The Thermotogota are a

phylum In biology, a phylum (; plural: phyla) is a level of classification or taxonomic rank below kingdom and above class. Traditionally, in botany the term division has been used instead of phylum, although the International Code of Nomenclature f ...

of the

domain Domain may refer to: Mathematics *Domain of a function, the set of input values for which the (total) function is defined **Domain of definition of a partial function **Natural domain of a partial function **Domain of holomorphy of a function * Do ...

Bacteria Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were among ...

. The phylum Thermotogota is composed of

Gram-negative Gram-negative bacteria are bacteria that do not retain the crystal violet stain used in the Gram staining method of bacterial differentiation. They are characterized by their cell envelopes, which are composed of a thin peptidoglycan cell wall ...

staining,

anaerobic Anaerobic means "living, active, occurring, or existing in the absence of free oxygen", as opposed to aerobic which means "living, active, or occurring only in the presence of oxygen." Anaerobic may also refer to: * Anaerobic adhesive, a bonding a ...

, and mostly

thermophilic A thermophile is an organism—a type of extremophile—that thrives at relatively high temperatures, between . Many thermophiles are archaea, though they can be bacteria or fungi. Thermophilic eubacteria are suggested to have been among the earl ...

and

hyperthermophilic A hyperthermophile is an organism that thrives in extremely hot environments—from 60 °C (140 °F) upwards. An optimal temperature for the existence of hyperthermophiles is often above 80 °C (176 °F). Hyperthermophiles are often within the doma ...

bacteria.Gupta, RS (2014) The Phylum Thermotogae. The Prokaryotes 989-1015. Springer Berlin Heidelberg.

Characteristics

The name of this phylum is derived from the existence of many of these organisms at high temperatures along with the characteristic sheath structure, or "toga", surrounding the cells of these species.Reysenbach, A.-L. (2001) Phylum BII. Thermotogae phy. nov. In: Bergey's Manual of Systematic Bacteriology, pp. 369-387. Eds D. R. Boone, R. W. Castenholz. Springer-Verlag: Berlin. Recently, some Thermotogota existing at moderate temperatures have also been identified. Although Thermotogota species exhibit

staining, they are bounded by a single-unit lipid membrane, hence they are

monoderm In bacteriology, gram-positive bacteria are bacteria that give a positive result in the Gram stain test, which is traditionally used to quickly classify bacteria into two broad categories according to their type of cell wall. Gram-positive bacte ...

bacteria. Because of the ability of some Thermotogota species to thrive at high temperatures, they are considered attractive targets for use in industrial processes. The metabolic ability of Thermotogota to utilize different complex-carbohydrates for production of hydrogen gas led to these species being cited as a possible biotechnological source for production of energy alternative to fossil fuels.

Molecular signatures

Until recently, no biochemical or

molecular marker A molecular marker is a molecule, sampled from some source, that gives information about its source. For example, DNA is a molecular marker that gives information about the organism from which it was taken. For another example, some proteins can be ...

s were known that could distinguish the species from the phylum Thermotogota from all other bacteria. However, a recent comparative genomic study has identified large numbers of

conserved signature indels Conserved signature inserts and deletions (CSIs) in protein sequences provide an important category of molecular markers for understanding phylogenetic relationships. CSIs, brought about by rare genetic changes, provide useful phylogenetic markers ...

(CSIs) in important proteins that are specific for either all Thermotogota species or a number of its subgroups. Many of these CSIs in important housekeeping proteins such as Pol1,

RecA RecA is a 38 kilodalton protein essential for the repair and maintenance of DNA. A RecA structural and functional homolog has been found in every species in which one has been seriously sought and serves as an archetype for this class of homolog ...

, and

TrpRS Tryptophanyl-tRNA synthetase, mitochondrial is an enzyme that in humans is encoded by the ''WARS2'' gene In biology, the word gene (from , ; "... Wilhelm Johannsen coined the word gene to describe the Mendelian units of heredity..." meanin ...

, and

ribosomal Ribosomes ( ) are macromolecular machines, found within all cells, that perform biological protein synthesis (mRNA translation). Ribosomes link amino acids together in the order specified by the codons of messenger RNA (mRNA) molecules to fo ...

proteins L4, L7/L12, S8, S9, etc. are uniquely present in different sequenced Thermotogota species providing novel molecular markers for this phylum. These studies also identified CSIs specific for each order and each family. These indels are the premise for the current taxonomic organization of the Thermotogota, and are strongly supported by phylogenomic analyses. Additional CSIs have also been found that are specific for ''

Thermotoga ''Thermotoga'' is a genus of the phylum ''Thermotogota''. Members of ''Thermotoga'' are hyperthermophilic bacteria whose cell is wrapped in a unique sheath-like outer membrane, called a "toga". The members of the phylum stain Gram-negative as th ...

'', '' Pseudothermotoga'', '' Fervidobacterium'', and ''

Thermosipho ''Thermosipho'' is a genus of Gram-negative staining, anaerobic, and mostly thermophilic and hyperthermophilic bacteria in the family Family (from la, familia) is a group of people related either by consanguinity (by recognized birth) or ...

''. These CSIs are specific for all species within each respective genus, and absent in all other bacteria, thus are specific markers. A clade consisting of the deep-branching species ''Petrotoga mobilis'', ''Kosmotoga olearia'', and ''Thermotogales bacterium'' mesG1 was also supported by seven CSIs. Additionally, some CSIs that provided evidence of LGT among the Thermotogota and other prokaryotic groups were also reported. The newly discovered molecular markers provide novel means for identification and circumscription of species from the phylum in molecular terms and for future revisions to its taxonomy. Additionally, a 51 aa insertion CSI was identified to be specific for all ''Thermotogales'' as well as ''

Aquificales The ''Aquificota'' phylum is a diverse collection of bacteria that live in harsh environmental settings. The name ''Aquificota'' was given to this phylum based on an early genus identified within this group, ''Aquifex'' (“water maker”), which ...

'', another order comprising hyperthermophilic species. Phylogenetic studies demonstrated that the presence of the same CSI within these two unrelated groups of bacteria is not due to

lateral gene transfer Horizontal gene transfer (HGT) or lateral gene transfer (LGT) is the movement of genetic material between unicellular and/or multicellular organisms other than by the ("vertical") transmission of DNA from parent to offspring ( reproduction). ...

, rather the CSI likely developed independently in these two groups of thermophiles due to

selective pressure Any cause that reduces or increases reproductive success in a portion of a population potentially exerts evolutionary pressure, selective pressure or selection pressure, driving natural selection. It is a quantitative description of the amount of ...

. The insert is located on the surface of the protein in the ATPase domain, near the binding site of ADP/ATP. Molecular dynamic stimulations revealed a network of hydrogen bonds formed between water molecules, residues within the CSI and a ADP/ATP molecule. It is thought that this network helps to maintain ADP/ATP binding to the SecA protein at high temperatures, contributing to the overall thermostable phenotype some ''Thermotogales'' species.

Phylogeny

Taxonomy

This phylum presently consists of a single class (Thermotogae), four orders (

Thermotogales The Thermotogota are a phylum of the domain Bacteria. The phylum Thermotogota is composed of Gram-negative staining, anaerobic, and mostly thermophilic and hyperthermophilic bacteria.Gupta, RS (2014) The Phylum Thermotogae. The Prokaryotes 989- ...

, Kosmotogales, Petrotogales, and Mesoaciditogales) and five families (Thermatogaceae, Fervidobacteriaceae, Kosmotogaceae, Petrotogaceae, and Mesoaciditogaceae). It contains a total of 15 genera and 52 species.Euzeby JP. List of prokaryotic names with standing in nomenclature. http://www.bacterio.cict.fr/t/thermotogales. In the 16S rRNA trees, the Thermotogota have been observed to branch with the

Aquificota The ''Aquificota'' phylum is a diverse collection of bacteria that live in harsh environmental settings. The name ''Aquificota'' was given to this phylum based on an early genus identified within this group, ''Aquifex'' (“water maker”), which ...

(another phylum comprising

organisms) in close proximity to the archaeal-bacterial branch point. However, a close relationship of the Thermotogota to the Aquificota, and the deep branching of the latter group of species, is not supported by phylogenetic studies based upon other gene/protein sequences. and also by conserved signature indels in several highly conserved universal proteins. The Thermotogota have also been scrutinized for their supposedly profuse

Lateral gene transfer Horizontal gene transfer (HGT) or lateral gene transfer (LGT) is the movement of genetic material between unicellular and/or multicellular organisms other than by the ("vertical") transmission of DNA from parent to offspring ( reproduction). ...

with

Archaea Archaea ( ; singular archaeon ) is a domain of single-celled organisms. These microorganisms lack cell nuclei and are therefore prokaryotes. Archaea were initially classified as bacteria, receiving the name archaebacteria (in the Archaebac ...

l organisms. However, recent studies based upon more robust methodologies suggest that incidence of LGT between Thermotogota and other groups including Archaea is not as high as suggested in earlier studies. The currently accepted taxonomy is based on the

List of Prokaryotic names with Standing in Nomenclature List of Prokaryotic names with Standing in Nomenclature (LPSN) is an online database that maintains information on the naming and taxonomy of prokaryotes, following the taxonomy requirements and rulings of the International Code of Nomenclature ...

(LPSN) and

National Center for Biotechnology Information The National Center for Biotechnology Information (NCBI) is part of the United States National Library of Medicine (NLM), a branch of the National Institutes of Health (NIH). It is approved and funded by the government of the United States. The ...

(NCBI) * Class Thermotogae Reysenbach 2002 ** Genus '' Caldotoga'' Xue et al. 1999 ** Order

Reysenbach 2002 *** Family Fervidobacteriaceae Bhandari & Gupta 2014 **** Genus '' Fervidobacterium'' Patel et al. 1985 **** Genus ''

'' Huber et al. 1989 non Kantor et al. 2013 *** Family Thermotogaceae Reysenbach 2002 **** Genus '' Pseudothermotoga'' Bhandari & Gupta 2014 **** Genus '' Thermopallium'' Duckworth et al. 1996 **** Genus ''

'' Stetter and Huber 1986 ** Order Kosmotogales Bhandari & Gupta 2014 *** Family Kosmotogaceae Bhandari & Gupta 2014 **** Genus '' Kosmotoga'' DiPippo et al. 2009 'Thermococcoides''_Feng_et_al._2010.html" ;"title="Thermococcoides.html" ;"title="'Thermococcoides">'Thermococcoides'' Feng et al. 2010">Thermococcoides.html" ;"title="'Thermococcoides">'Thermococcoides'' Feng et al. 2010**** Genus ''Mesotoga'' Nesbo et al. 2013 ** Order Mesoaciditogales Itoh et al. 2015 *** Family Mesoaciditogaceae Itoh et al. 2015 **** Genus ''Athalassotoga'' Itoh et al. 2015 **** Genus '' Mesoaciditoga'' Reysenbach et al. 2013 ** Order Petrotogales Bhandari & Gupta 2014 *** Family Petrotogaceae Bhandari & Gupta 2014 **** Tribe "Marinitogeae" Pelletier 2012 ***** Genus '' Marinitoga'' Wery et al. 2001 **** Tribe "Petrotogeae" Pelletier 2012 ***** Genus '' Defluviitoga'' Ben Hania et al. 2012 ***** Genus '' Geotoga'' Davey et al. 1993 ***** Genus '' Oceanotoga'' Jayasinghearachchi and Lal 2011 ***** Genus '' Petrotoga'' Davey et al. 1993 ***** Genus '' Tepiditoga'' Mori et al. 2021

References

{{Taxonbar, from=Q1146853 Bergey's volume 1 Thermophiles Thermozoa Bacteria phyla