etc.), but some of them live in association with animals (e.g.,
Cenarchaeum symbiosum, a sponge symbiont): Worth noticing, Takuro Nunoura and colleagues have recently assembled a composite genome (“Candidatus Caldiarchaeum
subterraneum”) from a metagenomic library prepared from
a geothermal water stream collected in a subsurface gold
mine, which was proposed to represent an additional phylum
tentatively called “Aigarchaeota” (corresponding to the formerly uncultured HWCG I group). However, subsequent
phylogenetic and comparative genomics analyses suggest
that “Aigarchaeota” rather represent an early branching lineage within Thaumarchaeota (Brochier-Armanet et al. 2011).
Thaumarchaeota are the subject of much attention since
environmental metagenomic surveys have shown that some
members of this phylum carry ammonia monooxygenase
genes, suggesting that they are nitrifiers (Treusch et al.
2005). This was confirmed after the isolation of
Nitrosopumilus maritimus, a marine thaumarchaeon that
grows chemolithoautotrophically by aerobically oxidizing
ammonia to nitrite (Ko ¨nneke et al. 2005). This key and
limiting step of the nitrogen cycle was previously thought
to be restricted to a few sublineages of autotrophic
betaproteobacteria and gammaproteobacteria and a few heterotrophic nitrifiers. The discovery of nitrifying archaea
extends the taxonomic range of microorganisms capable of
nitrification and therefore opens up new perspectives on the
origin and evolution of this key metabolism on Earth. Moreover, the widespread distribution of putative archaeal
nitrifiers and their numerical dominance over their bacterial
counterparts in most marine and terrestrial environments
suggested that ammonia oxidizer thaumarchaeota play a
major role in global nitrification (Pester et al. 2011). However, recent studies suggest that thaumarchaeotal nitrifiers
dominate over bacteria only in environments containing
low ammonium concentrations. Three orders of Thaumarchaeota have been proposed to date: Cenarchaeales,
Nitrosopumilales, and Nitrososphaerales. The first two
correspond to the former group I.1a, whereas the latter
was previously referred as group I.1b. Cenarchaeales and
Nitrososphaerales contain a single family and a single genus
(Cenarchaeaceae/Cenarchaeum and Nitrososphaeraceae/
Nitrososphaera, respectively), whereas Nitrosopumilales
contains a single family (Nitrosopumilaceae) and two genera
(Candidatus Nitrosoarchaeum and Nitrosopumilus). However, these lineages represent a small part of the real
diversity of Thaumarchaeota, meaning that additional
thaumarchaeota taxonomic groups should be proposed in
the near future. Currently, it is not clear whether ammoniaoxidizing thaumarchaeota are strict autotrophs or also able to
use other substrates (such as amino acids, oligopeptides, and
glycerol) for their growth, indicating they could also be
mixotrophs or even heterotrophs. Phylogenetic analyses of
various conserved proteins support a closer relationship
of Thaumarchaeota (including “Aigarchaeota”) with
Crenarchaeota and Korarchaeota than with Euryarchaeota
(Fig. 6.9).
6.6.2 Domain Bacteria
In the second edition of “Bergey’s Manual of Systematic
Bacteriology,” the domain is described with 30 bacterial
phyla. Relationships between these phyla are not yet
resolved and represent a major challenge in microbial
evolution.
The 30 bacterial phyla are presented in Table 6.2. They
bring together some 7,500 species characterized phenotypically from cultures of bacterial strains, and therefore they are
defined from these bacterial isolates fully characterized.
6.6.2.1 Phyla B1 to B9
Phyla B1 to B9 correspond to bacteria generally positioned
in the lower branches of the phylogenetic tree based on 16S
rRNA bacteria gene sequences (Fig. 6.11) or bacteria having
extremophilic characters and sometimes isolated from
extreme environments. However, this position is not found
in most phylogenetic analyses based on protein markers
(Lopez-Garcia and Moreira 2008). Many species belonging
to the phyla B1 to B9 are represented by bacteria capable of
living in environments considered extreme, either hyper-hot
or highly contaminated by metals or radiation. The phyla
Aquificae and Thermotogae, and genus Thermus contain the
most known thermophilic members among domain Bacteria.
The Phylum Aquificae
These
Gram-negative
aerobic
autotrophic
and
hydrogenophilic bacteria can grow up to temperatures
between 80 and 95
C. This phylum includes a single
class (Aquificae) containing a single order, Aquificales, in
which there is a single family Aquificaceae. The main genera
are Aquifex, Calderobacterium, Hydrogenobacter, and
Thermocrinis. Representatives of these genera are hyperthermophilic bacteria isolated from marine and terrestrial
hot springs, and developing either aerobic or
microaerophilic or anaerobic and are chemoorganotrophs
and some chemolithotrophs with hydrogen or thiosulfate as
electron donors. These microorganisms occupy a basal position in the phylogenetic tree of Bacteria based on 16S rRNA.
It was therefore suggested that these were very old lines
having inherited from LUCA (cf. Sect. 4.1.1) the ability to
live at high temperatures. However, this phylogenetic position is controversial, and these microorganisms may actually
6 Taxonomy and Phylogeny of Prokaryotes
175
Cenarchaeum symbiosum, a sponge symbiont): Worth noticing, Takuro Nunoura and colleagues have recently assembled a composite genome (“Candidatus Caldiarchaeum
subterraneum”) from a metagenomic library prepared from
a geothermal water stream collected in a subsurface gold
mine, which was proposed to represent an additional phylum
tentatively called “Aigarchaeota” (corresponding to the formerly uncultured HWCG I group). However, subsequent
phylogenetic and comparative genomics analyses suggest
that “Aigarchaeota” rather represent an early branching lineage within Thaumarchaeota (Brochier-Armanet et al. 2011).
Thaumarchaeota are the subject of much attention since
environmental metagenomic surveys have shown that some
members of this phylum carry ammonia monooxygenase
genes, suggesting that they are nitrifiers (Treusch et al.
2005). This was confirmed after the isolation of
Nitrosopumilus maritimus, a marine thaumarchaeon that
grows chemolithoautotrophically by aerobically oxidizing
ammonia to nitrite (Ko ¨nneke et al. 2005). This key and
limiting step of the nitrogen cycle was previously thought
to be restricted to a few sublineages of autotrophic
betaproteobacteria and gammaproteobacteria and a few heterotrophic nitrifiers. The discovery of nitrifying archaea
extends the taxonomic range of microorganisms capable of
nitrification and therefore opens up new perspectives on the
origin and evolution of this key metabolism on Earth. Moreover, the widespread distribution of putative archaeal
nitrifiers and their numerical dominance over their bacterial
counterparts in most marine and terrestrial environments
suggested that ammonia oxidizer thaumarchaeota play a
major role in global nitrification (Pester et al. 2011). However, recent studies suggest that thaumarchaeotal nitrifiers
dominate over bacteria only in environments containing
low ammonium concentrations. Three orders of Thaumarchaeota have been proposed to date: Cenarchaeales,
Nitrosopumilales, and Nitrososphaerales. The first two
correspond to the former group I.1a, whereas the latter
was previously referred as group I.1b. Cenarchaeales and
Nitrososphaerales contain a single family and a single genus
(Cenarchaeaceae/Cenarchaeum and Nitrososphaeraceae/
Nitrososphaera, respectively), whereas Nitrosopumilales
contains a single family (Nitrosopumilaceae) and two genera
(Candidatus Nitrosoarchaeum and Nitrosopumilus). However, these lineages represent a small part of the real
diversity of Thaumarchaeota, meaning that additional
thaumarchaeota taxonomic groups should be proposed in
the near future. Currently, it is not clear whether ammoniaoxidizing thaumarchaeota are strict autotrophs or also able to
use other substrates (such as amino acids, oligopeptides, and
glycerol) for their growth, indicating they could also be
mixotrophs or even heterotrophs. Phylogenetic analyses of
various conserved proteins support a closer relationship
of Thaumarchaeota (including “Aigarchaeota”) with
Crenarchaeota and Korarchaeota than with Euryarchaeota
(Fig. 6.9).
6.6.2 Domain Bacteria
In the second edition of “Bergey’s Manual of Systematic
Bacteriology,” the domain is described with 30 bacterial
phyla. Relationships between these phyla are not yet
resolved and represent a major challenge in microbial
evolution.
The 30 bacterial phyla are presented in Table 6.2. They
bring together some 7,500 species characterized phenotypically from cultures of bacterial strains, and therefore they are
defined from these bacterial isolates fully characterized.
6.6.2.1 Phyla B1 to B9
Phyla B1 to B9 correspond to bacteria generally positioned
in the lower branches of the phylogenetic tree based on 16S
rRNA bacteria gene sequences (Fig. 6.11) or bacteria having
extremophilic characters and sometimes isolated from
extreme environments. However, this position is not found
in most phylogenetic analyses based on protein markers
(Lopez-Garcia and Moreira 2008). Many species belonging
to the phyla B1 to B9 are represented by bacteria capable of
living in environments considered extreme, either hyper-hot
or highly contaminated by metals or radiation. The phyla
Aquificae and Thermotogae, and genus Thermus contain the
most known thermophilic members among domain Bacteria.
The Phylum Aquificae
These
Gram-negative
aerobic
autotrophic
and
hydrogenophilic bacteria can grow up to temperatures
between 80 and 95
C. This phylum includes a single
class (Aquificae) containing a single order, Aquificales, in
which there is a single family Aquificaceae. The main genera
are Aquifex, Calderobacterium, Hydrogenobacter, and
Thermocrinis. Representatives of these genera are hyperthermophilic bacteria isolated from marine and terrestrial
hot springs, and developing either aerobic or
microaerophilic or anaerobic and are chemoorganotrophs
and some chemolithotrophs with hydrogen or thiosulfate as
electron donors. These microorganisms occupy a basal position in the phylogenetic tree of Bacteria based on 16S rRNA.
It was therefore suggested that these were very old lines
having inherited from LUCA (cf. Sect. 4.1.1) the ability to
live at high temperatures. However, this phylogenetic position is controversial, and these microorganisms may actually
6 Taxonomy and Phylogeny of Prokaryotes
175