Aquificales

Desulfurobacterium thermolithotrophum, copyright HZI/Manfred Rohde.

Belongs within: Gracilicutes.

Standing the heat
Published 26 March 2008
Aquifex aeolicus, from here.

The Aquificae are a smallish group of thermophilic to hyperthermophilic bacteria whose main claim to fame is that ribosomal DNA phylogenies suggest that it is the earliest-diverging branch of the Eubacteria, making them a key player in the theory that life as a whole may be descended from a thermophilic ancestor. The type genus of the Aquificae, Aquifex, was only formally described in 1992, but the numbers have swelled since then to about fifteen genera divided between three families. Because their thermophilic habits make them difficult to culture, the diversity of Aquificae is almost certainly underestimated. Environmental molecular analyses, for instance, indicate that near neutral pH terrestrial thermal springs may be dominated by Aquificae, while examples of Aquificae have been isolated from deep-sea, shallow marine and terrestrial hydrothermal systems, subsurface mines, and even heated compost (Aguiar et al. 2004). Aquificae found in thermal springs form extensive microbial mats stained black or yellow by iron or sulphur mineral deposits, leading to their being referred to as “black filaments” or “sulphur-turf”.

Aquificae are all chemolithoautotrophs—that is, they produce their own energy directly from the reaction of inorganic sources. This is acheived through the oxidation of molecular hydrogen, which is a major component of emissions from deep-sea hydrothermal vents. Aquifex reacts hydrogen and oxygen to produce water, while other species of Aquificae use such substrates as elemental sulphur or nitrates as electron acceptors. Hydrogen oxidation is a common metabolic process in archaebacteria, but is unusual in eubacteria—the only hydrogen-oxidising eubacteria other than Aquificae belong to the ε-proteobacteria. Aquificae may be anaerobes or microaerophiles.

Microbial filaments containing Aquifex growing in water at 83°C (from MicrobeWiki).

Phylogenetically, Aquificae are something of a puzzle. As already noted, the ribosomal DNA phylogenies place the Aquificae basal to all other eubacterial groups. However, it has been fairly conclusively shown that the eukaryote section of the rDNA tree is quite severely compromised by long-branch attraction, and it is quite possible that the bacterial section of the tree suffers the same problem. In the case of the Aquificae, there is evidence that they may not be as basal as they appear.

Bacteria can be divided into two major groups, the Gram-positive and Gram-negative bacteria. While this originally referred only to the ability of the bacterium to be stained with Gram’s iodine and crystal violet, the results actually reflect a far more fundamental distinction between the two groups. Gram-positive bacteria have a single cell membrane surrounded by a thick cell wall. Gram-negative bacteria, on the other hand, have a thinner cell wall with a second membrane overlying it. Many molecular phylogenetic trees also show a sort of rough division between the two groups, with Gram-positive bacteria tending to sit closer than Gram-negative bacteria to the archaebacteria and eukaryotes, which like Gram-positive bacteria have a single cell membrane. Gupta (1998) formalised this distinction by dividing prokaryotes between the Monodermata (Gram-positive bacteria and archaebacteria) and Didermata (Gram-negative bacteria), suggesting only a single loss or gain (depending on where exactly the root of the tree of life sits) of the second cell membrane.

Aquificae, however, are Gram-negative, complete with second cell membrane. If their position on the ribosomal DNA trees is accurate, this would require either that the outer membrane was gained or lost multiple times. If the membrane gain or loss was a unque event, then Aquificae must be closer to the other Gram-negative bacteria. Cavalier-Smith (2002) placed Aquificae in a position within or near the Epsilonproteobacteria, as suggested by RNA polymerase and a few other molecular phylogenies. As already mentioned, it is notable that ε-proteobacteria include the only other hydrogen-oxidising eubacteria (Takai et al. 2003). Insertions in the alanyl-tRNA synthetase and RNA polymerase β genes also support a position for Aquificae among the other Gram-negative bacteria, possibly close to the Proteobacteria. It seems possible (though it must be stressed that it is far from well-established) that the rDNA tree has been compromised by long-branch attraction, probably due to the high G+C content of the Aquificae genome, which is itself believed to be an adaptation to a thermophilic lifestyle.

Systematics of Aquificales
<==Aquificales [Aquificota]LR06
    |--Desulfurobacteriaceae [Desulfurobacteriales, Desulfurobacteriia]TN03
    |    |--Balnearium Takai, Nakagawa et al. 2003TN03
    |    |    `--*B. lithotrophicum Takai, Nakagawa et al. 2003TN03
    |    `--+--ThermovibrioTN03
    |       |    |--T. ammonificansCD21
    |       |    |--T. guaymasensis L’Haridon, Reysenbach et al. 2006LR06
    |       |    `--T. ruberTN03
    |       `--Desulfurobacterium L’Haridon, Cilia et al. 1998VP TN03, R01
    |            |--+--*D. thermolithotrophum L’Haridon, Cilia et al. 1998VP R01, LR06, R01
    |            |  `--D. crinifexLR06
    |            `--+--D. atlanticum L’Haridon, Reysenbach et al. 2006LR06
    |               `--D. pacificum L’Haridon, Reysenbach et al. 2006LR06
    `--AquificaeCD21
         |--Hydrogenothermaceae [Hydrogenothermales]TN03
         |    |--PersephonellaABR04
         |    |    |--P. marinaABR04
         |    |    `--+--P. guaymasensisABR04
         |    |       `--P. hydrogeniphilaTN03
         |    `--+--Hydrogenothermus marinusABR04
         |       `--SulfurihydrogenibiumABR04
         |            |--S. azorense Aguiar, Beveridge & Reysenbach 2004ABR04
         |            `--S. subterraneumABR04
         `--AquificaceaeTN03
              |  i. s.: HydrogenivirgaLR06
              |--Hydrogenobaculum acidophilumTN03
              `--+--Aquifex Huber & Stetter 1992VP R01
                 |    `--*A. pyrophilus Huber & Stetter 1992VP R01
                 `--+--Thermocrinis Huber, Eder et al. 1999VP R01
                    |    |--*T. ruber Huber, Eder et al. 1999VP R01
                    |    `--T. minervaeCD21
                    `--+--Calderobacterium Kryukov, Savel’eva & Pusheva 1984VP R01
                       |    `--*C. hydrogenophilum Kryukov, Savel’eva & Pusheva 1984VP R01
                       `--Hydrogenobacter Kawasumi, Igarashi et al. 1984VP R01
                            |--*H. thermophilus Kawasumi, Igarashi et al. 1984VP R01
                            `--H. acidophilus Shima & Suzuki 1993VP R01
Nomina invalida: Aquifex aeolicusR01
                 Hydrogenobacter halophilus Nishihara, Igarashi & Kodama 1990R01
                 Hydrogenobacter subterraneus Takai et al. 2001JC08

*Type species of generic name indicated

References

[ABR04] Aguiar, P., T. J. Beveridge & A.-L. Reysenbach. 2004. Sulfurihydrogenibium azorense, sp. nov., a thermophilic hydrogen-oxidizing microaerophile from terrestrial hot springs in the Azores. International Journal of Systematic and Evolutionary Microbiology 54: 33–39.

Cavalier-Smith, T. 2002. The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification. International Journal of Systematic and Evolutionary Microbiology 52: 7–76.

[CD21] Coleman, G. A., A. A. Davín, T. A. Mahendrarajah, L. L. Szánthó, A. Spang, P. Hugenholtz, G. J. Szöllősi & T. A. Williams. 2021. A rooted phylogeny resolves early bacterial evolution. Science 372: 588.

Gupta, R. S. 1998. Life’s third domain (Archaea): an established fact or an endangered paradigm? A new proposal for classification of organisms based on protein sequences and cell structure. Theoretical Population Biology 54 (2): 91–104.

[JC08] Judicial Commission of the International Committee on Systematics of Prokaryotes. 2008. Status of strains that contravene Rules 27 (3) and 30 of the International Code of Nomenclature of Bacteria. Opinion 81. International Journal of Systematic and Evolutionary Microbiology 58: 1755–1763.

[LR06] L’Haridon, S., A.-L. Reysenbach, B. J. Tindall, P. Schönheit, A. Banta, U. Johnsen, P. Schumann, A. Gambacorta, E. Stackebrandt & C. Jeanthon. 2006. 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. International Journal of Systematic and Evolutionary Microbiology 56 (12): 2843–2852.

[R01] Reysenbach, A. L. 2001. Phylum BI. Aquificae phy. nov. In: Boone, D. R., R. W. Castenholz & G. M. Garrity (eds) Bergey’s Manual of Systematic Bacteriology 2nd ed. vol. 1. The Archaea and the Deeply Branching and Phototrophic Bacteria pp. 359–367. Springer.

[TN03] Takai, K., S. Nakagawa, Y. Sako & K. Horikoshi. 2003. Balnearium lithotrophicum gen. nov., sp. nov., a novel thermophilic, slightly anaerobic, hydrogen-oxidizing chemolithoautotroph isolated from a black smoker chimney in the Suiyo Seamount hydrothermal system. International Journal of Systematic and Evolutionary Microbiology 53: 1947–1954.

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