Thermotogae

The Thermotogae are a phylum of the domain Bacteria. The phylum Thermotogae is composed of Gram-negative staining, anaerobic, and mostly thermophilic and hyperthermophilic bacteria.^[1][2]

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.^[3] Recently, some Thermotogae existing at moderate temperatures have also been identified.^[4] Although Thermotogae species exhibit Gram-negative staining, they are bounded by a single-unit lipid membrane, hence they are monoderm bacteria.^[2][5][6] Because of the ability of some Thermotogae species to thrive at high temperatures, they are considered attractive targets for use in industrial processes.^[7] The metabolic ability of Thermotogae 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.^[8]

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).^{[1][2][3][9][10][11][12]} It contains a total of 15 genera and 52 species.^[13] In the 16S rRNA trees, the Thermotogae have been observed to branch with the Aquificae (another phylum comprising hyperthermophilic organisms) in close proximity to the archaeal-bacterial branch point.^[1][3] However, a close relationship of the Thermotogae 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.^{[2][14][15][16][17]} and also by conserved signature indels in several highly conserved universal proteins.^[18][19] The Thermotogae have also been scrutinized for their supposedly profuse Lateral gene transfer with Archaeal organisms.^[20][21] However, recent studies based upon more robust methodologies suggest that incidence of LGT between Thermotogae and other groups including Archaea is not as high as suggested in earlier studies.^{[22][23][9][24]}

Molecular signatures

Until recently, no biochemical or molecular markers were known that could distinguish the species from the phylum Thermotogae from all other bacteria.^[1] However, a recent comparative genomic study has identified large numbers of conserved signature indels (CSIs) in important proteins that are specific for either all Thermotogae species or a number of its subgroups.^[2][9] 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 Thermotogae species providing novel molecular markers for this phylum. These studies also identified CSIs specific for each order and each family.^[12] These indels are the premise for the current taxonomic organization of the Thermotogae, and are strongly supported by phylogenomic analyses.^[2][9] 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.^[2][9] A clade consisting of the deep-branching species Petrotoga mobilis, Kosmotoga olearia, and Thermotogales bacterium mesG1 was also supported by seven CSIs.^[9] Additionally, some CSIs that provided evidence of LGT among the Thermotogae and other prokaryotic groups were also reported.^[9] 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.

Phylogeny

The phylogeny based on the work of the All-Species Living Tree Project.^[25]

Taxonomy

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LSPN)^[26] and the National Center for Biotechnology Information (NCBI).^[27]

• Phylum Thermotogae Reysenbach 2002 emend. Bhandari & Gupta 2014 [Thermotogaeota Oren et al. 2015]
  • Class Thermotogae Reysenbach 2002 [Togobacteria Cavalier-Smith 2002]
    • Genus Caldotoga ♥ Xue et al. 1999
      • Species Caldotoga fontana ♥ Xue et al. 1999
    • Order Thermotogales Reysenbach 2002 emend. Bhandari & Gupta 2014
      • Family Fervidobacteriaceae Bhandari & Gupta 2014
        • Genus Fervidobacterium Patel et al. 1985
          • Species ?F. pennivorans 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 F. nodosum Patel et al. 1985 (type sp.)
          • Species F. riparium Podosokorskaya et al. 2011
        • Genus Thermosipho Huber et al. 1989 emend. Ravot et al. 1996
          • Species ?T. ferriphilus ♠ Kendall et al. 2002
          • Species T. activus Podosokorskaya et al. 2014
          • Species T. affectus Podosokorskaya et al. 2011
          • Species T. africanus Huber et al. 1989 emend. Ravot et al. 1996 (type sp.)
          • Species T. atlanticus Urios et al. 2004
          • Species T. geolei L'Haridon et al. 2001
          • Species T. globiformans Kuwabara et al. 2011
          • Species T. japonicus Takai and Horikoshi 2000
          • Species T. melanesiensis Antoine et al. 1997
      • Family Thermotogaceae Reysenbach 2002 emend. Bhandari & Gupta 2014
        • Genus Pseudothermotoga Bhandari & Gupta 2014
          • Species P. elfii (Ravot et al. 1995) Bhandari & Gupta 2014 [Thermotoga elfii Ravot et al. 1995]
          • Species P. hypogea (Fardeau et al. 1997) Bhandari & Gupta 2014 [Thermotoga hypogea Fardeau et al. 1997]
          • Species P. lettingae (Balk, Weijma & Stams 2002) Bhandari & Gupta 2014 [Thermotoga lettingae Balk, Weijma & Stams 2002]
          • Species P. thermarum (Windberger et al. 1992) Bhandari & Gupta 2014 [Thermotoga thermarum Windberger et al. 1992]
          • Species P. subterranea (Jeanthon et al. 2000) Bhandari & Gupta 2014 [Thermotoga subterranea Jeanthon et al. 2000]
        • Genus ?Thermopallium ♠ Duckworth et al. 1996
          • Species Thermopallium natronophilum ♠ Duckworth et al. 1996
        • Genus Thermotoga Stetter and Huber 1986
          • Species ?T. katamachii ♥ Takahata et al. 2000
          • Species ?T. kuroii ♥ 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 Kosmotogales Bhandari & Gupta 2014
      • Family Kosmotogaceae Bhandari & Gupta 2014
        • Genus Kosmotoga DiPippo et al. 2009 emend. Nunoura et al. 2010 [Thermococcoides Feng et al. 2010]
          • Species K. arenicorallina Nunoura et al. 2011
          • Species K. olearia DiPippo et al. 2009 (type sp.)
          • Species K. pacifica L'Haridon et al. 2016
          • Species K. shengliensis (Feng et al. 2010) Nunoura et al. 2013 [Thermococcoides shengliensis Feng et al. 2010]
        • Genus Mesotoga Nesbo et al. 2013
          • Species M. infera Ben et al. 2013
          • Species M. prima Nesbo et al. 2013
    • Order Mesoaciditogales Itoh et al. 2015
      • Family Mesoaciditogaceae Itoh et al. 2015
        • Genus Athalassotoga Itoh et al. 2015
          • Species Athalassotoga saccharophila Itoh et al. 2015
        • Genus Mesoaciditoga Reysenbach et al. 2013
          • Species Mesoaciditoga lauensis Reysenbach et al. 2013
    • Order Petrotogales Bhandari & Gupta 2014
      • Family Petrotogaceae Bhandari & Gupta 2014
        • Genus Defluviitoga Ben Hania et al. 2012
          • Species Defluviitoga tunisiensis Ben Hania et al. 2012
        • Genus Geotoga Davey et al. 1993
          • Species G. aestuarianus ♠ Holton et al. 2002
          • Species G. petraea Davey et al. 1993 (type sp.)
          • Species G. subterranea Davey et al. 1993
        • Genus Marinitoga Wery et al. 2001
          • Species M. hydrogenitolerans Postec et al. 2005
          • Species M. camini Wery et al. 2001 (type sp.)
          • Species M. litoralis Postec et al. 2010
          • Species M. okinawensis Nunoura et al. 2007
          • Species M. piezophila Alain et al. 2002
        • Genus Oceanotoga Jayasinghearachchi and Lal 2011
          • Species Oceanotoga teriensis Jayasinghearachchi and Lal 2011
        • Genus Petrotoga Davey et al. 1993
          • Species P. halophila Miranda-Tello et al. 2007
          • Species P. mexicana Miranda-Tello et al. 2004
          • Species P. miotherma Davey et al. 1993 (type sp.)
          • Species P. mobilis Lien et al. 1998
          • Species P. olearia L'Haridon et al. 2002
          • Species P. sibirica 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