Thermotogae

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Thermotogae
Scientific classification
Domain: Bacteria
Phylum: Thermotogae Reysenbach 2002 emend. Bhandari & Gupta 2014
Class: Thermotogae Reysenbach 2002 emend. Bhandari & Gupta 2014
Order
Synonyms
  • Togobacteria Cavalier-Smith 2002
  • Thermotogaeota Oren et al. 2015

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[edit]

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[edit]

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[edit]

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[edit]

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


Thermotogales
Thermotogaceae
Thermotoga

T. naphthophila




T. petrophila




T. maritima (type sp.)



T. neapolitana





Pseudothermotoga


P. hypogea



P. thermarum





P. subterranea




P. elfii



P. lettingae






Fervidobacteriaceae
Fervidobacterium


F. changbaicum



F. islandicum





F. nodosum (type sp.)




F. gondwanense



F. riparium





Thermosipho

T. activus




T. geolei




T. atlanticus





T. affectus



T. melanesiensis





T. globiformans




T. africanus (type sp.)



T. japonicus











Kosmotogaceae

Kosmotoga arenicorallina



Mesotoga

M. infera



M. prima



Kosmotoga

K. olearia (type sp.)



K. shengliensis






Mesoaciditogaceae

Mesoaciditoga lauensis


Petrotogaceae
Marinitoga

M. hydrogenitolerans




M. litoralis




M. okinawensis




M. piezophila



M. camini (type sp.)









Oceanotoga teriensis


Geotoga

G. petraea (type sp.)



G. subterranea






Defluviitoga tunisiensis


Petrotoga

P. sibirica




P. olearia




P. mexicana




P. mobilis




P. halophila



P. miotherma (type sp.)













Taxonomy[edit]

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]

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[edit]

  1. ^ a b c d Huber R., Hannig M. (2006). "Thermotogales". Prokaryotes. 7: 899–922. 
  2. ^ a b c d e f g Gupta, RS (2014) The Phylum Thermotogae. The Prokaryotes 989-1015. Springer Berlin Heidelberg.
  3. ^ a b c 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.
  4. ^ Nesbo C.L.; Kumaraswamy R.; Dlutek M.; Doolittle W.F. & Foght J. (2010). "Searching for mesophilic Thermotogales bacteria: "mesotogas" in the wild". Appl Environ Microbiol. 76: 4896–4900. doi:10.1128/AEM.02846-09. PMC 2901743Freely accessible. PMID 20495053. 
  5. ^ Gupta R.S. (1998). "Protein phylogenies and signature sequences: A reappraisal of evolutionary relationships among archaebacteria, eubacteria, and eukaryotes". Microbiol Mol Biol Rev. 62 (4): 1435–1491. PMC 98952Freely accessible. PMID 9841678. 
  6. ^ Gupta R.S. (2011). "Origin of diderm (Gram-negative) bacteria: antibiotic selection pressure rather than endosymbiosis likely led to the evolution of bacterial cells with two membranes". Antonie van Leeuwenhoek. 100: 171–182. doi:10.1007/s10482-011-9616-8. PMC 3133647Freely accessible. PMID 21717204. 
  7. ^ Eriksen N.T.; Riis M.L.; Holm N.K. & Iversen N. (2010). "H(2) synthesis from pentoses and biomass in Thermotoga spp.". Biotechnol Lett. 33 (2): 293–300. doi:10.1007/s10529-010-0439-x. PMID 20960218. 
  8. ^ Conners S.B.; Mongodin E.F.; Johnson M.R.; Montero C.I.; Nelson K.E. & Kelly R.M. (2006). "Microbial biochemistry, physiology, and biotechnology of hyperthermophilic Thermotoga species". FEMS Microbiol Rev. 30 (6): 872–905. doi:10.1111/j.1574-6976.2006.00039.x. PMID 17064285. 
  9. ^ a b c d e f g Gupta R.S. & Bhandari V. (2011). "Phylogeny and molecular signatures for the phylum Thermotogae and its subgroups". Antonie Van Leeuwenhoek. 100: 1–34. doi:10.1007/s10482-011-9576-z. PMID 21503713. 
  10. ^ Oren A, Garrity GM (2015). "List of new names and new combinations previously effectively, but not validly, published" (PDF). Int. J. Syst. Evol. Microbiol. 65 (7): 2017–2025. doi:10.1099/ijs.0.000317. 
  11. ^ Itoh T, Onishi M, Kato S, Iino T, Sakamoto M, Kudo T, Takashina T, Ohkuma M (December 2015). "Athalassotoga saccharophila gen. nov. sp. nov. isolated from an acidic terrestrial hot spring of Japan, and proposal of Mesoaciditogales ord. nov., Mesoaciditogaceae fam. nov. in the phylum Thermotogae". Int. J. Syst. Evol. Microbiol. in press: 1045–1051. doi:10.1099/ijsem.0.000833. PMID 26651491. 
  12. ^ a b Bhandari V, Gupta RS (January 2014). "Molecular signatures for the phylum (class) Thermotogae and a proposal for its division into three orders (Thermotogales, Kosmotogales ord. nov. and Petrotogales ord. nov.) containing four families (Thermotogaceae, Fervidobacteriaceae fam. nov., Kosmotogaceae fam. nov. and Petrotogaceae fam. nov.) and a new genus Pseudothermotoga gen. nov. with five new combinations". Antonie Van Leeuwenhoek. 105 (1): 143–168. doi:10.1007/s10482-013-0062-7. PMID 24166034. 
  13. ^ Euzeby JP. List of prokaryotic names with standing in nomenclature. http://www.bacterio.cict.fr/t/thermotogales .
  14. ^ Klenk H.P.; Meier T.D.; Durovic P.; et al. (1999). "RNA polymerase of Aquifex pyrophilus: Implications for the evolution of the bacterial rpoBC operon and extremely thermophilic bacteria". J Mol Evol. 48 (5): 528–541. doi:10.1007/pl00006496. PMID 10198119. 
  15. ^ Gupta R.S. (2000). "The phylogeny of Proteobacteria: relationships to other eubacterial phyla and eukaryotes". FEMS Microbiol Rev. 24 (4): 367–402. doi:10.1111/j.1574-6976.2000.tb00547.x. PMID 10978543. 
  16. ^ Ciccarelli F.D.; Doerks T.; von Mering C.; Creevey C.J.; Snel B. & Bork P. (2006). "Toward automatic reconstruction of a highly resolved tree of life". Science. 311: 1283–1287. doi:10.1126/science.1123061. PMID 16513982. 
  17. ^ Di Giulio M. (2003). "The universal ancestor was a thermophile or a hyperthermophile: Tests and further evidence". J Theor Biol. 221 (3): 425–436. doi:10.1006/jtbi.2003.3197. PMID 12642117. 
  18. ^ Bhandari V, Naushad HS, Gupta RS (2012). "Protein based molecular markers provide reliable means to understand prokaryotic phylogeny and support Darwinian mode of evolution". Front Cell Infect Microbiol. 2: 98. doi:10.3389/fcimb.2012.00098. PMC 3417386Freely accessible. PMID 22919687. 
  19. ^ Griffiths E. & Gupta R.S. (2004). "Signature sequences in diverse proteins provide evidence for the late divergence of the order Aquificales.". International Microbiology. 7 (1): 41–52. PMID 15179606. 
  20. ^ Nelson K.E.; Clayton R.; Gill S.; et al. (1999). "Evidence for lateral gene transfer between Archaea and Bacteria from genome sequence of Thermotoga maritima". Nature. 399 (6734): 323–329. doi:10.1038/20601. PMID 10360571. 
  21. ^ Nesbo C.L.; L'Haridon S.; Stetter K.O. & Doolittle W.F. (2001). "Phylogenetic analyses of two "Archaeal" genes in Thermotoga maritima reveal multiple transfers between Archaea and Bacteria". Mol Biol Evol. 18 (3): 362–375. doi:10.1093/oxfordjournals.molbev.a003812. PMID 11230537. 
  22. ^ Ochman H.; Lawrence J.G. & Groisman E.A. (2000). "Lateral gene transfer and the nature of bacterial innovation". Nature. 405 (6784): 299–304. doi:10.1038/35012500. PMID 10830951. 
  23. ^ Zhaxybayeva O.; Swithers K.S.; Lapierre P.; et al. (2009). "On the chimeric nature, thermophilic origin, and phylogenetic placement of the Thermotogales". Proc Natl Acad Sci U S A. 106: 5865–5870. doi:10.1073/pnas.0901260106. PMC 2667022Freely accessible. PMID 19307556. 
  24. ^ Kunisawa T (2011). "Inference of the phylogenetic position of the phylum Deferribacteres from gene order comparison". Antonie van Leeuwenhoek. 99: 417–422. doi:10.1007/s10482-010-9492-7. PMID 20706870. 
  25. ^ "16S rRNA-based LTP release 123 (full tree)" (PDF). Silva Comprehensive Ribosomal RNA Database. Retrieved 2016-03-20. 
  26. ^ J.P. Euzéby. "Thermotogae". List of Prokaryotic names with Standing in Nomenclature (LPSN). Retrieved 2016-03-20. 
  27. ^ Sayers; et al. "Thermotogae". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2016-03-20.