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Archaea

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Archaea (AmE [ɑɹˈkiə], BrE [ɑːˈkiːə]; from Greek αρχαία, "old ones"; singular Archaeum, Archaean, or Archaeon), also called Archaebacteria (AmE [ɑɹkɪbækˈtɪɹɪə], BrE [ɑːkɪbækˈtɪəɹɪə]), is a major division of living organisms. Although there is still uncertainty in the exact phylogeny of the groups, Archaea, Eukaryota and Bacteria are the fundamental classifications in what is called the three-domain system. Like bacteria, Archaea are single-celled organisms lacking nuclei and are therefore classified as Prokaryota — known as Monera in the five-kingdom taxonomy. They were originally described in extreme environments, but have since been found in all types of habitats.

A single organism from this domain has been called an "archaean." Furthermore, this biologic term is also used as an adjective.

Contents

History

Archaea 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, 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 comprise three Domains of living things.

The biological term, Archaea, should not be confused with the geologic phrase Archean eon, also known as the Archeozoic era. This latter term 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 3.8 billion years ago (3800 mya).

A phylogenetic tree based on rRNA data, showing the separation of bacteria, archaea, and eukaryotes.
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A phylogenetic tree based on rRNA data, showing the separation of bacteria, archaea, and eukaryotes.

Archaea, Bacteria and Eukaryotes

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. Archeal tRNA and rRNA genes harbor unique archeal 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:

Although dramatic, this adaptation is most common in the extremely thermophilic archaea. Although not unique, the archaeal cell walls are also unusual. For instance, the cell walls of most archaea 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. Even in this case, 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. Bacterial flagella 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.

Habitats

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, sea water 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 are known to cause disease.

Archaea are usually placed into three groups based on preferred habitat. These are the halophiles, methanogens, and thermophiles. Halophiles live in extremely saline environments. Methanogens live in anaerobic environments and produce methane. These can be found in sediments or in the intestines of animals. Thermophiles live in places that have high temperatures, such as hot springs. These groups do not necessarily agree with molecular phylogenies, are not necessarily complete, nor are they mutually exclusive. Nonetheless, they are a useful starting point for more detailed studies.

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 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 (Giovannoni and Stingl, 2005). 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 (Könneke et al, 2006) has shown, however, that one group of marine crenarchaeota are capable of nitrification, a trait previously unknown among the archaea.

Form

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. 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.

Evolution and classification

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.

Single gene sequencing for systematics has led to whole genome sequencing; currently 24 archaeal genomes have been completed with 22 partially completed [link].

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