Details for environmental samples

Some major characteristics of the Archaea include absence of peptidoglycan in cell walls and the presence of either-linked lipds and complex RNA polymerases. Despite these unifying properties, Archaea show enormous phenotypic diversity.

The phylogenetic tree of Archaea bifurcates into two major phyla called the Crenarchaeota and the Euryarchaeota. A third phylum, the "Korarchaeota" branches off close to the root. Among cultured representatives, the Crenarchaeota contain mostly hyperthermophilic species including those able to grow at the highest temperatures of all known organisms. Many hyperthermophiles are chemolithotrophic autotrophs; and because their habitats are devoid of photosynthetic life, these organisms are thus the only primary producers in these harsh environments.

Hyperthermophilic crenarchaeotes tend to cluster closely together and occupy short branches on the 16S ribosomal RNA-based tree of life. This suggests that these organisms have "slow evolutionary clocks" and have evolved the least away from the hypothetical universal ancestor of all life. Such organisms should thus be good models for study of early life on Earth.

Euryarchaeota comprise a physiologically diverse group of Archaea, many of which, like crenarchaeotes, inhabit extreme environments of one sort or the other. Groups of euryarchaeotes include the hyperthermophiles Thermococcus and Pyrococcus and the cell wall-less prokaryote Thermoplasma.

The "Korarchaeota" were originally discovered by community sampling of an unusual Yellowstone hot spring (Obsidian Pool), but now they exist in laboratory culture.

Several Archaea are chemoorganotrophic and thus use organic compounds as energy sources for growth. Catabolism of glucose in Archaea proceeds via slight modifications of the Entner-Doudoroff pathway or glycolytic pathway. Oxidation of acetate to CO₂ in Archaea proceeds through the citric acid cycle or some slight variation of this reaction series, or by the acetyl-CoA pathway. Little is known concerning biosynthesis of amino acids and other macromolecular precursors in Archaea, but presumably key monomers are produced from the central biosynthetic intermediates.

Electron transport chains including cytochromes of the a, b, and c types exist in some Archaea. Employing these and other electron carriers, chemoorganotrophic metabolism in most Archaea probably proceeds by introduction of electrons from organic electron donors into an electron transport chain, leading to the reduction of O₂, S⁰, or some other electron acceptor, with concurrent establishment of a proton motive force that drives adenosine triphosphate (ATP) synthesis through membrane-bound ATPases. Chemolithotrophy is also well established in the Archaea, with H₂ being a common electron donnor.

Autotrophy is widespread among Archaea and occurs by several different means. In methanogens, and presumably in most chemolithotrophic hyperthermophiles, CO₂ is incorporated via the acetyl-CoA pathway or some modification thereof. In other hyperthermophiles CO₂ fixation occurs via the reverse citric acid cycle, a reaction series that functions as the autotrophic pathway in the green sulfur bacteria, or via the Calvin cycle, the most widespread autotrophic pathway in Bacteria and eukaryotes. In this connection, genes encoding functional and very thermostable RubisCO enzymes (RubisCO catalyzes the first step in the Calvin cycle) have been characterized from the methanogen Methanocaldococcus jannaschii and from Pyrococcus species, both hyperthermophiles.