Aquificota

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Aquificota
Scientific classification Edit this classification
Domain: Bacteria
Phylum: Aquificota
Reysenbach 2021[1]
Class
Synonyms
  • "Aquificae" Reysenbach 2001
  • "Aquithermota" Cavalier-Smith 2020
  • "Aquificota" Whitman et al. 2018
  • "Aquificaeota" Oren et al. 2015

The Aquificota

Gram-negative, non-spore-forming rods.[5] They are true bacteria (domain Bacteria) as opposed to the other inhabitants of extreme environments, the Archaea
.

Taxonomy

The Aquificota currently contain 15 genera and 42 validly published species.[6] The phylum comprises three class with each of them having their respective order.[7][8] Aquificales consists of the families Aquificaceae and Hydrogenothermaceae, while the Desulfurobacteriaceae are the only family within the Desulfurobacteriales. Thermosulfidibacter takaii is not assigned to a family within the phylum based on its phylogenetic distinctness from both orders.[9] It is currently classified as a member of Aquificales, but it has shown more physiological similarity to the Desulfobacteriaceae.

Molecular signatures and phylogenetic position

Comparative genomic studies have identified several conserved signature indels (CSIs) that are specific for all species belonging to the phylum Aquificota and provide potential molecular markers.[8] The order Aquificales can be distinguished from Desulfobacteriales by several CSIs across different proteins that are specific for each group. Additional CSIs have been found at the family level, and can be used to demarcate Aquificota and Hydrogenothermaceae from all other bacteria.[8] In parallel with the observed CSI distribution, the orders within the Aquificota are also physiologically distinct from one another. Members of the Desulfurobacteriales are strict anaerobes that exclusively oxidize hydrogen for energy, whereas those belonging to the Aquificales are microaerophilic, and capable of oxidizing other compounds (such as sulfur or thiosulfate) in addition to hydrogen.[10][11][12]

Several CSIs have also been identified that are specific for the species from the Aquificota and provide potential molecular markers for this phylum.

lateral gene transfer, rather the CSI likely developed independently in these two groups of thermophiles due to selective pressure.[13] The 51 amino acid insertion is located on the surface of SecA near the binding site of ADP/ATP. Molecular dynamic simulations revealed a network water molecules forming an intermediate interaction between residues of the 51 aa CSI and ADP molecules, which serves to stabilize the hydrogen bonds formed between ADP/ATP and the protein. It is suggested that the network of hydrogen bonds formed between the water molecules, CSI residues and ADP/ATP helps to maintain ATP/ADP binding to the SecA protein at high temperatures, which contributes to the bacteria’s overall thermostability.[13]

In the 16S rRNA gene trees, the Aquificota species branch in the proximity of the phylum

Cavalier-Smith has also suggested that the Aquificota are closely related to the Proteobacteria.[21] In contrast to the above cited analyses that are based on a few indels or on single genes, analyses on informational genes, which appeared to be less often transferred to the Aquifex lineage than noninformational genes, most often placed the Aquificales close to the Thermotogales.[22] These authors explain the frequently observed grouping of Aquificota with Campylobacterota as result of frequent horizontal gene transfer
due to shared ecological niches.

Along with the Thermotogota, the Aquificota are

thermophilic eubacteria.[3]

Phylogeny

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN)[23] and National Center for Biotechnology Information (NCBI)[24][25]

16S rRNA based
LTP_08_2023[26][27][28]
 120 single copy marker proteins based GTDB 08-RS214[29][30][31]
Aquificales
"Thermosulfidibacterota"
"Thermosulfidibacterales"

"Thermosulfidibacteraceae" Cavalier-Smith 2020 ex Chuvochina et al. 2023

"Thermosulfidibacteria"
Aquificota
"Desulfurobacteriia"
Desulfurobacteriales

Desulfurobacteriaceae L'Haridon et al. 2006

"Aquificia"
"Hydrogenothermales"

Hydrogenothermaceae Eder and Huber 2003

Aquificales

"Hydrogenobaculaceae"

Aquificaceae Reysenbach 2002


See also

References

  1. S2CID 239887308
    .
  2. ^
    PMID 16403873. Archived from the original
    on 2018-01-27. Retrieved 2009-04-28.
  3. ^
    PMID 19000750
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  4. doi:10.1016/S0723-2020(11)80206-7
    .
  5. PMID 17158986
    .
  6. ^ J.P. Euzéby. "Aquificae". List of Prokaryotic names with Standing in Nomenclature (LPSN). Archived from the original on 2011-06-13. Retrieved 2016-09-09.
  7. PMID 28891789
    .
  8. ^
    S2CID 559778
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  9. PMID 18319474
    .
  10. PMID 23046953. {{cite book}}: |journal= ignored (help
    )
  11. ^ a b 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.
  12. ^ Gupta, RS (2014) The Phylum Aquificae. The Prokaryotes 417-445. Springer Berlin Heidelberg.
  13. ^
    PMID 31905784
    .
  14. ^ Huber, R. and Hannig, M. (2006) Thermotogales. Prokaryotes 7: 899-922.
  15. ^ Klenk, H. P., Meier, T. D., Durovic, P. and others (1999) RNA polymerase of Aquifex pyrophilus: Implications for the evolution of the bacterial rpoBC operon and extremely thermophilic bacteria. J Mol Evol 48: 528-541.
  16. ^ Gupta, R. S. (2000) The phylogeny of Proteobacteria: relationships to other eubacterial phyla and eukaryotes. FEMS Microbiol Rev 24: 367-402.
  17. ^ Ciccarelli, F. D., Doerks, T., von Mering, C., Creevey, C. J., Snel, B., and Bork, P. (2006) Toward automatic reconstruction of a highly resolved tree of life. Science 311: 1283-1287.
  18. ^ Di Giulio, M. (2003) The universal ancestor was a thermophile or a hyperthermophile: Tests and further evidence. J Theor Biol 221: 425-436.
  19. ^ a b c Griffiths, E. and Gupta, R. S. (2004) Signature sequences in diverse proteins provide evidence for the late divergence of the order Aquificales. International Microbiol 7: 41-52.
  20. ^ Meyer, T. E. and Bansal, A. K. (2005) Stabilization against hyperthermal denaturation through increased CG content can explain the discrepancy between whole genome and 16S rRNA analyses. Biochemistry 44: 11458-11465.
  21. ^ Catalogue of Organisms: Standing the Heat
  22. doi:10.1186/1471-2148-8-272
    .
  23. ^ J.P. Euzéby. "Aquificota". List of Prokaryotic names with Standing in Nomenclature (LPSN). Retrieved 2022-09-09.
  24. ^ Sayers; et al. "Aquificae". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2022-09-09.
  25. ^ Ludwig, W.; Euzéby, J. & Whitman W.B. (2008). "Bergey's Taxonomic Outlines: Volume 4 - Draft Taxonomic Outline of the Bacteroidetes, Planctomycetes, Chlamydiae, Spirochaetes, Fibrobacteres, Fusobacteria, Acidobacteria, Verrucomicrobia, Dictyoglomi, and Gemmatimonadetes" (PDF). Bergey's Manual Trust: 15. Archived from the original (PDF) on 2009-04-24. Retrieved 2011-06-27.
  26. ^ "The LTP". Retrieved 20 November 2023.
  27. ^ "LTP_all tree in newick format". Retrieved 20 November 2023.
  28. ^ "LTP_08_2023 Release Notes" (PDF). Retrieved 20 November 2023.
  29. ^ "GTDB release 08-RS214". Genome Taxonomy Database. Retrieved 10 May 2023.
  30. ^ "bac120_r214.sp_label". Genome Taxonomy Database. Retrieved 10 May 2023.
  31. ^ "Taxon History". Genome Taxonomy Database. Retrieved 10 May 2023.
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