Aquificae

Aquificae
Scientific classification
Domain:	Bacteria
Phylum:	Aquificae Reysenbach 2001
Class:	Aquificae Reysenbach 2002
Order:	Aquificales Reysenbach 2002
Families
Thermosulfidibacter Nunoura et al. 2008 Aquificaceae Reysenbach 2002 Aquifex Huber and Stetter 1992 Hydrogenivirga Nakagawa et al. 2004 Hydrogenobacter Kawasumi et al. 1984 Hydrogenobaculum Stöhr et al. 2001 Thermocrinis Huber et al. 1999 Desulfurobacteriaceae L'Haridon et al. 2006 Balnearium Takai et al. 2003 Desulfurobacterium L'Haridon et al. 1998 emend. L'Haridon et al. 2006 Phorcysium Pérez-Rodríguez et al. 2012 Thermovibrio Huber et al. 2002 Hydrogenothermaceae Eder and Huber 2003 Hydrogenothermus Stöhr et al. 2001 Persephonella Götz et al. 2002 Sulfurihydrogenibium Takai et al. 2003 emend. O'Neill et al. 2008 Venenivibrio Hetzer et al. 2008

The Aquificae phylum is a diverse collection of bacteria that live in non-harsh environmental settings.^[1][2] They have been found in spring, pools, and ocean. Members of the genus Aquifex, for example, are productive in water between 105 and 138 °C. They are the dominant members of most terrestrial neutral to spring above 6.4 degrees Celsius. They are autotrophs, and are the primary carbon fixers in these environments. They are true bacteria (domain bacteria) as opposed to the other inhabitants of extreme environments, the Archaea.

Molecular signatures and phylogenetic position

Comparative genomic studies have identified 6 conserved signature indels (CSIs) that are specific for the species from the phylum Aquificae and provide potential molecular markers for this phylum.^[3] Of these 6 CSIs, 3 CSIs consisting of a 2 amino acid insertion, a 5-6 amino acid insertion and a 6 amino acid deletion are found in DNA polymerase I. The other 3 CSIs include a 6 to 7 amino acid insert in the GidA protein, a 52 amino acid insertion in RpoC beta’ subunit, and a 4 amino acid insertion in the EF-Tu proteins. Of these CSIs, the insert in EF-Tu was only found in members of family Aquificaceae. Additionally, a 51 amino acid insertion has been identified in SecA preprotein translocase which is shared by various members of the phylum Aquificae as well as 2 Thermotoga species. The presence of the insertion in the Thermotoga species may be due to a horizontal gene transfer.^[3] 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.^[4][5] However, a close relationship of the Aquificae to Thermotogae and the deep branching of Aquificae is not supported by some phylogenetic studies based upon other gene/protein sequences^[6][7][8][9] and also by conserved signature indels in several highly conserved universal proteins.^[10] The deep branching of Aquificae species in the rRNA gene tree was ascribed to be an artefact resulting from the very high G+C content of their 16S-23S-5S operons.^[10] 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^[11] The inference that the Aquificae species do not constitute a deep branch lineage is also independently strongly supported by conserved signature indels 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.^[10] A specific relationship of the Aquificae to Proteobacteria is supported by a 2 aa conserved signature indel in the protein inorganic pyrophosphatase, which is uniquely found in species from these two phyla.^[10] Cavalier-Smith has also suggested that Aquificae is closely related to Proteobacteria.^[12] In contrast to the above cited analyses that are based on a few indels or on single genes, analyses informational genes, which appeared to be less often transferred to the Aquifex lineage than non-informational genes, most often placed Aquificales close to Thermotogales.^[13] These authors explain the frequently observed grouping of Aquificae with Epsilonproteobacteria as result of frequent horizontal gene transfer due to shared ecological niche.

Along with Thermotogae, members of Aquificae are thermophilic eubacteria.^[2]

Phylogeny

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN) ^[14] and National Center for Biotechnology Information (NCBI)^[15] and the phylogeny is based on 16S rRNA-based LTP release 111 by The All-Species Living Tree Project ^{[16] [17]}

Thermosulfidibacter takaii Nunoura et al. 2008   Desulfurobacteriaceae ?Phorcysia thermohydrogeniphila Pérez-Rodríguez et al. 2012 ?Desulfurobacterium crinifex ♠ Alain et al. 2003 Desulfurobacterium thermolithotrophum L'Haridon et al. 1998 (type sp.) Desulfurobacterium atlanticum L'Haridon et al. 2006 Desulfurobacterium pacificum L'Haridon et al. 2006 Thermovibrio T. ruber Huber et al. 2002 (type sp.) Balnearium lithotrophicum Takai et al. 2003 T. ammonificans Vetriani et al. 2004 T. guaymasensis L'Haridon et al. 2006   Hydrogenothermaceae   Persephonella P. guaymasensis Götz et al. 2002 P. hydrogeniphila Nakagawa et al. 2003 P. marina Götz et al. 2002 (type sp.) Venenivibrio stagnispumantis Hetzer et al. 2008 Hydrogenothermus marinus Stöhr et al. 2001   Sulfurihydrogenibium S. yellowstonense Nakagawa et al. 2005 S. kristjanssonii Flores et al. 2008 S. subterraneum Takai et al. 2003 emend. Nakagawa et al. 2005 (type sp.) S. azorense Aguiar et al. 2004 emend. Nakagawa et al. 2005 S. rodmanii O'Neill et al. 2008   Aquificaceae Hydrogenobaculum acidophilum (Shima and Suzuki 1993) Stöhr et al. 2001   Hydrogenobacter Thermothrix azorensis Odintsova EV et al. (1996) [was Burkholderiaceae] H. subterraneus Takai et al. 2001 H. hydrogenophilus (Kryukov et al. 1984) Stöhr et al. 2001 H. thermophilus Kawasumi et al. 1984 (type sp.) Thermocrinis minervae Huber et al. 1999 Thermocrinis ruber Huber et al. 1999 (type sp.) Thermocrinis albus Eder and Huber 2002   Aquifex A. aeolicus ♠ Huber and Stetter 2001 A. pyrophilus Huber and Stetter 1992 (type sp.)   Hydrogenivirga H. calditorris Nakagawa et al. 2004 (type sp.) H. okinawensis Nunoura et al. 2008

Note:
♠ Strain found at the National Center for Biotechnology Information (NCBI) but not listed in the List of Prokaryotic names with Standing in Nomenclature (LPSN)

References

1. Griffiths E, Gupta RS (January 2006). "Molecular signatures in protein sequences that are characteristics of the phylum Aquificae". Int. J. Syst. Evol. Microbiol. 56 (Pt 1): 99–107. doi:10.1099/ijs.0.63927-0. PMID 16403873.
2. Horiike T, Miyata D, Hamada K; et al. (January 2009). "Phylogenetic construction of 17 bacterial phyla by new method and carefully selected orthologs". Gene 429 (1–2): 59–64. doi:10.1016/j.gene.2008.10.006. PMC 2648810. PMID 19000750.
3. Griffiths, E. and Gupta, R. S. (2006). Molecular signatures in protein sequences that are characteristics of the phylum Aquificae. International Journal of Systematic and Evolutionary Microbiology. 56:99-107. doi:10.1099/ijs.0.63927-0.
4. Huber, R. and Hannig, M. (2006) Thermotogales. Prokaryotes 7: 899-922.
5. 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.
6. 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.
7. Gupta, R. S. (2000) The phylogeny of Proteobacteria: relationships to other eubacterial phyla and eukaryotes. FEMS Microbiol Rev 24: 367-402.
8. 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.
9. Di Giulio, M. (2003) The universal ancestor was a thermophile or a hyperthermophile: Tests and further evidence. J Theor Biol 221: 425-436.
10. 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.
11. 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.
12. Catalogue of Organisms: Standing the Heat
13. 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.
14. J.P. Euzéby. "Aquificae". List of Prokaryotic names with Standing in Nomenclature (LPSN). Retrieved 2013-03-20.
15. Sayers; et al. "Aquificae". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2013-03-20.
16. All-Species Living Tree Project."16S rRNA-based LTP release 111 (full tree)" (PDF). Silva Comprehensive Ribosomal RNA Database. Retrieved 2013-03-20.
17. 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.