Phylum Nanoarchaeota The Archaea are a major group of prokaryotes. Their classification among living things is difficult because they are similar to bacteria in some respects but similar to eukaryotes in others.
They were identified in 1977 by Carl Woese and George Fox based on their separation from other prokaryotes on 16S rRNA phylogenetic trees. These two groups were originally named the Archaebacteria and Eubacteria, treated as kingdoms or subkingdoms. Woese argued that they represented fundamentally different branches of living things. He later renamed the groups Archaea and Bacteria to emphasize this, and argued that together with Eukarya they comprise three domains of living things.
Archaea are similar to other prokaryotes in most aspects of cell structure and metabolism. However, their genetic transcription and translation - the two central processes in molecular biology - do not show the typical bacterial features, but are extremely similar to those of eukaryotes. For instance, archaean translation uses eukaryotic initiation and elongation factors, and their transcription involves TATA-binding proteins and TFIIB as in eukaryotes.
Several other characteristics also set the Archaea apart. Unlike most bacteria, they have a single cell membrane that lacks a peptidoglycan wall. Further, both bacteria and eukaryotes have membranes composed mainly of glycerol-ester lipids, whereas archaea have membranes composed of glycerol-ether lipids. These differences may be an adaptation on the part of Archaea to hyperthermophily. Archaeans also have flagella that are notably different in composition and development from the superficially similar flagella of bacteria.
Many archaeans are extremophiles. Some live at very high temperatures, often above 100°C, as found in geysers and black smokers. Others are found in very cold habitats or in highly saline, acidic, or alkaline water. However, other archaeans are mesophiles, and have been found in environments like marshland, sewage, and soil. Many methanogenic archaea are found in the digestive tracts of animals such as ruminants, termites, and humans. Archaea are usually harmless to other organisms and none is known to cause disease.
Individual archaeans range from 0.1 to over 15 μm in diameter, and some form aggregates or filaments up to 200 μm in length. They occur in various shapes, such as spherical, rod-shaped, spiral, lobed, or rectangular. They also exhibit a variety of different types of metabolism. Of note, the halobacteria can use light to produce ATP, although no Archaea conduct photosynthesis with an electron transport chain, as occurs in other groups.
Archaea are divided into two main groups based on rRNA trees, the Euryarchaeota and Crenarchaeota. Two other groups have been tentatively created for certain environmental samples and the peculiar species Nanoarchaeum equitans, discovered in 2002 by Karl Stetter, but their affinities are uncertain.
Woese argued that the bacteria, archaea, and eukaryotes each represent a primary line of descent that diverged early on from an ancestral progenote with poorly developed genetic machinery. This hypothesis is reflected in the name Archaea, from the Greek archae or ancient. Later he treated these groups formally as domains, each comprising several kingdoms. This division has become very popular, although the idea of the progenote itself is not generally supported. Some biologists, however, have argued that the archaebacteria and eukaryotes arose from specialized eubacteria.
The relationship between Archaea and Eukarya remains an important problem. Aside from the similarities noted above, many genetic trees group the two together. Some place eukaryotes closer to Eurarchaeota than Crenarchaeota are, although the membrane chemistry suggests otherwise. However, the discovery of archaean-like genes in certain bacteria, such as Thermotoga, makes their relationship difficult to determine. Some have suggested that eukaryotes arose through fusion of an archaean and eubacterium, which became the nucleus and cytoplasm, which accounts for various genetic similarities but runs into difficulties explaining cell structure.