Methanothermococcus. All Methanococcales produce CH 4 by
using H 2 to reduce CO 2 , but Methanococcaceae are also able
to use formate are electron donors. Cells occur as irregular
flagellated cocci ranging from 0.9 to 3 μm in diameter occurring singly or in pairs. This order gathers mesophiles (e.g.,
Methanococcus vannielii), thermophiles (e.g., Methanothermococcus thermolithotrophicus), and hyperthermophiles (e.
g., Methanotorris igneus, Methanocaldococcus infernus) at
weakly acidic (e.g., Methanotorris igneus), neutral (e.g.,
Methanothermococcus okinawensis), or weakly alkaliphilic
pH. Most members of this order are fast growing and require
salt for growth. From an evolutionary point of view,
Methanococcales belong to class I methanogens and are
closely related to Methanopyrales and Methanobacteriales
(Fig. 6.9). For additional information on Methanococcales,
see Dworkin and collaborators (2006).
The Halobacteriales
This order was proposed by William D. Grant and Helge
Larsen in 1989. Halobacteriales live in environments
containing high salt levels exceeding 150–200 g/l. Most
Halobacteriales cannot grow at salt concentrations below
2.5–3 M and are irreversibly damaged (or even lyse) when
suspended in solutions containing less than 1–2 M salt.
It comprises a single family the Halobacteriaceae, which
gather 42 genera: Haladaptatus, Halalkalicoccus,
Halarchaeum, Haloarchaeobius, Haloarcula, Halobacterium,
Halobaculum, Halobellus, Halobiforma, Halococcus,
Haloferax, Halogeometricum, Halogranum, Halomarina,
Halomicrobium, Halonotius, Halopelagius, Halopenitus,
Halopiger, Haloplanus, Haloquadratum, Halorhabdus,
Halorientalis, Halorubellus, Halorubrum, Halorussus,
Halosarcina, Halosimplex, Halostagnicola, Haloterrigena,
Halovivax, Natrialba, Natrinema, Natronoarchaeum,
Natronobacterium, Natronococcus, Natronolimnobius, Natronomonas, Natronorubrum, Salarchaeum, and Salinarchaeum.
Most representatives of this order live in hypersaline marine
biotopes or freshwaters, such as salt lakes (e.g., the Great Salt
Lake, the Dead Sea, etc.) or saltern crystallizer ponds. These
environments can be thalassohaline, meaning that they are
dominated by Na
+ and Cl
À ions. In contrast, athalassohaline
environments present greatly different ionic compositions.
Among them, the Dead Sea is dominated by Mg
2+ and Ca
2+
,
in addition to Na
+ and K
+
. Halobacteriales are also present in
saline soils, mines, and arid areas (e.g., coasts, plains,
mountains, deserts, etc.). Some Halobacteriales develop on
products preserved by salt (e.g., food, hides, etc.) but
contaminated through the use of crude solar salt. Indeed,
during crystallization of halite, Halobacteriales cells can be
trapped inside the growing crystals, and these may remain
viable for a long time. The economic damages caused by
these halophilic Archaea have triggered many of the early
researches on Halobacteriales. In many hypersaline
environments, Halobacteriales coexist with eukaryotes (such
as green algae Dunaliella) and diverse bacteria such as
Salinibacter ruber (Cytophagales). However, in the most
extreme ones, Halobacteriales dominate microbial
communities over bacteria. Some Halobacteriales (e.g.,
Natronobacterium) are haloalkaliphilic, living in alkaline
hypersaline lakes characterized by salinity at (or close) to
saturation and very high pH (9–11) due to high concentrations
of carbonates. Many Halobacteriales are mesophilic to moderate thermophilic, having optimal growth temperatures ranging from 35 to 50
C. This is not surprising given that many
hypersaline environments inhabited by Halobacteriales are
formed by evaporation processes occurring in warm areas.
However, psychrotolerant members of Halobacteriales exist,
such as those living in the very cold (but ice-free) hypersaline
Deep Lake (Antarctica), which water temperature varies seasonally between below 0 and +11.5
C. Some Halobacteriales
cells are flagellated. Halobacteriales present many different
morphotypes: rods, cocci, flat pleomorphic types, perfectly
square flat cells, or even triangular and trapezoid cells.
Halobacteriales are also known to carry the largest plasmids
known to date, some of them being referred as to
minichromosomes due to the presence of important or essential genes. For instance, 547 of the 2,674 (20 %) of the genes of
Halobacterium sp. NRC1 are located on two megaplasmids,
whereas 27 % of the Haloferax volcanii genes are carried on
two megaplasmids and two small plasmids. In addition, many
Halobacteriales are polyploid, for instance, there are 15–30
genome copies in Haloferax volcanii and Halobacterium
salinarum.
The Halobacteriales are chemoorganotrophic. They oxidize various organic compounds under aerobic conditions
and use O 2 as terminal electron acceptor. However, the
availability of O 2 is often limited due to high microbial
densities and the limited solubility of O 2 at high salt
concentrations. Without surprise many Halobacteriales are
able to use alternative pathways to produce their energy
under microaerophilic or anaerobic conditions, including
denitrification or fermentation of L-arginine. They are also
able to use various compounds as electron acceptors, such as
DMSO, TMAO, and fumarate. In addition, some
Halobacteriales (e.g., Halobacterium) are phototrophic,
meaning that they can use light to produce ATP. This process is carried out by a membrane protein called bacteriorhodopsin (cf. Sect. 3.3.4, Fig. 3.30) under anaerobic
conditions. This protein is a light-driven H
+ pump that
expulses H
+ from the cell, generating a H
+ gradient which in
turn is converted into ATP by ATP synthases. Bacteriorhodopsin may be very abundant in cell membranes. It is responsible for the pink/red coloration of the cells. This phototrophic
process is different from chlorophyll-based photosynthesis
because it requires neither chlorophyll nor electron transport
chains. Furthermore and contrarily to bacteriorhodopsin6 Taxonomy and Phylogeny of Prokaryotes
171
using H 2 to reduce CO 2 , but Methanococcaceae are also able
to use formate are electron donors. Cells occur as irregular
flagellated cocci ranging from 0.9 to 3 μm in diameter occurring singly or in pairs. This order gathers mesophiles (e.g.,
Methanococcus vannielii), thermophiles (e.g., Methanothermococcus thermolithotrophicus), and hyperthermophiles (e.
g., Methanotorris igneus, Methanocaldococcus infernus) at
weakly acidic (e.g., Methanotorris igneus), neutral (e.g.,
Methanothermococcus okinawensis), or weakly alkaliphilic
pH. Most members of this order are fast growing and require
salt for growth. From an evolutionary point of view,
Methanococcales belong to class I methanogens and are
closely related to Methanopyrales and Methanobacteriales
(Fig. 6.9). For additional information on Methanococcales,
see Dworkin and collaborators (2006).
The Halobacteriales
This order was proposed by William D. Grant and Helge
Larsen in 1989. Halobacteriales live in environments
containing high salt levels exceeding 150–200 g/l. Most
Halobacteriales cannot grow at salt concentrations below
2.5–3 M and are irreversibly damaged (or even lyse) when
suspended in solutions containing less than 1–2 M salt.
It comprises a single family the Halobacteriaceae, which
gather 42 genera: Haladaptatus, Halalkalicoccus,
Halarchaeum, Haloarchaeobius, Haloarcula, Halobacterium,
Halobaculum, Halobellus, Halobiforma, Halococcus,
Haloferax, Halogeometricum, Halogranum, Halomarina,
Halomicrobium, Halonotius, Halopelagius, Halopenitus,
Halopiger, Haloplanus, Haloquadratum, Halorhabdus,
Halorientalis, Halorubellus, Halorubrum, Halorussus,
Halosarcina, Halosimplex, Halostagnicola, Haloterrigena,
Halovivax, Natrialba, Natrinema, Natronoarchaeum,
Natronobacterium, Natronococcus, Natronolimnobius, Natronomonas, Natronorubrum, Salarchaeum, and Salinarchaeum.
Most representatives of this order live in hypersaline marine
biotopes or freshwaters, such as salt lakes (e.g., the Great Salt
Lake, the Dead Sea, etc.) or saltern crystallizer ponds. These
environments can be thalassohaline, meaning that they are
dominated by Na
+ and Cl
À ions. In contrast, athalassohaline
environments present greatly different ionic compositions.
Among them, the Dead Sea is dominated by Mg
2+ and Ca
2+
,
in addition to Na
+ and K
+
. Halobacteriales are also present in
saline soils, mines, and arid areas (e.g., coasts, plains,
mountains, deserts, etc.). Some Halobacteriales develop on
products preserved by salt (e.g., food, hides, etc.) but
contaminated through the use of crude solar salt. Indeed,
during crystallization of halite, Halobacteriales cells can be
trapped inside the growing crystals, and these may remain
viable for a long time. The economic damages caused by
these halophilic Archaea have triggered many of the early
researches on Halobacteriales. In many hypersaline
environments, Halobacteriales coexist with eukaryotes (such
as green algae Dunaliella) and diverse bacteria such as
Salinibacter ruber (Cytophagales). However, in the most
extreme ones, Halobacteriales dominate microbial
communities over bacteria. Some Halobacteriales (e.g.,
Natronobacterium) are haloalkaliphilic, living in alkaline
hypersaline lakes characterized by salinity at (or close) to
saturation and very high pH (9–11) due to high concentrations
of carbonates. Many Halobacteriales are mesophilic to moderate thermophilic, having optimal growth temperatures ranging from 35 to 50
C. This is not surprising given that many
hypersaline environments inhabited by Halobacteriales are
formed by evaporation processes occurring in warm areas.
However, psychrotolerant members of Halobacteriales exist,
such as those living in the very cold (but ice-free) hypersaline
Deep Lake (Antarctica), which water temperature varies seasonally between below 0 and +11.5
C. Some Halobacteriales
cells are flagellated. Halobacteriales present many different
morphotypes: rods, cocci, flat pleomorphic types, perfectly
square flat cells, or even triangular and trapezoid cells.
Halobacteriales are also known to carry the largest plasmids
known to date, some of them being referred as to
minichromosomes due to the presence of important or essential genes. For instance, 547 of the 2,674 (20 %) of the genes of
Halobacterium sp. NRC1 are located on two megaplasmids,
whereas 27 % of the Haloferax volcanii genes are carried on
two megaplasmids and two small plasmids. In addition, many
Halobacteriales are polyploid, for instance, there are 15–30
genome copies in Haloferax volcanii and Halobacterium
salinarum.
The Halobacteriales are chemoorganotrophic. They oxidize various organic compounds under aerobic conditions
and use O 2 as terminal electron acceptor. However, the
availability of O 2 is often limited due to high microbial
densities and the limited solubility of O 2 at high salt
concentrations. Without surprise many Halobacteriales are
able to use alternative pathways to produce their energy
under microaerophilic or anaerobic conditions, including
denitrification or fermentation of L-arginine. They are also
able to use various compounds as electron acceptors, such as
DMSO, TMAO, and fumarate. In addition, some
Halobacteriales (e.g., Halobacterium) are phototrophic,
meaning that they can use light to produce ATP. This process is carried out by a membrane protein called bacteriorhodopsin (cf. Sect. 3.3.4, Fig. 3.30) under anaerobic
conditions. This protein is a light-driven H
+ pump that
expulses H
+ from the cell, generating a H
+ gradient which in
turn is converted into ATP by ATP synthases. Bacteriorhodopsin may be very abundant in cell membranes. It is responsible for the pink/red coloration of the cells. This phototrophic
process is different from chlorophyll-based photosynthesis
because it requires neither chlorophyll nor electron transport
chains. Furthermore and contrarily to bacteriorhodopsin6 Taxonomy and Phylogeny of Prokaryotes
171