Archaea

Overview
The Archaea, or archaebacteria, are a major group of microorganisms. Like bacteria, archaea are single-celled organisms that lack nuclei and are therefore prokaryotes, classified in kingdom Monera in the traditional five-kingdom taxonomy. Although there is still uncertainty in the phylogeny, Archaea, Eukaryota and Bacteria are the fundamental classifications of what is called the three-domain system. Although their prokaryotic features are diagnostic of that clade, archaea are more closely related to eukaryotes than to bacteria. To account for this, archaeans and eukaryotes are grouped together in the clade Neomura, which is thought to have arisen from gram-positive bacteria. Archaea were originally described in extreme environments, but have since been found in all habitats and may contribute up to 20% of total biomass.

A single individual or species from this domain is called an archaeon (sometimes spelled "archeon"), while the adjectival form is archaeal or archaean. The etymology is Greek, from αρχαία meaning "ancient ones".

Habitats


Multiple archaeans are extremophiles, and some would say this is their ecological niche. They can survive high temperatures, often above 100°C, as found in geysers, black smokers, and oil wells. Some are found in very cold habitats and others in highly saline, acidic, or alkaline water. Mesophiles favor milder conditions in marshland, sewage and soil. Many methanogenic archaea are found in the digestive tracts of animals such as ruminants, termites, and humans. As of 2007, no clear examples of archaeal pathogens are known, although a relationship has been proposed between the presence of some methanogens and human periodontal disease.

Archaea are commonly placed into three physiological groups. These are the halophiles, thermophiles and acidophiles. These groups are not necessarily comprehensive or monophyletic, nor even mutually exclusive. Nonetheless, they are a useful starting point for ecological studies. Halophiles, including the genus Halobacterium, live in extremely saline environments and start outnumbering their bacterial counterparts at salinities greater than 20-25%. These can be found in sediments or in the intestines of animals. Thermophiles live in places that have high temperatures, such as hot springs. Where optimal growth occurs at greater than 80°C, the archaeon is a hyperthermophyle, and the highest recorded temperature survived was 121°C. Although thermophilic bacteria predominate at some high temperatures, archaea generally have the edge when acidity exceeds pH 5. True acidophiles withstand pH 0 and below.

Recently, several studies have shown that archaea exist not only in mesophilic and thermophilic environments but are also present, sometimes in high numbers, at low temperatures as well. It is increasingly becoming recognised that methanogens are commonly present in low-temperature environments such as cold sediments. Some studies have even suggested that at these temperatures the pathway by which methanogenesis occurs may change due to the thermodynamic constraints imposed by low temperatures. Perhaps even more significant are the large numbers of archaea found throughout most of the world's oceans, a predominantly cold environment. These archaea, which belong to several deeply branching lineages unrelated to those previously known, can be present in extremely high numbers (up to 40% of the microbial biomass) although almost none have been isolated in pure culture. Currently we have almost no information regarding the physiology of these organisms, meaning that their effects on global biogeochemical cycles remain unknown. One recent study has shown, however, that one group of marine crenarchaeota are capable of nitrification, a trait previously unknown among the archaea.

History of archaean microbiology
Archaea were identified in 1977 by Carl Woese and George E. Fox as being a separate branch 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, which Woese and Fox termed Urkingdoms. 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 compose three Domains of living organisms.

Size and shape
Individual archaeans range from 0.1 μm 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-shape, spiral, lobed, or rectangular. Archaea have no murein in their cell walls. Recently, a species of flat, square archaean that lives in hypersaline pools has been discovered.

Comparison of archaeal, bacterial and eukaryotic cells
Archaea are similar to other prokaryotes in most aspects of cell structure and metabolism. However, their genetic transcription and translation &mdash; the two central processes in molecular biology &mdash; do not show many typical bacterial features, and are in many aspects similar to those of eukaryotes. For instance, archaeal translation uses eukaryotic-like initiation and elongation factors, and their transcription involves TATA Binding Proteins and TFIIB as in eukaryotes. Many archaeal tRNA and rRNA genes harbor unique archaeal introns which are neither like eukaryotic introns, nor like bacterial (type I and type II etc which can "home") introns.

Several other characteristics also set the Archaea apart. Like bacteria and eukaryotes, archaea possess glycerol-based phospholipids. However, three features of the archaeal lipids are unusual:
 * The archaeal lipids are unique because the stereochemistry of the glycerol is the reverse of that found in bacteria and eukaryotes. This is strong evidence for a different biosynthetic pathway.
 * Most bacteria and eukaryotes have membranes composed mainly of glycerol-ester lipids, whereas archaea have membranes composed of glycerol-ether lipids. Even when bacteria have ether-linked lipids, the stereochemistry of the glycerol is the bacterial form. These differences may be an adaptation on the part of Archaea to hyperthermophily. However, it is worth noting that even mesophilic archaea have ether-linked lipids.
 * Archaeal lipids are based upon the isoprenoid sidechain. This is a five-carbon unit that is also common in rubber and as a component of some bacterial and eukaryotic vitamins. However, only the archaea incorporate these compounds into their cellular lipids, frequently as C-20 (four monomers) or C-40 (eight monomers) side-chains. In some archaea, the C-40 isoprenoid side-chain is long enough to span the membrane, forming a monolayer for a cell membrane with glycerol phosphate moieties on both ends. Although dramatic, this adaptation is most common in the extremely thermophilic archaea.

Cell wall and flagella
Although not unique, archaeal cell walls are also unusual. For instance, in most archaea they are formed by surface-layer proteins or an S-layer. S-layers are common in bacteria, where they serve as the sole cell-wall component in some organisms (like the Planctomyces) or an outer layer in many organisms with peptidoglycan. With the exception of one group of methanogens, archaea lack a peptidoglycan wall (and in the case of the exception, the peptidoglycan is very different from the type found in bacteria).

Archaeans also have flagella that are notably different in composition and development from the superficially similar flagella of bacteria. The bacterial flagellum is a modified type III secretion system, while archeal flagella resemble type IV pilli which use a sec dependent secretion system somewhat similar to but different from type II secretion system.

Metabolism
Archaea exhibit a variety of different types of metabolism; there are nitrifiers, methanogens and anaerobic methane oxidisers. Methanogens live in anaerobic environments and produce methane. Of note are the halobacteria, which use light to produce energy. Although no archaea conduct photosynthesis with an electron transport chain, light-activated ion pumps like bacteriorhodopsin and halorhodopsin play a role in generating ion gradients, which are harnessed into adenosine triphosphate (ATP).

Genetics and propagation
Archaea have one circular chromosome although up to 30% of their genetic material may be contained in plasmids, as evidenced by comparisons of GC content. Archaea can reproduce by binary and multiple fission, fragmentation, and budding.

Phylogeny
Archaea are divided into two main groups based on rRNA trees, the Euryarchaeota and Crenarchaeota. Three other groups have been tentatively created for certain environmental samples, the peculiar species Nanoarchaeum equitans, discovered in 2002 by Karl Stetter, and the Archael Richmond Mine Acidophilic Nanoorganisms (ARMAN) groups discovered by Brett Baker, 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. 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 Euryarchaeota 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, as horizontal gene transfer may have occurred. 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.

Single gene sequencing for systematics has led to whole genome sequencing; by January, 2007, 31 archaeal genomes have been completed with 29 partially completed.

Origin and early evolution
The Archaea should not be confused with the geological term Archean eon, also known as the Archeozoic era. This refers to the primordial period of earth history when Archaea and Bacteria were the only cellular organisms living on the planet. Probable fossils of these microbes have been dated to almost 3.5 billion years ago, and the remains of lipids that may be either archaean or eukaryotic have been detected in shales dating from 2.7 billion years ago.

The last common ancestor of Bacteria and Archaea was probably a non-methanogenic thermophile, raising the possibility that lower temperatures are extreme environments in archaeal terms, and organisms that can survive in cooler environments evolved later on.