Classification of the Archaea

According to the second edition of Bergey, the Archaea are divided into two phyla, the Euryarchaeota and Crenarchaeota. A third phylum, the Korarchaeota has been

Figure 7.3 Membrane lipids in Archaea and Bacteria. Compositional differences in membrane lipids between (a) Bacteria and (b) Archaea. Note the ether linkages and branched fatty acids in (b)

proposed, whose members are known only from molecular studies, while the recent discovery of Nanoarchaeum equitans has led to the proposal of yet another archaean phylum (see Box 7.1). Countless more species of archaea are thought to exist, which like the Korarchaeota, have not yet been successfully cultured in the laboratory.

Box 7.1 A new phylum?

In 2002 a novel microorganism, Nanoarchaeum equitans was isolated from a hydrothermal vent deep below the sea off the Icelandic coast. Found at temperatures around boiling point, its tiny spherical cells were attached to the surface of another archaean, Ignicoccus sp., without which it cannot apparently be cultured. Ribosomal RNA studies showed N. equitans to be sufficiently unlike other members of the Archaea to justify the creation of a new archaean phylum, the Nanoar-chaeota. Now fully sequenced, the genome of N. equitans is one of the smallest living things to date (490kb). It appears to belong to a very deeply rooted branch of the Archaea, leading to speculation that it may resemble the first living cells. At 0.4 ¡m in diameter, n. equitans is also among the smallest known living organisms. Although at present it is the only recognised species of the Nanarchaeota, it seems likely to be joined by isolates reported from other locations around the world.

The phylum Eurychaeota is a bigger group than the Crenarchaeota, and includes halophilic and methanogenic forms. The former are aerobic heterotrophs, requiring a chloride concentration of at least 1.5 m (generally 2.0-4.0 m) for growth. One species, Halobacterium salinarum, is able to carry out a unique form of photosynthesis using the bacterial pigment bacteriorhodopsin, and uses the ATP so generated for the active transport into the cell of the chloride ions it requires.

Members of the Euryarchaeota such as Methanococcus and Methanobacterium are unique among all life forms in their ability to generate methane from simple carbon compounds. They are strict anaerobes found in environments such as hot springs, marshes and the gut of ruminant mammals. The methane is derived from the metabolism of various simple carbon compounds such as carbon dioxide or methanol in reactions linked to the production of ATP. e.g.

In addition, a few species can cleave acetate to produce methane:

This acetotrophic reaction is responsible for the much of the methane production in sewage sludges. Although sharing the unique facility to generate methane, some of the methanogenic genera are quite distantly related to one another.

Other representatives of the Eurychaeota include the Thermoplasmata and the Thermococci. Thermo-plasmata are highly acidophilic and moderately ther-mophilic; they completely lack a cell wall, and are pleomorphic. A unique membrane lipid composition allows them to withstand temperatures of well over 50 °C. Thermococci are anaerobic extreme thermophiles found in anoxic thermal waters at temperatures as high as 95 °C. Enzymes isolated from thermococci have found a variety of applications. A thermostable DNA polymerase from Pyrococcus furiosus is used as an alternative to Taq polymerase (see Phylum 'Deinococcus-Thermus' later in this chapter) in the polymerase chain reaction (PCR).

Representative genera: Methanobacterium, Halobacterium

Members of the Crenarchaeota are nearly all extreme thermophiles, many of them capable of growth at temperatures in excess of 100 °C, including Pyrolobus fumarii, which has an optimum growth temperature of 106 °C, and can survive autoclaving at 121 °C.

Many utilise inorganic sulphur compounds as either a source or acceptor of electrons (respectively, oxidation to H2SO4 or reduction to H2S).

Crenarchaeotes are mostly anaerobic, and are thought by many to resemble the common ancestors of all bacteria.

Representative genera: Thermoproteus, Sulfolobus

Pleomorphic means lacking a regular shape.

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