2. THERMOTOGAE
The phylumThermotogae is comprised of anaerobic, thermophilic, as well as
mesophilic bacteria that are surrounded by an outer sheathlike envelope referred
to as a ‘‘toga.’’
The species from this deep-branching group exhibit Gram-negative staining, but
due to the absence of an archetypal outer cell membrane, they are considered
monoderm (or atypical diderm) bacteria.
This phylum presently contains 10 genera harboring 41 validated species which
are all part of a single family,Thermotogaceae, within the orderThermotogales
3.
4. The first genome sequence of a species from the phylumThermotogae, Thermotoga maritima
MSB8, was published in 1999
. In the 1,860,725 bp chromosome, 7 % of all genes were related to carbohydrate metabolism
pathways
Since then, completed genomes for 15 other species, representing six genera of the phylum, have
been sequenced
The G+C content of the sequenced species varied from 26 % to 50 %.
All of the sequenced species contained a single chromosomal genome around 2 Mb in size with
Tt. naphthophila containing the smallest of these at 1.81 Mb, while Mesotoga prima contains the
largest at 2. 97 Mb.
5.
6. PLAMIDS
Though most species lack extrachromosomal elements, plasmids have been
discovered in someThermotogae species.
A small plasmid, named pRQ7, 846-bp in size inThermotoga sp. RQ7 was the first
to be discovered among this group.
The plasmid was suggested to contain a single protein, possibly involved in
plasmid replication.
The pRQ7 plasmid was also inferred to replicate by rolling cycle replication based
on its sequence similarity to a family of other plasmids replicating through this
mechanism
7. CRISPR SEQUENCES
Prophages in theThermotogae have not been identified; however, the presence of several
CRISPR elements is observed in mostThermotogae species.
CRISPR sequences, or Clustered Regularly Interspaced Short Palindromic Repeats, consist of 24–
47 bp repeats that are interspersed with ‘‘spacer’’ sequences of an equal length.
The spacer regions are homologous in sequence to foreign DNA, often of a virus or a plasmid,
and they have been implicated in defense against foreign genetic material.
The presence of these elements may provide clues to the various viral particles that are likely
present in the environment of these bacteria
8. GENOMIC ISLANDS
TheThermotogae have been proposed to harbor a large contingent of foreign DNA in their
genomes.
With the publication ofTt. maritima genome, it was predicted that as much as 24 % of their genomic
content had best BLAST matches to archaeal species genes.
As many of these genes were found in clusters and had atypical compositions, the clusters were
termed ‘‘archaeal islands.’’
Numerically, 15 such genomic islands were highlighted, ranging in size from 4 to 20 kb and
containing a total of 81 genes.
An example of such a horizontally transferred genomic island is a 13 gene cluster in theTt. maritima
which has been indicated to share closest similarity to an operon in the archaeal species Pyrococcus
furiosus genome.
The cluster, also present inTs. africanus and F. nodosum, is suggested to contain an operon of a
putative membrane associated photon translocating ferredoxin-NAD(P) H oxidoreductase.
9. THERMOTOGAE AND LGT
Sequence similarity analysis performed during the sequencing of T. maritima genome indicated
that a large percentage (24 %) of their genes were possibly derived from archaeal sources.
As many archaeal species of the Archaeoglobus andThermococcus groups are known to exist in
oil reservoirs, a habitat for manyThermotogales
It was deemed possible that species from the Archaea andThermotogae could be sharing genes
in the common environment
With 21 % of the rest of its genome most similar to the Firmicute species Bacillus subtilis and 15
% similar to Aquifex aeolicus
It was suggested that perhaps theThermotoga maritima genome was a collage composed of
genes from multiple sources shaped together through constant lateral transfer of genes
10. THERMOTOGAE PHYSIOLOGY
Members of this family are generally rod-shaped, fermentative, anaerobic,
chemoorganotrophic organisms.
Oxygen tolerance is variable in this phylum withThermotoga, Fervidobacterium, and Geotoga
unable to grow at all in oxygen, while K. olearia can survive at oxygen levels reaching 15 %
Cell length is usually less than 10 μm , but P. miotherma cells of 50 μm have been observed.
The cells grow singly and in pairs, but in rare cases many species form chains with multiple cells
surrounded by the sheath.
Since their identification, species of the phylum have been recognized for their existence at
thermophilic and hyperthermophilic temperatures.
11. THERMOTOGAE PHYSIOLOGY
Recently identified species Ms. prima and K. shengliensis have displayed features previously not
found among the species of the group.
Ms. prima was found to have a mesophilic optimum growth temperature, while K. shengliensis is
the only known species of the group with a coccoid cell morphology rather than rod-shaped
Additionally, though most species of the phylum stain Gram-negative, Defluviitoga tunisiensis
was observed to stain Gram-positive
12. THERMOTOGAE MEMBRANES
Among numerous unusual features, perhaps the most characteristic of theThermotogae
bacteria is a sheath-like structure that surrounds the cell and is commonly referred to as the
‘‘toga’’
This outer toga structure is a membrane comprised of patches of regular, crystalline arrays
The crystalline arrays of the toga contain the oligomeric proteins Ompα and Ompβ porin,
present in relatively equal quantity, embedded within a lipid matrix
Among the features unusual to the membranes of the phylum is the presence of long-chained
C30, C32, and C34 dicarboxylic acids in lipids in species of the genera Kosmotoga,Thermotoga,
Fervidobacterium, andThermosipho thought to be an adaptation of growth in high-temperature
environments
13. METABOLISM
As organotrophs, theThermotogae ferment a variety of carbohydrates as well as complex
organic matter.
Genomic analysis has shown the use of both the Entner-Doudoroff and the Embden-Meyerhof-
Parnas pathways for sugar metabolism
Along with the utilization of the non-oxidative part of pentose phosphate pathway inTt.
maritima for breaking down glucose
.This diversity of pathways and substrate utilization is reflected in the genomic composition as
over 7 % of theTt. maritima genome was noted to encode genes required for sugar metabolism
14.
15. MOTILITY
Mobility has been observed in many species of the phylum where the species
often contain flagella.
The flagella are commonly polar, but species of the genusThermotoga contain
subpolar or peritrichous flagella.
Noticeably, while motility is variable by group, no species belonging to the
generaThermosipho and Kosmotoga have been observed to display motility,
though flagella are present inTs. geolei .
Thermotaxis was identified inTt. maritima which have been observed to be motile
to temperatures up to 105 C and Chemotaxis proteins have also been identified
16. ECOLOGY /HABITAT
TheThermotogae are cosmopolitan organisms which have been isolated from
deep-sea and terrestrial hydrothermal environments, from oil wells and oil
reservoirs, and from continental solfatara springs around the world
TheThermotogae are known for their thermophilic existence with most known
species growing best at temperatures of 45–80 C.
Most species of the group grow best in neutral pH, while optimum concentration
of NaCl varies among species.
Tolerance for salt is highest among Geotoga, Oceanotoga, and Petrotoga species,
many of which can survive in environments comprised of 10 % NaCl with P.
mexicana able to live at levels up to 20 % NaCl
17. ECOLOGY /HABITAT
Tt. maritima,Tt. neapolitana, andTt. hypogea harbor the ability to exist at or above temperatures
close to 90 C
Though most species exist and flourish at temperatures above 40 C, some species such as K.
olearia, Oceanotoga teriensis, and P. mexicana can thrive at mesophilic temperatures.
However, despite such meso-tolerant growth among theThermotogae, the recently described
Mesotoga prima species is the first organism of the group to have been isolated at a mesophilic
temperature
Additionally, unlike otherThermotogae, the Mesotoga species was isolated from an enrichment
PCB-dechlorinating culture in Baltimore harbor
19. MOLECULAR MARKERSTHAT ARE SPECIFIC FOR
DIFFERENTTHERMOTOGAE CLADES
Until recently, apart from phylogenetic analyses, no other methods existed that
provided reliable means to distinguish different groups of species from each other
or to infer the evolutionary relationships among them.
This important gap, however, is being filled by the availability of genomic
sequences from large numbers of prokaryotic species
The analyses of these genomes are enabling the discovery of numerous reliable
molecular markers for identification and clear demarcation of different groups of
prokaryotic organisms
20. CSI
One very useful category of molecular markers for evolutionary and systematic studies are
Conserved Signature Indels in protein sequences, that are specific for different groups of
prokaryotes at various phylogenetic depths
The CSIs that are useful for evolutionary studies are of defined lengths,
They are present at specific locations in widely distributed proteins,
They are flanked on both sides by conserved regions, and
They are restricted to homologous proteins from monophyletic groups of organisms
21. CSI
The simplest and most parsimonious explanation for these CSIs is that the rare
genetic changes responsible for them first occurred in the common ancestor of
these groups (or clades) of species and these changes were then vertically
inherited by various descendant species
Editor's Notes
surrounds the cell and is commonly referred to as the ‘‘toga,’’ providing the group with the latter part of its name
These long-chained lipids are absent in the mesophilic Ms. prima
(CSIs; indels refer to either inserts or deletions),
