Thermotogota

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Thermotogota
Scientific classification
Domain:
Bacteria
Superphylum:
Eurybacteria
Phylum:
Thermotogota

Reysenbach 2021 [1]
Class:
Thermotogae

Reysenbach 2002
Orders
Synonyms
  • Thermotogota:
    • "Synthermota" Cavalier-Smith 2020
    • "Thermotogae" Reysenbach 2001
    • "Thermotogaeota" Oren et al. 2015
    • "Thermotogota" Whitman et al. 2018
  • Thermotogae:
    • "Thermotogia" Cavalier-Smith 2020
    • Togobacteria Cavalier-Smith 2002

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. [2] [3]

Contents

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. [4] Recently, some Thermotogota existing at moderate temperatures have also been identified. [5] Although Thermotogota species exhibit Gram-negative staining, they are bounded by a single-unit lipid membrane, hence they are monoderm bacteria. [3] [6] [7] Because of the ability of some Thermotogota species to thrive at high temperatures, they are considered attractive targets for use in industrial processes. [8] 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. [9]

Molecular signatures

Until recently, no biochemical or molecular markers were known that could distinguish the species from the phylum Thermotogota from all other bacteria. [2] However, a recent comparative genomic study has identified large numbers of conserved signature indels (CSIs) in important proteins that are specific for either all Thermotogota species or a number of its subgroups. [3] [10] Many of these CSIs in important housekeeping proteins such as Pol1, RecA, and TrpRS, and ribosomal 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. [11] These indels are the premise for the current taxonomic organization of the Thermotogota, and are strongly supported by phylogenomic analyses. [3] [10] Additional CSIs have also been found that are specific for Thermotoga , Pseudothermotoga , Fervidobacterium , and Thermosipho . These CSIs are specific for all species within each respective genus, and absent in all other bacteria, thus are specific markers. [3] [10] A clade consisting of the deep-branching species Petrotoga mobilis, Kosmotoga olearia, and Thermotogales bacterium mesG1 was also supported by seven CSIs. [10] Additionally, some CSIs that provided evidence of LGT among the Thermotogota and other prokaryotic groups were also reported. [10] 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 , another order comprising hyperthermophilic species. [12] Phylogenetic studies demonstrated that the presence of the same CSI within these two unrelated groups of bacteria is not due to lateral gene transfer, rather the CSI likely developed independently in these two groups of thermophiles due to selective pressure. [12] 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. [12]

Phylogeny

16S rRNA based LTP_12_2021 [13] [14] [15] 120 single copy marker proteins based GTDB 08-RS214 [16] [17] [18]
Mesoaciditogales
Mesoaciditogaceae

Athalassotoga

Mesoaciditoga

Kosmotogales
Kosmotogaceae

Mesotoga

Kosmotoga

Petrotogales
Petrotogaceae
"Marinitogeae"

Marinitoga

"Petrotogeae"

Tepiditoga

Oceanotoga

Geotoga

Defluviitoga

Petrotoga

Thermotogales
Thermotogaceae

Thermotoga

Pseudothermotoga

Fervidobacteriaceae

Fervidobacterium

Thermosipho

Mesoaciditogales
Mesoaciditogaceae

Athalassotoga

Mesoaciditoga

Petrotogales
Kosmotogaceae

Mesotoga

Kosmotoga

Petrotogaceae
"Marinitogeae"

Marinitoga

"Petrotogeae"

Tepiditoga

Oceanotoga

Geotoga

Defluviitoga

Petrotoga

Thermotogales
Thermotogaceae

Thermotoga

"Pseudothermotogaceae"

Pseudothermotoga

Fervidobacteriaceae

Fervidobacterium

Thermosipho

Taxonomy

This phylum presently consists of a single class (Thermotogae), four orders (Thermotogales, Kosmotogales, Petrotogales, and Mesoaciditogales) and five families (Thermatogaceae, Fervidobacteriaceae, Kosmotogaceae, Petrotogaceae, and Mesoaciditogaceae). [2] [3] [4] [10] [19] [20] [11] It contains a total of 15 genera and 52 species. [21] In the 16S rRNA trees, the Thermotogota have been observed to branch with the Aquificota (another phylum comprising hyperthermophilic organisms) in close proximity to the archaeal-bacterial branch point. [2] [4] 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. [3] [22] [23] [24] [25] and also by conserved signature indels in several highly conserved universal proteins. [26] [27] The Thermotogota have also been scrutinized for their supposedly profuse Lateral gene transfer with Archaeal organisms. [28] [29] 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. [30] [31] [10] [32]

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN) [33] and National Center for Biotechnology Information (NCBI) [34]

Related Research Articles

<span class="mw-page-title-main">Spirochaete</span> Phylum of bacteria

A spirochaete or spirochete is a member of the phylum Spirochaetota, which contains distinctive diderm (double-membrane) gram-negative bacteria, most of which have long, helically coiled cells. Spirochaetes are chemoheterotrophic in nature, with lengths between 3 and 500 μm and diameters around 0.09 to at least 3 μm.

<span class="mw-page-title-main">Nanoarchaeota</span> Phylum of archaea

Nanoarchaeota is a proposed phylum in the domain Archaea that currently has only one representative, Nanoarchaeum equitans, which was discovered in a submarine hydrothermal vent and first described in 2002.

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, which is able to produce water by oxidizing hydrogen. They have been found in springs, pools, and oceans. They are autotrophs, and are the primary carbon fixers in their environments. These bacteria are Gram-negative, non-spore-forming rods. They are true bacteria as opposed to the other inhabitants of extreme environments, the Archaea.

The Chloroflexia are a class of bacteria in the phylum Chloroflexota. Chloroflexia are typically filamentous, and can move about through bacterial gliding. It is named after the order Chloroflexales.

<span class="mw-page-title-main">Deinococcota</span> Phylum of Gram-negative bacteria

Deinococcota is a phylum of bacteria with a single class, Deinococci, that are highly resistant to environmental hazards, also known as extremophiles. These bacteria have thick cell walls that give them gram-positive stains, but they include a second membrane and so are closer in structure to those of gram-negative bacteria.

<span class="mw-page-title-main">Verrucomicrobiota</span> Phylum of bacteria

Verrucomicrobiota is a phylum of Gram-negative bacteria that contains only a few described species. The species identified have been isolated from fresh water, marine and soil environments and human faeces. A number of as-yet uncultivated species have been identified in association with eukaryotic hosts including extrusive explosive ectosymbionts of protists and endosymbionts of nematodes residing in their gametes.

<span class="mw-page-title-main">Chlamydiota</span> Phylum of bacteria

The Chlamydiota are a bacterial phylum and class whose members are remarkably diverse, including pathogens of humans and animals, symbionts of ubiquitous protozoa, and marine sediment forms not yet well understood. All of the Chlamydiota that humans have known about for many decades are obligate intracellular bacteria; in 2020 many additional Chlamydiota were discovered in ocean-floor environments, and it is not yet known whether they all have hosts. Historically it was believed that all Chlamydiota had a peptidoglycan-free cell wall, but studies in the 2010s demonstrated a detectable presence of peptidoglycan, as well as other important proteins.

<span class="mw-page-title-main">Xanthomonadales</span> Order of bacteria

The Xanthomonadales are a bacterial order within the Gammaproteobacteria. They are one of the largest groups of bacterial phytopathogens, harbouring species such as Xanthomonas citri, Xanthomonas euvesicatoria, Xanthomonas oryzae and Xylella fastidiosa. These bacteria affect agriculturally important plants including tomatoes, bananas, citrus plants, rice, and coffee. Many species within the order are also human pathogens. Species within the genus Stenotrophomonas are multidrug resistant opportunistic pathogens that are responsible for nosocomial infections in immunodeficient patients.

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<i>Thermotoga</i> Genus of bacteria

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".

<span class="mw-page-title-main">PVC superphylum</span> Superphylum of bacteria

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The Synergistota is a phylum of anaerobic bacteria that show Gram-negative staining and have rod/vibrioid cell shape. Although Synergistota have a diderm cell envelope, the genes for various proteins involved in lipopolysaccharides biosynthesis have not yet been detected in Synergistota, indicating that they may have an atypical outer cell envelope. The Synergistota inhabit a majority of anaerobic environments including animal gastrointestinal tracts, soil, oil wells, and wastewater treatment plants and they are also present in sites of human diseases such as cysts, abscesses, and areas of periodontal disease. Due to their presence at illness related sites, the Synergistota are suggested to be opportunistic pathogens but they can also be found in healthy individuals in the microbiome of the umbilicus and in normal vaginal flora. Species within this phylum have also been implicated in periodontal disease, gastrointestinal infections and soft tissue infections. Other species from this phylum have been identified as significant contributors in the degradation of sludge for production of biogas in anaerobic digesters and are potential candidates for use in renewable energy production through their production of hydrogen gas. All of the known Synergistota species and genera are presently part of a single class (Synergistia), order (Synergistiales), and family (Synergistaceae).

<i>Deinococcus</i> Genus of bacteria

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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 that are generally of defined size and they are flanked on both sides by conserved regions to ensure their reliability. While indels can be arbitrary inserts or deletions, CSIs are defined as only those protein indels that are present within conserved regions of the protein.

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The Eggerthellaceae are a family of Gram-positive, rod- or coccus-shaped Actinomycetota. It is the sole family within the order Eggerthellales.

References

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