinforced by the discovery in the genome of Archaeoglobus
fulgidus of almost all genes encoding enzymes and cofactors
involved in methanogenesis. The only missing genes are those
encoding methyl CoM reductase (the enzyme involved in the
6 Taxonomy and Phylogeny of Prokaryotes
173