Biology:Aquificae

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Short description: Phylum of bacteria

Aquificae
Scientific classification
Domain:
Bacteria
Phylum:
Aquificae

Reysenbach 2002 emend. Gupta & Lali 2014
Class
  • "Aquificia"
  • "Desulfurobacteriia"
  • "Thermosulfidibacteria"
Synonyms
  • Aquificaeota Oren et al. 2015
  • "Aquificota" Whitman et al. 2018

The Aquificae phylum is a diverse collection of bacteria that live in harsh environmental settings.[1][2] The name 'Aquificae' was given to this phylum based on an early genus identified within this group, Aquifex (“water maker”), which is able to produce water by oxidizing hydrogen.[3] They have been found in springs, pools, and oceans. They are autotrophs, and are the primary carbon fixers in their environments. These bacteria are Gram-negative, non-spore-forming rods.[4] They are true bacteria (domain Bacteria) as opposed to the other inhabitants of extreme environments, the Archaea.

Taxonomy

The Aquificae currently contain 15 genera and 42 validly published species.[5] The phylum comprises a single class and two orders.[6][7] Aquificales consists of the families Aquificaceae and Hydrogenothermaceae, while the Desulfurobacteriaceae are the only family within the Desulfobacteriales. Thermosulfidibacter takaii is not assigned to a family within the phylum based on its phylogenetic distinctness from both orders.[8] 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 Aquificae and provide potential molecular markers.[7] 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 Aquificae and Hydrogenothermaceae from all other bacteria.[7] In parallel with the observed CSI distribution, the orders within the Aquificae 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.[9][10][11]

Several CSIs have also been identified that are specific for the species from the Aquificae and provide potential molecular markers for this phylum.[1] Additionally, a 51-amino-acid insertion has been identified in SecA preprotein translocase which is shared by all members of the Aquificae, as well as all members of the order Thermotogales.[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 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.[12]

In the 16S rRNA gene trees, the Aquificae species branch in the proximity of the phylum Thermotogae (another phylum comprising hyperthermophilic organisms) close to the archaeal-bacterial branch point.[13][10] However, a close relationship of the Aquificae to the Thermotogae and the deep branching of the Aquificae is not supported by some phylogenetic studies based upon other gene/protein sequences[14][15][16][17] and also by CSIs in several highly conserved universal proteins 16S-23S-5S operons.[18] In contrast to the very high G+C content of their rRNAs (i.e. more than 62%), which is required for stability of their secondary structures at high growth temperatures,[19] the inference that the Aquificae do not constitute a deep-branch lineage is also independently strongly supported by CSIs in a number of important proteins (viz. Hsp70, Hsp60, RpoB, RpoB and AlaRS), which support its placement in the proximity of the phylum Proteobacteria, particularly the Epsilonproteobacteria.[18] A specific relationship of the Aquificae to the Proteobacteria is supported by a two-amino-acid CSI in the protein inorganic pyrophosphatase, which is uniquely found in species from these two phyla.[18] Cavalier-Smith has also suggested that the Aquificae are closely related to the Proteobacteria.[20] 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.[21] These authors explain the frequently observed grouping of Aquificae with Epsilonproteobacteria as result of frequent horizontal gene transfer due to shared ecological niches.

Along with the Thermotogae, the Aquificae are thermophilic eubacteria.[2]

Phylogeny

Phylogeny is based on 16S rRNA-based LTP release 132 by The All-Species Living Tree Project[22][23]

 
"Thermosulfidibacteraceae"

Thermosulfidibacter takaii

 
 
Desulfurobacteriales

Desulfurobacteriaceae

 
"Aquificia"
"Hydrogenothermales"

Hydrogenothermaceae

 
Aquificales
"Hydrogenobaculaceae"

Hydrogenobaculum acidophilum

 
 

Aquificaceae

 
 
 
 
 

Taxonomy

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LSPN),[24] the National Center for Biotechnology Information (NCBI)[25] and the GTDB 05-RS95 (Genome Taxonomy Database).[26][27]

  • Class "Thermosulfidibacteria" Cavalier-Smith 2020
    • Order "Thermosulfidibacterales" Cavalier-Smith 2020
      • Family "Thermosulfidibacteraceae" Cavalier-Smith 2020
  • Class "Desulfurobacteriia"
    • Order Desulfurobacteriales Gupta & Lali 2014
  • Class "Aquificia" Cavalier-Smith 2020
    • Order "Hydrogenothermales"
    • Order Aquificales Reysenbach 2002 em. Gupta & Lali 2013
      • Family "Hydrogenobaculaceae"
      • Family Aquificaceae Reysenbach 2002 em. Gupta & Lali 2013

References

  1. ↑ 1.0 1.1 "Molecular signatures in protein sequences that are characteristics of the phylum Aquificae". Int. J. Syst. Evol. Microbiol. 56 (Pt 1): 99–107. January 2006. doi:10.1099/ijs.0.63927-0. PMID 16403873. http://ijs.sgmjournals.org/cgi/pmidlookup?view=long&pmid=16403873. 
  2. ↑ 2.0 2.1 "Phylogenetic construction of 17 bacterial phyla by new method and carefully selected orthologs". Gene 429 (1–2): 59–64. January 2009. doi:10.1016/j.gene.2008.10.006. PMID 19000750. 
  3. ↑ "Aquifex pyrophilus gen. nov. sp. nov., Represents a Novel Group of Marine Hyperthermophilic Hydrogen-Oxidizing Bacteria". Syst. Appl. Microbiol. 15 (3): 340–351. 1992. doi:10.1016/S0723-2020(11)80206-7. 
  4. ↑ "Desulfurobacterium atlanticum sp. nov., Desulfurobacterium pacificum sp. nov. and Thermovibrio guaymasensis sp. nov., three thermophilic members of the Desulfurobacteriaceae fam. nov., a deep branching lineage within the bacteria". Int. J. Syst. Evol. Microbiol. 56 (Pt 12): 2843–2852. December 2006. doi:10.1099/ijs.0.63994-0. PMID 17158986. 
  5. ↑ J.P. Euzéby. "Aquificae". List of Prokaryotic names with Standing in Nomenclature (LPSN). http://www.bacterio.cict.fr/classifphyla.html#Aquificae. 
  6. ↑ "List of new names and new combinations previously effectively, but not validly, published". Int. J. Syst. Evol. Microbiol. 65 (7): 2017–2025. 2015. doi:10.1099/ijs.0.000317. PMID 28891789. 
  7. ↑ 7.0 7.1 7.2 "Molecular signatures for the phylum Aquificae and its different clades: proposal for division of the phylum Aquificae into the emended order Aquificales, containing the families Aquificaceae and Hydrogenothermaceae, and a new order Desulfurobacteriales ord. nov., containing the family Desulfurobacteriaceae". Antonie van Leeuwenhoek 104 (3): 349–368. September 2013. doi:10.1007/s10482-013-9957-6. PMID 23812969. 
  8. ↑ "Thermosulfidibacter takaii gen. nov., sp. nov., a thermophilic, hydrogen-oxidizing, sulfur-reducing chemolithoautotroph isolated from a deep-sea hydrothermal field in the Southern Okinawa Trough". Int. J. Syst. Evol. Microbiol. 58 (Pt 3): 659–665. March 2008. doi:10.1099/ijs.0.65349-0. PMID 18319474. 
  9. ↑ The hyperthermophilic bacterium Aquifex aeolicus: from respiratory pathways to extremely resistant enzymes and biotechnological applications. Advances in Microbial Physiology. 61. 2012. 125–194. doi:10.1016/B978-0-12-394423-8.00004-4. ISBN 9780123944238. 
  10. ↑ 10.0 10.1 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.
  11. ↑ Gupta, RS (2014) The Phylum Aquificae. The Prokaryotes 417-445. Springer Berlin Heidelberg.
  12. ↑ 12.0 12.1 12.2 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. http://dx.doi.org/10.3390/microorganisms8010059. 
  13. ↑ Huber, R. and Hannig, M. (2006) Thermotogales. Prokaryotes 7: 899-922.
  14. ↑ 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.
  15. ↑ Gupta, R. S. (2000) The phylogeny of Proteobacteria: relationships to other eubacterial phyla and eukaryotes. FEMS Microbiol Rev 24: 367-402.
  16. ↑ 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.
  17. ↑ Di Giulio, M. (2003) The universal ancestor was a thermophile or a hyperthermophile: Tests and further evidence. J Theor Biol 221: 425-436.
  18. ↑ 18.0 18.1 18.2 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.
  19. ↑ 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.
  20. ↑ Catalogue of Organisms: Standing the Heat
  21. ↑ Boussau B, Guéguen L, Gouy M. Accounting for horizontal gene transfers explains conflicting hypotheses regarding the position of Aquificales in the phylogeny of Bacteria. BMC Evol Biol. 2008 Oct 3;8:272. doi:10.1186/1471-2148-8-272.
  22. ↑ All-Species Living Tree Project."16S rRNA-based LTP release 132". Silva Comprehensive Ribosomal RNA Database. https://itol.embl.de/tree/37201229170412631528207598. Retrieved 2015-08-20. 
  23. ↑ 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". Bergey's Manual Trust: 15. http://bergeys.org/outlines/Bergeys_Vol_4_Outline.pdf. Retrieved 2011-06-27. 
  24. ↑ "Aquificae". List of Prokaryotic names with Standing in Nomenclature (LPSN). https://lpsn.dsmz.de/class/aquificae. 
  25. ↑ Sayers. "Aquificae". National Center for Biotechnology Information (NCBI) taxonomy database. https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=200783&lvl=3&srchmode=1&keep=1&unlock. 
  26. ↑ "GTDB release 05-RS95". https://gtdb.ecogenomic.org/about#4%7C. 
  27. ↑ Parks, DH; Chuvochina, M; Chaumeil, PA; Rinke, C; Mussig, AJ; Hugenholtz, P (September 2020). "A complete domain-to-species taxonomy for Bacteria and Archaea.". Nature Biotechnology 38 (9): 1079–1086. doi:10.1038/s41587-020-0501-8. PMID 32341564. https://www.researchgate.net/publication/340954053. 

Wikidata ☰ Q597831 entry




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