Thermotogota

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]

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]

Taxonomy[]

This phylum presently consists of a single class (Thermotogae), four orders (Thermotogales, , , and ) and five families (Thermatogaceae, Fervidobacteriaceae, Kosmotogaceae, Petrotogaceae, and Mesoaciditogaceae).^{[2][3][4][10][11][12][13]} It contains a total of 15 genera and 52 species.^[14] In the 16S rRNA trees, the Thermotogota have been observed to branch with the Aquificae (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 Aquificae, and the deep branching of the latter group of species, is not supported by phylogenetic studies based upon other gene/protein sequences.^{[3][15][16][17][18]} and also by conserved signature indels in several highly conserved universal proteins.^[19][20] The Thermotogota have also been scrutinized for their supposedly profuse Lateral gene transfer with Archaeal organisms.^[21][22] 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.^{[23][24][10][25]}

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.^[13] 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, , , and . 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.^[26] 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.^[26] 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.^[26]

Phylogeny[]

The phylogeny based on the work of the All-Species Living Tree Project.^[27]

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LSPN)^[28] and the National Center for Biotechnology Information (NCBI).^[29]

• Phylum Thermotogota Reysenbach 20201
  • Class Thermotogae Reysenbach 2002 [Togobacteria Cavalier-Smith 2002]
    • Genus ♥ Xue et al. 1999
      • Species ♥ Xue et al. 1999
    • Order Thermotogales Reysenbach 2002 emend. Bhandari & Gupta 2014
      • Family Bhandari & Gupta 2014
        • Genus Patel et al. 1985
          • Species ? Friedrich and Antranikian 1999
          • Species F. changbaicum Cai et al. 2007
          • Species F. gondwanense Andrews and Patel
          • Species F. islandicum Huber et al. 1991
          • Species Patel et al. 1985 (type sp.)
          • Species Podosokorskaya et al. 2011
        • Genus Huber et al. 1989 emend. Ravot et al. 1996
          • Species ? ♠ Kendall et al. 2002
          • Species Podosokorskaya et al. 2014
          • Species Podosokorskaya et al. 2011
          • Species Huber et al. 1989 emend. Ravot et al. 1996 (type sp.)
          • Species Urios et al. 2004
          • Species L'Haridon et al. 2001
          • Species Kuwabara et al. 2011
          • Species Takai and Horikoshi 2000
          • Species Antoine et al. 1997
      • Family Reysenbach 2002 emend. Bhandari & Gupta 2014
        • Genus Bhandari & Gupta 2014
          • Species (Ravot et al. 1995) Bhandari & Gupta 2014 [Thermotoga elfii Ravot et al. 1995]
          • Species (Fardeau et al. 1997) Bhandari & Gupta 2014 [Thermotoga hypogea Fardeau et al. 1997]
          • Species (Balk, Weijma & Stams 2002) Bhandari & Gupta 2014 [Thermotoga lettingae Balk, Weijma & Stams 2002]
          • Species (Windberger et al. 1992) Bhandari & Gupta 2014 [Thermotoga thermarum Windberger et al. 1992]
          • Species (Jeanthon et al. 2000) Bhandari & Gupta 2014 [Thermotoga subterranea Jeanthon et al. 2000]
        • Genus ? ♠ Duckworth et al. 1996
          • Species ♠ Duckworth et al. 1996
        • Genus Thermotoga Stetter and Huber 1986
          • Species ? ♥ Takahata et al. 2000
          • Species ? ♥ Takahata et al. 2000
          • Species T. maritima Stetter and Huber 1986 (type sp.)
          • Species T. naphthophila Takahata et al. 2001
          • Species T. neapolitana Jannasch et al. 1989
          • Species T. petrophila Takahata et al. 2001
    • Order Bhandari & Gupta 2014
      • Family Bhandari & Gupta 2014
        • Genus DiPippo et al. 2009 emend. Nunoura et al. 2010 [ Feng et al. 2010]
          • Species Nunoura et al. 2011
          • Species DiPippo et al. 2009 (type sp.)
          • Species L'Haridon et al. 2016
          • Species (Feng et al. 2010) Nunoura et al. 2013 [Thermococcoides shengliensis Feng et al. 2010]
        • Genus Nesbo et al. 2013
          • Species Ben et al. 2013
          • Species Nesbo et al. 2013
    • Order Itoh et al. 2015
      • Family Itoh et al. 2015
        • Genus Itoh et al. 2015
          • Species Itoh et al. 2015
        • Genus Reysenbach et al. 2013
          • Species Reysenbach et al. 2013
    • Order Bhandari & Gupta 2014
      • Family Bhandari & Gupta 2014
        • Genus Ben Hania et al. 2012
          • Species Ben Hania et al. 2012
        • Genus Davey et al. 1993
          • Species ♠ Holton et al. 2002
          • Species Davey et al. 1993 (type sp.)
          • Species Davey et al. 1993
        • Genus Wery et al. 2001
          • Species Postec et al. 2005
          • Species Wery et al. 2001 (type sp.)
          • Species Postec et al. 2010
          • Species Nunoura et al. 2007
          • Species M. piezophila Alain et al. 2002
        • Genus Jayasinghearachchi and Lal 2011
          • Species Jayasinghearachchi and Lal 2011
        • Genus Davey et al. 1993
          • Species Miranda-Tello et al. 2007
          • Species Miranda-Tello et al. 2004
          • Species Davey et al. 1993 (type sp.)
          • Species Lien et al. 1998
          • Species L'Haridon et al. 2002
          • Species L'Haridon et al. 2002

Notes:
♠ Strain found at the National Center for Biotechnology Information (NCBI) but not listed in the List of Prokaryotic names with Standing in Nomenclature (LPSN)
♥ No strains lodged at National Center for Biotechnology Information NCBI and or listed in the List of Prokaryotic names with Standing in Nomenclature (LPSN)

References[]