Phylum Aquificae (Aquifex and relatives)

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  • Phylum Aquificae
    • Class Aquificae
      • Order Aquificales
        • Family Aquificaceae
          • Genus Aquifex
          • Genus Calderobacterium
          • Genus Hydrogenivirga
          • Genus Hydrogenobaculum
          • Genus Hydrogenobacter
          • Genus Hydrogenothermus
          • Genus Persephonella
          • Genus Sulfurihydrogenibium
          • Genus Thermocrinus
          • Genus Venenivibrio
      • Incertae sedis
          • Genus Balnearium
          • Genus Desulfurobacterium
          • Genus Thermovibrio

General characteristics of the Aquificae


Less than 2 dozen species have been described in this group, only one or a few species in each genus, and they are relatively homogenous in phenotype, especially among the Aquificales (the genera that are currently incertae sedis are more phenotypically distinct).


These organisms are all thermophilic or extremely thermophilic, and obtain energy by respirative hydrogen oxidation. This reaction is known as the “Knallgas” reaction. They are obligate aerobes, generally microaerophilic (the solubility of oxygen in water at the temperatures these organisms grow at is very low in any case). Reduced sulfur compounds such as sulfide, thiosulfate (S2O32-), or elemental sulfur can generally replace hydrogen, but nitrate cannot replace oxygen as the terminal electron acceptor in most species. These organisms are autotrophic, fixing carbon dioxide via the reverse TCA cycle. Few have been grown heterotrophically; they are generally considered to be obligate autotrophs.


These organisms are rod-shaped (ca. 0.5 x 2-8μm) to filamentous, with a typical Gram-negative type envelop, some with an external crystalline protein “S-layer”. Some are motile and flagellated, but other appendages have not been seen. During growth on sulfide or thiosulfate, elemental sulfur granules can appear, but no storage granules or internal membranous structures been observed. Some produce carotenoid pigments.


These organisms are common inhabitants of near-neutral pH, high temperature geothermal springs, including hot springs and submarine vents.

Example species

Aquifex pyrophilus

Aquifex pyrophilus
Aquifex pyrophilus : K. Stetter and R. Rachel, University of Regensburg

A. pyrophilus is, like the other members of this group, a thermophilic hydrogen oxidizer. A. pyrophilus is an extreme thermophile, growing optimally at 85°C and maximally at 95°C. This makes it the most extremely thermophilic isolated and characterized bacterium. It is unusual amongst its relatives in that it can use nitrate as a terminal electron acceptor, and so can grow anaerobically. It is also more sensitive to oxygen than most members of this group, and when grown without nitrate is an obligate microaerophile.

A. pyrophilus was isolated in 1992 from a deep sea hydrothermal vent on the Kolbeinsey Ridge North of Iceland (which is an outcropping of the Mid-atlantic ridge, where the two large plates underlying the ever-enlarging Atlantic Ocean come together, or more properly are coming apart).

The phylum is named after this organism because it was the first of its members to be characterized phylogenetically and discovered to represent a distinct, deeply-branching and primitive branch of the Bacteria. It was only later discovered that previously isolated species (Hydrogenobacter and Calderobacterium) were related to A. pyrophilus.

Thermocrinis ruber

Thermocrinus ruber
Thermocrinus ruber : Huber, R., et al. 1998 Appl. Env. Microbiol. 64:3576-3583

T. ruber is also a thermophilic hydrogen oxidizer, growing optimally at 80°C but up to 89°C. Grows either as individual rod-shaped cells (0.5 x 1-3μm) that are motile by monopolar polytrichous flagella (multiple flagella at one end of the cell only), or as filaments. T. ruber can grow heterotrophically using formate or formamide, as well as autotrophically using hydrogen and reduced sulfur compounds, as electron donors, but cannot replace oxygen with nitrate as an alternative electron acceptor, and so it is an obligate microaerophile.

Octopus Spring
Octopus Spring, Yellowstone National Park : James W. Brown

T. ruber was isolated from pink filamentous growth in Octopus Spring, Yellowstone National Park. This pink filamentous growth is common in the 80-90°C temperature zones of neutral to slightly alkaline hot springs throughout the park, and has been described since the early work of Thomas Brock in the 1960’s. Numerous attempts to cultivate the pink filamentous organism failed, although Thermus aquaticus (the source of Taq polymerase, that made PCR amplification a reasonable technology) was isolated as a by-product of these attempts.

Ultimately, of course, T. ruber was isolated from the pink filaments of Octopus Spring, using insight gained by molecular phylogenetic analysis of the organism prior to cultivation. This story is described in detail later in the semester.