Thermotogae

The Thermotogota are a phylum of the domain Bacteria. The phylum contains a single class, Thermotogae. The phylum Thermotogota is composed of Gram-negative staining, anaerobic, and mostly thermophilic and hyperthermophilic bacteria.^[2][3]

Thermotogae
Scientific classification
Domain:	Bacteria
Phylum:	Thermotogota Reysenbach 2021[1]
Class:	Thermotogae Reysenbach 2002
Orders
Kosmotogales Mesoaciditogales Petrotogales Thermotogales
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

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]

• Class Thermotogae Reysenbach 2002
  • Genus ?Caldotoga Xue et al. 1999
  • Order Kosmotogales Bhandari & Gupta 2014
    • Family Kosmotogaceae Bhandari & Gupta 2014
      • Genus Kosmotoga DiPippo et al. 2009 [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
  • Order Thermotogales Reysenbach 2002
    • Family Fervidobacteriaceae Bhandari & Gupta 2014
      • Genus Fervidobacterium Patel et al. 1985
      • Genus Thermosipho Huber et al. 1989 non Kantor et al. 2013
    • Family Thermotogaceae Reysenbach 2002 ["Pseudothermotogaceae" Pallen, Rodriguez-R & Alikhan 2022]
      • Genus Pseudothermotoga Bhandari & Gupta 2014
      • Genus ?Thermopallium Duckworth et al. 1996
      • Genus Thermotoga Stetter and Huber 1986

References

1. Oren A, Garrity GM (2021). "Valid publication of the names of forty-two phyla of prokaryotes". Int J Syst Evol Microbiol. 71 (10): 5056. doi:10.1099/ijsem.0.005056. PMID 34694987.
2. Huber R., Hannig M. (2006). "Thermotogales". The Prokaryotes. Vol. 7: Proteobacteria: Delta and Epsilon Subclasses. Deeply Rooting Bacteria. pp. 899–922. doi:10.1007/0-387-30747-8_38. ISBN 978-0-387-25497-5.
3. Gupta, RS (2014) The Phylum Thermotogae. The Prokaryotes 989-1015. Springer Berlin Heidelberg.
4. 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.
5. 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 (14): 4896–4900. Bibcode:2010ApEnM..76.4896N. doi:10.1128/AEM.02846-09. PMC 2901743. PMID 20495053.
6. 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. doi:10.1128/MMBR.62.4.1435-1491.1998. PMC 98952. PMID 9841678.
7. 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 (2): 171–182. doi:10.1007/s10482-011-9616-8. PMC 3133647. PMID 21717204.
8. Eriksen N.T.; Riis M.L.; Holm N.K. & Iversen N. (2010). "H(2) synthesis from pentoses and biomass in Thermotoga spp" (PDF). Biotechnol Lett. 33 (2): 293–300. doi:10.1007/s10529-010-0439-x. PMID 20960218. S2CID 35392547.
9. 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.
10. Gupta R.S. & Bhandari V. (2011). "Phylogeny and molecular signatures for the phylum Thermotogae and its subgroups". Antonie van Leeuwenhoek. 100 (1): 1–34. doi:10.1007/s10482-011-9576-z. PMID 21503713. S2CID 24995263.
11. 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. S2CID 6547323.
12. Khadka, Bijendra; Persaud, Dhillon; Gupta, Radhey S. (2019-12-29). "Novel Sequence Feature of SecA Translocase Protein Unique to the Thermophilic Bacteria: Bioinformatics Analyses to Investigate Their Potential Roles". Microorganisms. 8 (1): 59. doi:10.3390/microorganisms8010059. ISSN 2076-2607. PMC 7023208. PMID 31905784.
13. "The LTP". Retrieved 23 February 2021.
14. "LTP_all tree in newick format". Retrieved 23 February 2021.
15. "LTP_12_2021 Release Notes" (PDF). Retrieved 23 February 2021.
16. "GTDB release 08-RS214". Genome Taxonomy Database. Retrieved 10 May 2023.
17. "bac120_r214.sp_label". Genome Taxonomy Database. Retrieved 10 May 2023.
18. "Taxon History". Genome Taxonomy Database. Retrieved 10 May 2023.
19. 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. PMID 28056215.
20. 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. 66 (2): 1045–1051. doi:10.1099/ijsem.0.000833. PMID 26651491.
21. Euzeby JP. List of prokaryotic names with standing in nomenclature. http://www.bacterio.cict.fr/t/thermotogales%5B%5D.
22. 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. Bibcode:1999JMolE..48..528K. doi:10.1007/pl00006496. PMID 10198119. S2CID 224169.
23. 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.
24. 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 (5765): 1283–1287. Bibcode:2006Sci...311.1283C. CiteSeerX 10.1.1.381.9514. doi:10.1126/science.1123061. PMID 16513982. S2CID 1615592.
25. Di Giulio M. (2003). "The universal ancestor was a thermophile or a hyperthermophile: Tests and further evidence". J Theor Biol. 221 (3): 425–436. Bibcode:2003JThBi.221..425G. doi:10.1006/jtbi.2003.3197. PMID 12642117.
26. 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 3417386. PMID 22919687.
27. 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.
28. 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. Bibcode:1999Natur.399..323N. doi:10.1038/20601. PMID 10360571. S2CID 4420157.
29. 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.
30. Ochman H.; Lawrence J.G. & Groisman E.A. (2000). "Lateral gene transfer and the nature of bacterial innovation". Nature. 405 (6784): 299–304. Bibcode:2000Natur.405..299O. doi:10.1038/35012500. PMID 10830951. S2CID 85739173.
31. 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 (14): 5865–5870. Bibcode:2009PNAS..106.5865Z. doi:10.1073/pnas.0901260106. PMC 2667022. PMID 19307556.
32. Kunisawa T (2011). "Inference of the phylogenetic position of the phylum Deferribacteres from gene order comparison". Antonie van Leeuwenhoek. 99 (2): 417–422. doi:10.1007/s10482-010-9492-7. PMID 20706870. S2CID 38697982.
33. J.P. Euzéby. "Thermotogota". List of Prokaryotic names with Standing in Nomenclature (LPSN). Retrieved 2022-03-20.
34. Sayers; et al. "Thermotogae". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2022-03-20.