final step of methanogenesis), which prevents the biosynthesis
of methane by this organism. Instead these genes are used in
the reverse direction during the oxidation of lactate. For additional information on Archaeoglobales, see Dworkin and
collaborators (2006).
The Nanoarchaeota
This lineage was first described as a new phylum tentatively
named “Nanoarchaeota” by Harald Huber and colleagues in
2002. The only representative of this group is
“Nanoarchaeum equitans,” a nanometric hyperthermophilic
archaeon that grows attached to the surface of the surface of
Ignicoccus hospitalis (Desulfurococcales). The nature of the
association (i.e., symbiotic or parasitic) between these two
archaea remains debated, even if most recent analyses favor
the latter hypothesis. Environmental surveys suggest that
members of the “Nanoarchaeota” are broadly distributed in
hot biotopes, such as the deep-sea hydrothermal vents, shallow marine areas, and terrestrial solfataric fields.
Nanoarchaeota are anaerobic cocci of only 400 nm in diameter. “Nanoarchaeum equitans” cells are not flagellated.
They grow under strictly anaerobic conditions at
temperatures ranging from 75 to 98
C. Early phylogenetic
analyses suggested that “Nanoarchaeota” branch deeply in
archaeal tree, meaning before to the speciation of
Crenarchaeota and Euryarchaeota. However, later analyses
suggested that this position results from a tree reconstruction
artifact called long branch attraction and that
“Nanoarchaeota” represent in fact a fast-evolving lineage
of Euryarchaeota, likely related to Thermococcales
(Brochier et al. 2005) (Fig. 6.9). The relationship between
“Nanoarchaeota” and Euryarchaeota has been strengthened
by comparative genomic analyses. The 16S rRNA of
“Nanoarchaeota” are highly divergent even in previously
“universally” conserved regions, meaning that they cannot
be easily amplified by PCR using universal 16S rRNA
primers. The genome of “Nanoarchaeum equitans” is the
smallest genome of archaea known to date (490 kb,
corresponding to ~552 genes). It is G + C poor (31.6 %),
has high gene density (95 %), and presents a number of
unique genomic rearrangements (e.g., split genes such as
tRNA, etc.) that were sometime interpreted as ancestral
archaeal features in agreement with the deeply branching
position of “Nanoarchaeota” observed in initial studies.
Many biosynthetic pathways (e.g., lipids, cofactors, amino
acids, nucleotides, etc.) and metabolic pathways (e.g., glycolysis, pentose phosphate pathway, carbon assimilation,
etc.) are lacking. This suggests that “Nanoarchaeum
equitans” is strictly dependent of its host and why all isolation attempts were unsuccessful so far. The genome
sequence of a second representative of “Nanoarchaeota”
(distantly related to “Nanoarchaeum equitans”) has been
obtained from an enrichment culture obtained from a terrestrial hot spring (Podar et al. 2013). In contrast to
“Nanoarchaeum equitans,” this new strain could be a symbiont of an uncultured Sulfolobales, but this remains to be
formerly demonstrated. The genome of this new
nanoarchaeon is larger than the genome of “Nanoarchaeum
equitans,” which contains less split genes, suggesting that
the former has experienced less severe genome reduction
than the latter. It encodes a complete gluconeogenesis pathway as well as a full set of archaeal flagellum proteins,
suggesting that this new nanoarchaeon is motile. Altogether
these findings indicate that the features of “Nanoarchaeum
equitans” that were interpreted as ancestral are in fact
derived characters linked to their particular lifestyle (Podar
et al. 2013).
The Korarchaeota
Korarchaeota (from the Greek “koros” meaning young) was
proposed by Susan M. Barns and colleagues in 1996 based on
16S rRNA environmental surveys of a hot spring in the
Yellowstone National Park in the USA (Barns et al. 1996).
This phylum is represented by a handful of 16S rRNA gene
sequences from uncultured representatives. For a long time,
these archaea remained elusive. This situation has changed
following the report of the genome sequencing of the
“Candidatus Korarchaeum cryptofilum” from an enrichment
culture (Elkins et al. 2008). This ultrathin filamentous
korarchaeaon is 0.16–0.18 μm wide  26 μm long. The analysis of the genome suggests that “Candidatus Korarchaeum
cryptofilum” ferments peptides to obtain carbon and energy.
It lacks the ability to synthesize de novo many compounds
and cofactors such as purines and CoA. Phylogenetic
analyses based on 16S rRNA genes and on various conserved
proteins support a closer relationship of Korarchaeota
with Crenarchaeota and Thaumarchaeota (including
“Aigarchaeota”) than with Euryarchaeota (Fig. 6.9).
The Thaumarchaeota
Thaumarchaeota (from the Greek “thaumas” meaning
wonder) was proposed in 2008 by Ce ´line Brochier-Armanet
and collaborators (Brochier-Armanet et al. 2008).
Thaumarchaeota (formerly referred as group I or mesophilic
crenarchaeota) have been discovered independently by the
teams of Jed Fuhrman and Ed DeLong in 1992 through 16S
rRNA surveys of environmental marine samples. This phylum constitutes one of the most abundant and diversified
archaeal taxonomic groups (Brochier-Armanet et al. 2012).
It gathers numerous sublineages (e.g., group I.1a, I.1b, I.1c,
1A/pSL12, ThAOA/HWCG III, SAGMCG-I, SCG, FSCG,
etc.). Most Thaumarchaeota are uncultured free-living
archaea occurring in very diverse environments (e.g.,
freshwaters, lakes, soils, sediments, oceans, hot springs,
174
P. Caumette et al.
of methane by this organism. Instead these genes are used in
the reverse direction during the oxidation of lactate. For additional information on Archaeoglobales, see Dworkin and
collaborators (2006).
The Nanoarchaeota
This lineage was first described as a new phylum tentatively
named “Nanoarchaeota” by Harald Huber and colleagues in
2002. The only representative of this group is
“Nanoarchaeum equitans,” a nanometric hyperthermophilic
archaeon that grows attached to the surface of the surface of
Ignicoccus hospitalis (Desulfurococcales). The nature of the
association (i.e., symbiotic or parasitic) between these two
archaea remains debated, even if most recent analyses favor
the latter hypothesis. Environmental surveys suggest that
members of the “Nanoarchaeota” are broadly distributed in
hot biotopes, such as the deep-sea hydrothermal vents, shallow marine areas, and terrestrial solfataric fields.
Nanoarchaeota are anaerobic cocci of only 400 nm in diameter. “Nanoarchaeum equitans” cells are not flagellated.
They grow under strictly anaerobic conditions at
temperatures ranging from 75 to 98
C. Early phylogenetic
analyses suggested that “Nanoarchaeota” branch deeply in
archaeal tree, meaning before to the speciation of
Crenarchaeota and Euryarchaeota. However, later analyses
suggested that this position results from a tree reconstruction
artifact called long branch attraction and that
“Nanoarchaeota” represent in fact a fast-evolving lineage
of Euryarchaeota, likely related to Thermococcales
(Brochier et al. 2005) (Fig. 6.9). The relationship between
“Nanoarchaeota” and Euryarchaeota has been strengthened
by comparative genomic analyses. The 16S rRNA of
“Nanoarchaeota” are highly divergent even in previously
“universally” conserved regions, meaning that they cannot
be easily amplified by PCR using universal 16S rRNA
primers. The genome of “Nanoarchaeum equitans” is the
smallest genome of archaea known to date (490 kb,
corresponding to ~552 genes). It is G + C poor (31.6 %),
has high gene density (95 %), and presents a number of
unique genomic rearrangements (e.g., split genes such as
tRNA, etc.) that were sometime interpreted as ancestral
archaeal features in agreement with the deeply branching
position of “Nanoarchaeota” observed in initial studies.
Many biosynthetic pathways (e.g., lipids, cofactors, amino
acids, nucleotides, etc.) and metabolic pathways (e.g., glycolysis, pentose phosphate pathway, carbon assimilation,
etc.) are lacking. This suggests that “Nanoarchaeum
equitans” is strictly dependent of its host and why all isolation attempts were unsuccessful so far. The genome
sequence of a second representative of “Nanoarchaeota”
(distantly related to “Nanoarchaeum equitans”) has been
obtained from an enrichment culture obtained from a terrestrial hot spring (Podar et al. 2013). In contrast to
“Nanoarchaeum equitans,” this new strain could be a symbiont of an uncultured Sulfolobales, but this remains to be
formerly demonstrated. The genome of this new
nanoarchaeon is larger than the genome of “Nanoarchaeum
equitans,” which contains less split genes, suggesting that
the former has experienced less severe genome reduction
than the latter. It encodes a complete gluconeogenesis pathway as well as a full set of archaeal flagellum proteins,
suggesting that this new nanoarchaeon is motile. Altogether
these findings indicate that the features of “Nanoarchaeum
equitans” that were interpreted as ancestral are in fact
derived characters linked to their particular lifestyle (Podar
et al. 2013).
The Korarchaeota
Korarchaeota (from the Greek “koros” meaning young) was
proposed by Susan M. Barns and colleagues in 1996 based on
16S rRNA environmental surveys of a hot spring in the
Yellowstone National Park in the USA (Barns et al. 1996).
This phylum is represented by a handful of 16S rRNA gene
sequences from uncultured representatives. For a long time,
these archaea remained elusive. This situation has changed
following the report of the genome sequencing of the
“Candidatus Korarchaeum cryptofilum” from an enrichment
culture (Elkins et al. 2008). This ultrathin filamentous
korarchaeaon is 0.16–0.18 μm wide  26 μm long. The analysis of the genome suggests that “Candidatus Korarchaeum
cryptofilum” ferments peptides to obtain carbon and energy.
It lacks the ability to synthesize de novo many compounds
and cofactors such as purines and CoA. Phylogenetic
analyses based on 16S rRNA genes and on various conserved
proteins support a closer relationship of Korarchaeota
with Crenarchaeota and Thaumarchaeota (including
“Aigarchaeota”) than with Euryarchaeota (Fig. 6.9).
The Thaumarchaeota
Thaumarchaeota (from the Greek “thaumas” meaning
wonder) was proposed in 2008 by Ce ´line Brochier-Armanet
and collaborators (Brochier-Armanet et al. 2008).
Thaumarchaeota (formerly referred as group I or mesophilic
crenarchaeota) have been discovered independently by the
teams of Jed Fuhrman and Ed DeLong in 1992 through 16S
rRNA surveys of environmental marine samples. This phylum constitutes one of the most abundant and diversified
archaeal taxonomic groups (Brochier-Armanet et al. 2012).
It gathers numerous sublineages (e.g., group I.1a, I.1b, I.1c,
1A/pSL12, ThAOA/HWCG III, SAGMCG-I, SCG, FSCG,
etc.). Most Thaumarchaeota are uncultured free-living
archaea occurring in very diverse environments (e.g.,
freshwaters, lakes, soils, sediments, oceans, hot springs,
174
P. Caumette et al.