The Aquificae phylum is a diverse collection of bacteria that live in harsh environmental settings. They have been found in hot springs, sulfur pools, and thermal ocean vents. 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 alkaline hot springs above 56.4 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. 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 inseret 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. 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. However, a close relationship of the Aquificae to Thermotogae and the deep branching of Aquificae is not supported by phylogenetic studies based upon other gene/protein sequences and also by conserved signature indels in several highly conserved universal proteins. The deep branching of Aquificae species in the rRNA gene tree appears to be an artefact resulting from the very high G+C content of their 16S-23S-5S operons. 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 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. A specific relationship of the Aquificae to Proteobacteria is supported by a 2 aa conserved signature indelin the protein inorganic pyrophosphatase, which is uniquely found in species from these two phyla. Cavalier-Smith has also suggested that Aquificae is closely related to Proteobacteria.
The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN)  and National Center for Biotechnology Information (NCBI) and the phylogeny is based on 16S rRNA-based LTP release 111 by The All-Species Living Tree Project  
♠ Strain found at the National Center for Biotechnology Information (NCBI) but not listed in the List of Prokaryotic names with Standing in Nomenclature (LPSN)
- 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.
- 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. Cite error: Invalid
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- 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.
- Huber, R. and Hannig, M. (2006) Thermotogales. Prokaryotes 7: 899-922.
- 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.
- 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.
- Gupta, R. S. (2000) The phylogeny of Proteobacteria: relationships to other eubacterial phyla and eukaryotes. FEMS Microbiol Rev 24: 367-402.
- 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.
- Di Giulio, M. (2003) The universal ancestor was a thermophile or a hyperthermophile: Tests and further evidence. J Theor Biol 221: 425-436.
- 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.
- 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.
- Catalogue of Organisms: Standing the Heat
- J.P. Euzéby. "Aquificae". List of Prokaryotic names with Standing in Nomenclature (LPSN) . Retrieved 2013-03-20.
- Sayers; et al. "Aquificae". National Center for Biotechnology Information (NCBI) taxonomy database . Retrieved 2013-03-20.
- All-Species Living Tree Project."16S rRNA-based LTP release 111 (full tree)" (PDF). Silva Comprehensive Ribosomal RNA Database . Retrieved 2013-03-20.
- 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.