Archaea: Difference between revisions

Archaea; Temporal range: Paleoarchean - Recent
	Halobacteria sp. strain NRC-1, each cell about 5 μm in length.
Scientific classification
Superdomain:	Neomura
Domain:	Archaea; Woese, Kandler & Wheelis, 1990
Phyla
	Crenarchaeota; Euryarchaeota; Korarchaeota; Nanoarchaeota;

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The Archaea [ɑrˈkiə]^ⓘ are a group of single-celled microorganisms. The word archaea comes from the Ancient Greek ἀρχαῖα, meaning "ancient things". A single individual or species from this domain is called an archaeon (sometimes spelled "archeon"). Archaea, like bacteria, are prokaryotes and have no cell nucleus or any other organelles within their cells. As a result, they were viewed initially as an unusual group of bacteria and named archaebacteria. It is now known that archaea have an independent evolutionary history and show many differences in their biochemistry from other forms of life, so they are classified as a separate domain in the three-domain system. In this system, which was introduced by Carl Woese in 1977, Archaea, Eukaryota and Bacteria are the three main branches of evolutionary descent. Classifying the Archaea is still difficult, since the vast majority of these organisms have never been studied in the laboratory and have only been detected by analysis of their nucleic acids in samples from the environment.

Generally, archaea and bacteria are quite similar in size and shape, although a few archaea have unusual shapes, such as the flat and square-shaped cells of Haloquadra walsbyi. Despite this visual similarity to bacteria, archaea possess genes and several metabolic pathways that are more closely related to those of eukaryotes. Other aspects of archaean biochemistry are unique, such as their reliance on ether lipids in their cell membranes. The archaea also exploit a much greater variety of sources of energy than eukaryotes: ranging from familiar organic compounds such as sugars, to using ammonia, metal ions or even hydrogen gas as nutrients. Salt-tolerant archaea (the Halobacteria) use sunlight as a source of energy, whereas other species of archaea fix carbon; however, unlike plants and cyanobacteria, no species of archaea is known that can do both.

Initially, archaea were seen as extremophiles that lived in harsh environments, such as hot springs and salt lakes, but they have since been found in a broad range of habitats, such as soils, oceans and marshlands. Archaea are particularly numerous in the oceans, and the archaea in plankton may be one of the most abundant groups of organisms on the planet. These prokaryotes are now recognized as a major part of life on Earth and may play an important role in both the carbon cycle and nitrogen cycle. No clear examples of archaeal pathogens or parasites are known, but they are often mutualists or commensals. One example are the methanogenic archaea that inhabit the gut of humans and ruminants, where they are present in vast numbers and aid in the digestion of food.

Discovery

Early in the 20th century, prokaryotes were regarded as a single group of organisms and classified based on their biochemistry, morphology and metabolism. For example, microbiologists tried to classify microorganisms based on the structures of their cell walls, their shapes, and the substances they consume.^[1] However, a new approach was proposed in 1965,^[2] using the sequences of the genes in these organisms to work out which prokaryotes are genuinely related to each other. This powerful approach, known as phylogenetics, is the main method used today.

Archaea were identified as a separate group of prokaryotes in 1977 by Carl Woese and George E. Fox in phylogenetic trees based on the sequences of ribosomal RNA (rRNA) genes.^[3] These two groups were originally named the Archaebacteria and Eubacteria and treated as kingdoms or subkingdoms, which Woese and Fox termed Urkingdoms. Woese argued that this group of prokaryotes is a fundamentally different sort of life. He later renamed the two groups of prokaryotes Archaea and Bacteria to emphasize this, and argued that together with Eukarya they are three domains of living organisms.^[4]

At first, only the methanogens were placed in this new domain, and the archaea were seen as extremophiles that exist only in habitats such as hot springs and salt lakes. By the end of the 20th century, microbiologists realized that the archaea are a large and diverse group of organisms that are widely distributed in nature and are common in much less extreme habitats, such as soils and oceans.^[5] This new appreciation of the importance and ubiquity of archaea came mostly from the use of molecular biology techniques to detect prokaryotes in samples of water or soil from their nucleic acids alone. Such techniques eliminate the need to culture organisms in the laboratory, which is often difficult.^[6]^[7]

Morphology

Individual archaeans range from 0.1 micrometers (μm) to over 15 μm in diameter, and occur in various shapes, commonly as spheres, rods, spirals or plates.^[8] Other morphologies in the Crenarchaeota include irregularly-shaped lobed cells in Sulfolobus, thin needle-like filaments that are less than half a micrometer in diameter in Thermofilum, and almost perfectly rectangular rods in Thermoproteus and Pyrobaculum.^[9] There is even a species of flat, square archaea called Haloquadra walsbyi that lives in hypersaline pools.^[10] These unusual shapes are probably maintained both by their cell walls and a prokaryotic cytoskeleton. Proteins related to the cytoskeleton components of other organisms exist in the archaea,^[11] and filaments are formed within their cells,^[12] but in contrast to bacteria, these cellular structures are poorly understood in archaea.^[13]

Some species of archaea form aggregates or filaments of cells up to 200 μm in length,^[8] and these organisms can be prominent members of the communities of microbes that make up biofilms.^[14] An extreme example is Thermococcus coalescens, as aggregates of these cells fuse together in culture, forming single giant cells.^[15] A particularly elaborate form of multicellular colony is produced by archaea in the genus Pyrodictium. Here, the cells produce arrays of long, thin hollow tubes called cannulae that stick out from the cells' surfaces and connect them together into a dense bush-like colony.^[16] The function of these cannulae is not known, but they may allow the cells to communicate or exchange nutrients with their neighbors.^[17] Colonies can also be produced by an association between different species. For example, in the "string-of-pearls" community that was discovered in 2001 in a German swamp, round whitish colonies of a novel species of archaea in the phylum Euryarchaeota are spaced along thin filaments that can be up to 15 centimetres (5.9 in) long; these filaments are made of a particular species of bacteria.^[18]

Origin and early evolution

Archaea are an ancient form of life. Probable fossils of these cells have been dated to almost 3.5 billion years ago,^[19] and the remains of lipids that may be either archaean or eukaryotic have been detected in shales dating from 2.7 billion years ago.^[20] Since most prokaryotes do not have distinctive morphologies, the shapes of fossils cannot be used to identify them as Archaea. Instead, chemical fossils, in the form of the unique lipids found in archaea, are more informative because such compounds do not occur in other groups of organisms.^[21] Such lipids have now been detected in rocks dating back to the Precambrian. The oldest known traces of these isoprene lipids come from the Isua district of west Greenland, which include sediments formed 3.8 billion years old and are the oldest on Earth.^[22] The origin of Archaea appears very old indeed and the archaeal lineage may be the most ancient that exists on earth.^[23]

Woese argued that the bacteria, archaea, and eukaryotes each represent a separate line of descent that diverged early on from an ancestral colony of organisms.^[25]^[26] A few biologists, however, have argued that the Archaea and Eukaryota arose from a group of bacteria.^[27] It is possible that the last common ancestor of the bacteria and archaea was a thermophile, which raises the possibility that lower temperatures are "extreme environments" in archaeal terms, and organisms that live in cooler environments appeared later in the history of life on Earth.^[28] Since the Archaea and Bacteria are no more related to each other than they are to eukaryotes, this has led to the argument that the term prokaryote has no real evolutionary meaning and should be discarded entirely.^[29]

The relationship between archaea and eukaryotes remains an important problem. Aside from the similarities in cell structure and function that are discussed below, many genetic trees group the two together. Some early analyses even suggested that the relationship between eukaryotes and the archaeal phylum Euryarchaeota is closer than the relationship between the Euryarchaeota and the phylum Crenarchaeota.^[30] However, it is now considered more likely that the ancestor of the eukaryotes diverged early from the Archaea.^[31]^[32] The discovery of archaean-like genes in certain bacteria, such as Thermotoga maritima, makes these relationships difficult to determine, since horizontal gene transfer has occurred.^[33] Some have suggested that eukaryotes arose through fusion of an archaean and eubacterium, which became the nucleus and cytoplasm; this accounts for various genetic similarities but runs into difficulties explaining cell structure.^[34]

Classification

The classification of archaea, and of prokaryotes in general, is a rapidly moving and contentious field. Current classification systems aim to organize archaea into groups of organisms that share structural features and common ancestors.^[35] These classifications rely heavily on the use of the sequence of ribosomal RNA genes to reveal relationships between organisms (molecular phylogenetics).^[36] Most of the culturable and well-investigated species of archaea are members of two main phyla, the Euryarchaeota and Crenarchaeota. Other groups have been tentatively created. For example, the peculiar species Nanoarchaeum equitans, which was discovered in 2003, has been given its own phylum, the Nanoarchaeota.^[37] A new phylum Korarchaeota has also been proposed, it contains a small group of unusual thermophilic species that are most closely related to the Crenarchaeota.^[38] Other recently detected species of archaea are only distantly related to any of these groups, such as the Archaeal Richmond Mine Acidophilic Nanoorganisms (ARMAN), which were discovered in 2006.^[39]

The current state of knowledge on archaean diversity is fragmentary.^[36] Estimates of the total number of phyla in the archaea range from 18 to 23, of which only 8 phyla have representatives that have been grown in culture and studied directly. Many of these hypothetical groups are known from only a single rRNA sequence, indicating that the vast majority of the diversity among these organisms remains completely unknown.^[40] The problem of how to study and classify uncultured microbes is also encountered in the Bacteria.^[41]

The classification of archaea is also controversial. In biology, a species is a group of related organisms. A popular definition of a species in animals is a set of organisms that can breed with each other and are reproductively isolated from other groups of organisms (i.e. they cannot breed with other species).^[42] However, efforts to classify prokaryotes such as archaea into species are complicated by the fact that they are asexual and show high levels of horizontal gene transfer between lineages. The area is contentious; with, for example, some arguing that in groups such as the genus Ferroplasma, populations of archaea show clusters of related cells that can be seen as species.^[43] On the other hand, studies in Halorubrum found significant genetic exchange between such population clusters.^[44] Such results have led to the argument that these species are points within an interconnected net of gene transfer events, rather than parts of a standard phylogenetic tree.^[45]

Cell structure

Archaea are similar to bacteria in many aspects of their cell structure, but other characteristics set the archaea apart. Like bacteria, archaea lack interior membranes so their cells do not contain organelles.^[29] They also resemble bacteria in that their cell membrane is usually bounded by a cell wall and they swim by the use of one or more flagella.^[46] In overall structure the archaea are most similar to gram-positive bacteria, as most have a single plasma membrane and cell wall, and lack a periplasmic space; the exception to this general rule is the archaean Ignicoccus, which possess a particularly large periplasm that contains membrane-bound vesicles and is enclosed by an outer membrane.^[47]

Cell membranes

Archaeal membranes are made of molecules that differ strongly from those in other forms of life, which is evidence that archaea are related only distantly to bacteria and eukaryotes.^[48] The membranes in all three domains of life (archaea, bacteria and eukaryotes) are made of molecules known as phospholipids. These molecules resemble soap molecules, in that they possess both a polar part that will dissolve in water (the phosphate "head", shown as green circles, labeled 4 and 8, in the Figure), and a "greasy" non-polar part that will not dissolve in water (the lipid tails, shown as pink ovals, labeled 1 and 5). These dissimilar parts are connected by a glycerol group (red ovals in Figure, labeled 3 and 7). In water, phospholipids assemble into a double-layered sheet (labeled 9 in the Figure), with the polar phosphate heads facing the water and the non-polar lipid tails clustering away from the water. This double sheet of phospholipids is the major structure in cell membranes, and is called a lipid bilayer.

The phospholipids in the membranes of archaea are unusual in four ways:

Most bacteria and eukaryotes have membranes composed mainly of glycerol-ester lipids, whereas archaea have membranes composed of glycerol-ether lipids.^[49] The difference between these two types of phospholipid is the type of bond that joins the lipids to the glycerol group; these two types of bonds are shown in yellow in the Figure at the right. In ester lipids this is an ester bond, (labeled 6 in the Figure), whereas in ether lipids this is an ether bond, (labeled 2 in the Figure). Ether bonds are more chemically-resistant then ester bonds, which might contribute to the ability of some archaea to survive at extremes of temperature and in very acidic or alkaline environments.^[50] Bacteria and eukaryotes do contain some ether lipids, but in contrast to archaea these lipids are not a major part of their membranes.
The archaeal lipids are also unique because the stereochemistry of the glycerol group (red oval at right) is the reverse of that found in bacterial and eukaryotic lipids. The glycerol group can occur in two forms that are mirror images of one another, which may be called the right-handed and left-handed forms; in chemical terms these forms are called enantiomers. Just as a right hand does not fit easily into a left-handed glove, a right-handed glycerol molecule generally cannot be used or made by enzymes adapted for the left-handed form. This suggests that archaea use entirely different enzymes for synthesizing their phospholipids than do bacteria and eukaryotes; since such enzymes developed very early in life's history, this in turn suggests that the archaea split off very early from the other two domains.^[48]
The lipid tails of the phospholipids of archaea are also chemically different from those in other organisms. Archaeal lipids are based upon the isoprenoid sidechain and are long chains with multiple side-branches and sometimes even cyclopropane or cyclohexane rings.^[51] This is in contrast to the fatty acids found in other organisms' membranes, which have straight chains with no branches or rings. Although isoprenoids play an important role in the biochemistry of many organisms, only the archaea use them to make phospholipids. These branched chains may help prevent archaean membranes from becoming leaky at high temperatures.^[52]
In some archaea the typical phospholipid bilayer (labeled 9 at the right) is replaced by a single monolayer (labeled 10 at the right). In effect, the archaea have fused the tails of two independent phospholipid molecules into a single molecule with two polar heads; this fusion may make their membranes more rigid and better able to resist harsh environments.^[53] For example, all the lipids in Ferroplasma are of this type, which is thought to aid this organism's survival in the extraordinarily acidic environments in which it thrives.^[54]

Cell wall and flagella

Most archaea possess a cell wall, with the exceptions being Thermoplasma and Ferroplasma.^[55] Although not unique in their structure and composition, archaeal cell walls are unusual. For instance, in most archaea the wall is assembled from surface-layer proteins, which form what is called an S-layer.^[56] An S-layer is made of a rigid array of protein molecules that cover the outside of the cell like chain mail.^[57] This layer provides both chemical and physical protection, and can act as a barrier preventing macromolecules from coming into contact with the cell membrane. S-layers are also found in some bacteria, where they serve as the sole cell wall component in the Planctomyces, or as an outer layer in bacteria possessing cell walls made from peptidoglycan. In contrast to these bacteria, archaea generally lack peptidoglycan in their cell walls.^[58] Some archaeal walls do contain pseudopeptidoglycan, which is found in Methanobacteriales, but this polymer differs from the peptidoglycan of bacteria since it lacks D-amino acids and N-acetylmuramic acid.^[59]

Archaea also have flagella, and while they are similar to bacterial flagella in that they are rotatory motors driven by a proton gradient, archaeal flagella are notably different in their composition and development.^[46] The bacterial flagellum is a modified type III secretion system, while archaeal flagella appear to have evolved from to the bacterial type IV pili.^[60] In contrast to the bacterial flagellum, where filament proteins move up a central pore and are added to the tip of the filament, archaeal filaments appear to be synthesized by adding subunits to their base.^[61]

Metabolism

Archaea exhibit a variety of different types of metabolism, obtaining the energy they need from a many different chemical reactions. Some archaea are lithotrophs and obtain their energy from inorganic compounds. These archaea include nitrifiers, methanogens and anaerobic methane oxidisers.^[62] Several other groups of archaea are phototrophs that use sunlight to directly power synthesis of adenosine triphosphate (ATP); however, oxygen-generating photosynthesis does not occur in any archaeal group.^[63] Many basic metabolic pathways are shared between archaea and bacteria, with archaea that grow on complex organic compounds (the chemoorganotrophs) having a modified form of glycolysis (the Entner–Doudoroff pathway) and either a complete or partial citric acid cycle.^[64] These similarities with other organisms probably reflect the early evolution of carbohydrate metabolism in the history of life.^[65]

Nutritional types in archaeal metabolism
Nutritional type	Source of energy	Source of carbon	Examples
Phototrophs	Sunlight	Organic compounds	Halobacteria
Lithotrophs	Inorganic compounds	Organic compounds or carbon fixation	Ferroglobus, Methanobacteria or Pyrolobus
Heterotrophs	Organic compounds	Organic compounds or carbon fixation	Pyrococcus, Sulfolobus or Methanosarcinales

Some Euryarchaeota are methanogens, which produce methane gas as a waste product in anaerobic environments such as swamps. This form of metabolism evolved early, and the first free-living organism may have been a methanogen.^[66] A common reaction in these organisms involves the use of carbon dioxide as an electron acceptor to oxidize hydrogen, as shown below:
${\mbox{CO}}_{2}+{\mbox{4H}}_{2}\rightarrow {\mbox{CH}}_{4}+{\mbox{2H}}_{2}{\mbox{O}}\,$

Methanogenesis involves a range of unique coenzymes, such as coenzyme M and methanofuran,^[67] and generates ATP through chemiosmosis.^[63] Other organic compounds such as alcohols, acetic acid or formic acid are also used as electron acceptors by methanogens. These reactions are common in the gut. Acetic acid is also broken down into methane and carbon dioxide directly, by acetotrophic archaea. These acetotrophs are archaea in the order Methanosarcinales, and dominate the microbial communities involved in biogas production.^[68]

Bacteriorhodopsin from *Halobacterium salinarum*. The retinol cofactor and residues involved in proton transfer are shown as ball-and-stick models.^[69]

Other archaea are autotrophs that fix carbon dioxide. This process involves either a highly-modified form of the Calvin cycle,^[70] or a recently-discovered metabolic pathway called the 3-hydroxypropionate/4-hydroxybutyrate cycle.^[71] The Crenarchaeota also use the reverse Krebs cycle and the Euryarchaeota also use the reductive acetyl-CoA pathway.^[72] In these organisms, carbon-fixation reactions are powered by lithotrophic metabolism rather than phototrophic metabolism, which is employed by plants and cyanobacteria. There are no known archaea that carry out photosynthesis, using light for energy as well as fixing carbon dioxide.^[73] The energy sources used by archaea to fix carbon are extremely diverse, and range from the oxidation of ammonia by the Nitrosopumilales in anammox metabolism^[74]^[75] to the oxidation of hydrogen sulfide or elemental sulfur by species of Sulfolobus, using either oxygen or metal ions as electron acceptors.^[63]

Phototrophic archaea use light to produce chemical energy in the form of ATP, although not by means of carbon fixation.^{[clarification needed]} In the Halobacteria, light-activated ion pumps like bacteriorhodopsin and halorhodopsin generate ion gradients by pumping the ions out of the cell across the plasma membrane. The energy stored in these electrochemical gradients is then converted into ATP by ATP synthase.^[8] This process is a form of photophosphorylation. The structure and function of these light-driven pumps has been studied in great detail, which has revealed that their ability to move ions across membranes depends on light-driven changes in the structure of a retinol cofactor buried in the center of the protein.^[76]

Genetics

Archaea are similar to bacteria in that they usually have a single circular chromosome,^[77] the size of which may be as great as 5,751,492 base pairs in Methanosarcina acetivorans,^[78] the largest archaean genome sequenced to date. At one-tenth of this size is the tiny 490,885 base-pair genome of Nanoarchaeum equitans, which is the smallest microbial genome known; it is estimated to contain only 537 protein-encoding genes.^[79] Smaller independent pieces of DNA, called plasmids, are also found in archaea. Plasmids may be transferred between cells by physical contact, in a process that may be similar to bacterial conjugation.^[80]^[81] Archaeal plasmids are increasingly important as genetic tools and allow the performance of genetic studies in archaea.^[82]

*Sulfolobus* infected with the DNA virus STSV1.^[83] Bar is 1 micrometer.

As with the bacteriophages that infect bacteria, some viruses replicate within archaea: these are double-stranded DNA viruses that appear to be unrelated to any other form of virus and have a variety of unusual shapes, with some resembling bottles, hooked rods, or teardrops.^[84] These viruses have been studied in most detail in the thermophilic archaea, particularly the orders Sulfolobales and Thermoproteales.^[85] Defenses against these viruses may involve RNA interference from repetitive DNA sequences within archaean genomes that are related to the genes of the viruses.^[86]^[87]

Archaea are genetically distinct from other organisms, with up to 15% of the proteins encoded by any one archaeal genome being unique to the Archaea, although most of these unique genes have no known function.^[88] Of the remainder of the genes that are unique to archaea and do have an identified function, most are involved in methanogenesis. The genes that are shared between archaea, bacteria and eukaryotes form a common core of cell function, relating mostly to transcription, translation, and nucleotide metabolism.^[89] Other characteristic features of archaean genomes are the organization of genes of related function—such as enzymes catalysing steps in the same metabolic pathway—into novel operons, and large differences in tRNA genes and their aminoacyl tRNA synthetases.^[89]

Transcription and translation in archaea are more similar to those in eukaryotes than in bacteria, with archaean RNA polymerase II and ribosomes being very similar to their equivalents in eukaryotes.^[77] The archaeal RNA polymerase in transcription also seems to function in a similar way to that of eukaryotes, with similar assemblies of proteins (the general transcription factors) directing the binding of the RNA polymerase to a gene's promoter. However, other archaean transcription factors are similar to those found in bacteria.^[90]

Reproduction

Archaea reproduce asexually by binary or multiple fission, fragmentation, or budding; meiosis does not occur, so if a species of archaea exists in more than one form, these will all have the same number of chromosomes (they have the same karyotype).^[8] Cell division is controlled in the archaea as part of a complex cell cycle; after the cell's chromosome is replicated and the two daughter chromosomes are separated, the cell divides.^[91] The details of the archaeal cell cycle have only been investigated in the genus Sulfolobus, but here it has characters that are similar to both bacterial and eukaryotic systems. In this archaean, the chromosomes are replicated from multiple starting-points (origins of replication) using DNA polymerases that are similar to the equivalent eukaryotic enzymes.^[92] However, the proteins that direct cell division, such as the protein FtsZ, which forms a contracting ring around the cell, and the components of the septum that is constructed across the center of the cell, are similar to their bacterial equivalents.^[91]

Spores, such as the endospores made by some bacteria, are not formed in any of the known archaea.^[93] Some species of Haloarchaea undergo phenotypic switching and grow as several different types of cell, including thick-walled structures that are resistant to osmotic shock and allow the archaea to survive in water at low concentrations of salt, but these are not reproductive structures and may instead help them disperse to new habitats.^[94]

Ecology

Habitats

Archaea exist in a broad range of habitats, and are a major part of global ecosystems,^[5] and may contribute up to 20% of the total biomass on Earth.^[95] Multiple archaeans are extremophiles, and historically this was seen as their ecological niche.^[62] Indeed, some archaea survive high temperatures, often above 100 °C, as found in geysers, black smokers, and oil wells. Others are found in very cold habitats and others in highly saline, acidic, or alkaline water. However, other archaea are mesophiles that grow in much milder conditions, in marshland, sewage, the oceans, and soils.^[5]

Extremophile archaea are members of four main physiological groups. These are the halophiles, thermophiles, alkaliphiles, and acidophiles.^[96] These groups are not comprehensive or related to which phylum the organisms belong to, nor are they mutually exclusive, since some archaea belong to several of these groups. Nonetheless, they are a useful starting point for classification. Halophiles, including the genus Halobacterium, live in extremely saline environments such as salt lakes and start outnumbering their bacterial counterparts at salinities greater than 20–25%.^[62] Thermophiles live in places that have high temperatures, such as hot springs. Hyperthermophilic archaea are defined as those that grow optimally at temperatures greater than 80 °C; the archaeal Strain 121 grows at 121 °C, which is the highest recorded temperature at which any organism will grow.^[97] Other archaea exist in very acid or alkali conditions.^[96] For example, one of the most extreme archaean acidophiles is Picrophilus torridus, which grows at pH 0, which is equivalent to thriving in 1.2 Molar sulfuric acid.^[98]

This resistance to extreme environments has made archaea the focus of speculation about the possible properties of extraterrestrial life.^[99] This has focused on the possibility that microbial life may exist on Mars,^[100] and has even led to the suggestion that viable microbes could be transferred between planets in meteorites.^[101]

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. For example, archaea are common in cold oceanic environments such as sea-floor sediments and polar seas.^[102]^[103] Even more significant are the large numbers of archaea found throughout the world's oceans.^[104] Although these archaea can be present in extremely high numbers (up to 40% of the microbial biomass), almost none of these species have been isolated and studied in pure culture.^[105] Consequently, our understanding of the role of archaea in the ecology of the oceans is rudimentary, so their full influence on global biogeochemical cycles remains largely unexplored.^[106] A recent study has shown, however, that one group of marine Crenarchaeota are capable of nitrification, suggesting these organisms may be important in the oceanic nitrogen cycle.^[107]

Role in chemical cycling

Archaea are part of the systems on Earth that recycle elements such as carbon, nitrogen and sulfur through the various habitats in ecosystems. Although these activities are vital for the normal function of ecosystems, archaea can also contribute to the changes that humans have made in the environment, and even cause pollution.

Archaea carry out many steps in the nitrogen cycle, this includes both dissimilatory reactions that remove nitrogen from ecosystems, such as nitrate-based respiration and denitrification: as well as assimilatory processes that introduce nitrogen, such as nitrate assimilation and nitrogen fixation.^[108] The involvement of archaea in anammox reactions was recently discovered, with these being particularly important in the oceans.^[109] The archaea also appear to be particularly important in ammonia oxidation is soils, this produces nitrite, which is then oxidized to nitrate by other microbes, and then taken up by plants and other organisms.^[110]

In the sulfur cycle archaea that grow by oxidizing sulfur compounds are important as they can release this element from rocks and make it available to other organisms. However, the archaea that do this, such as Sulfolobus, can cause environmental damage. This group of archaea produces sulfuric acid as a waste product, and the growth of these organisms in abandoned mines causes acid mine drainage.^[111]

In the carbon cycle, methanogen archaea are significant as methane producers. The ability of these archaea to remove hydrogen is important in the degradation of organic matter by the populations of microorganisms that act as decomposers in anaerobic ecosystems, such as sediments, marshes and sewage treatment works.^[112] However, methane is one of the most abundant greenhouse gases in Earth's atmosphere, constituting 18% of the global total.^[113] It is 25 times more potent as a greenhouse gas than carbon dioxide.^[114] Methanogens are the primary source of atmospheric methane, and are responsible for most of the world's yearly methane emissions. Most of this methane is produced in wetlands (including rice paddies) or in livestock,^[115] although a significant volume of methane is also produced by termites.^[116] As a consequence, these archaea contribute to global greenhouse gas emissions and global warming.

Interactions with other organisms

The well-characterized interactions between archaea and other organisms are either mutualism or commensal. As of 2007, no clear examples of archaeal pathogens or parasites are known.^[117]^[118] However, a relationship has been proposed between the presence of some species of methanogens and infections in the mouth,^[119]^[120] and Nanoarchaeum equitans may be parasitic, since it only survives and reproduces within the cells of the Crenarchaeon Ignicoccus hospitalis,^[121] and appears to offer no benefit to its host.^[122]

The best-understood example of archaean mutualists are the methanogenic archaea that are found in the digestive tracts of animals that digest cellulose, such as ruminants and termites.^[123] In these environments, the archaea consume the hydrogen produced during cellulose digestion by anaerobic protozoa, helping the protozoa gain energy from this process.^[124] These associations between methanogens and protozoa are taken a step further in several species of anaerobic protozoa, such as Plagiopyla frontata; here the archaea actually reside inside the protozoa and consume the hydrogen produced in their hydrogenosomes.^[125]^[126] Similar associations with larger organisms are now being found, with the discovery that the marine archaean Cenarchaeum symbiosum lives within (it is an endosymbiont of) the sponge Axinella mexicana.^[127]

Archaea can also be commensals, benefiting from an association without helping or harming the other organism. For example, the formate-consuming methanogen Methanobrevibacter smithii is by far the most common archaean in the human flora, with this species making up about one in ten of all the prokaryotes in the human gut.^[128] As in termites, these methanogens may in fact be mutualists in humans, interacting with other microbes in the gut to aid the digestion of food.^[129] Communities of archaea are also associated with a range of other organisms, such as on the surface of corals,^[130] and in the region of soil that surrounds plant roots (the rhizosphere).^[131]^[132]

Significance in technology and industry

Extremophile archaea, particularly those that are resistant either to heat or to extremes of acidity and alkalinity, are a source of enzymes that function under these harsh conditions.^[133]^[134] These enzymes have a wide range of uses. For example, thermostable DNA polymerases, such as the Pfu DNA polymerase from Pyrococcus furiosus, have revolutionized molecular biology by allowing the polymerase chain reaction to be used as a simple and rapid technique for cloning DNA. In industry, amylases, galactosidases and pullulanases in other species of Pyrococcus that function at over 100 °C allow food processing at high temperatures, such as the production of low lactose milk and whey.^[135] Enzymes from these thermophilic archaea also tend to be very stable in organic solvents, allowing their use in environmentally-friendly processes in green chemistry that synthesize organic compounds.^[134] The stability of thermophilic enzymes also makes them easier to use in structural biology, consequently the counterparts of bacterial or eukaryotic enzymes from extremophile archaea are often used in structural studies.^[136]

In contrast to the range of applications of archaean enzymes, the use of the organisms themselves in biotechnology is more restricted. However, methanogenic archaea are a vital part of sewage treatment, since they are part of the community of microorganisms that carry out anaerobic digestion and produce biogas.^[137] In mineral processing, Acidophillic archaea display promise for the extraction of metals from ores, including gold, cobalt and copper.^[138]

A new class of potentially useful antibiotics has been discovered in archaea. A few of these archaeocins have been characterized, but hundreds more are believed to exist, especially within Haloarchaea and Sulfobolous.^[139] These compounds are important since they are different in structure to bacterial antibiotics, so they may have novel modes of action. In addition, they may allow the creation of new selectable markers for use in archaeal molecular biology. The discovery of new archaeocins depends on successful recovery and cultivation of new species of archaea from the environment.^[140]

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External links

General

Introduction to the Archaea, ecology, systematics and morphology
Oceans of Archaea - E.F. DeLong, ASM News, 2003

Classification

NCBI taxonomy parge on Archaea
Tree of Life illustration showing how Archaea relates to other lifeforms
Shotgun sequencing finds nanoorganisms - discovery of the ARMAN group of archaea

Genomics

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 Generally, archaea and bacteria are quite similar in size and shape, although a few archaea have unusual shapes, such as the flat and square-shaped cells of ''[[Haloquadra|Haloquadra walsbyi]]''. Despite this visual similarity to bacteria, archaea possess genes and several [[metabolic pathway]]s that are more closely related to those of eukaryotes. Other aspects of archaean biochemistry are unique, such as their reliance on [[ether lipid]]s in their [[cell membrane]]s. The archaea also exploit a much greater variety of sources of energy than eukaryotes: ranging from familiar [[organic compounds]] such as [[sugar]]s, to using [[ammonia]], [[ion|metal ions]] or even [[hydrogen|hydrogen gas]] as nutrients. Salt-tolerant archaea (the [[Halobacteria]]) use sunlight as a source of energy, whereas other species of archaea [[carbon fixation|fix carbon]]; however, unlike [[plant]]s and [[cyanobacteria]], no species of archaea is known that can do both.
-Initially, archaea were seen as [[extremophile]]s that lived in harsh environments, such as [[hot spring]]s and [[salt lake]]s, but they have since been found in a broad range of [[habitat]]s, such as [[soil]]s, [[ocean]]s and [[marshland]]s. Archaea are particularly numerous in the oceans, and the archaea in [[plankton]] may be one of the most abundant groups of organisms on the planet. These prokaryotes are now recognized as a major part of life on Earth and may play an important role in both the [[carbon cycle]] and [[nitrogen cycle]]. No clear examples of archaeal [[pathogen]]s or [[parasite]]s are known, but they form [[mutualism|mutualistic]] or [[commensalism|commensal]] relationships with other organisms. One example are the [[methanogen]]ic archaea that inhabit the gut of humans and [[ruminant]]s, where they are present in vast numbers and aid in the [[digestion]] of food.
+Initially, archaea were seen as [[extremophile]]s that lived in harsh environments, such as [[hot spring]]s and [[salt lake]]s, but they have since been found in a broad range of [[habitat]]s, such as [[soil]]s, [[ocean]]s and [[marshland]]s. Archaea are particularly numerous in the oceans, and the archaea in [[plankton]] may be one of the most abundant groups of organisms on the planet. These prokaryotes are now recognized as a major part of life on Earth and may play an important role in both the [[carbon cycle]] and [[nitrogen cycle]]. No clear examples of archaeal [[pathogen]]s or [[parasite]]s are known, but they are often [[mutualism|mutualists]] or [[commensalism|commensals]]. One example are the [[methanogen]]ic archaea that inhabit the gut of humans and [[ruminant]]s, where they are present in vast numbers and aid in the [[digestion]] of food.
 ==Discovery==
@@ Line 27: / Line 27: @@
 Early in the 20th century, prokaryotes were regarded as a single group of organisms and classified based on their [[biochemistry]], [[morphology (biology)|morphology]] and [[metabolism]]. For example, microbiologists tried to classify microorganisms based on the structures of their [[cell wall]]s, their shapes, and the substances they consume.<ref>{{cite journal |author=Staley JT |title=The bacterial species dilemma and the genomic-phylogenetic species concept |journal=Philos. Trans. R. Soc. Lond., B, Biol. Sci. |volume=361 |issue=1475 |pages=1899&ndash;909 |year=2006 |pmid=17062409 |url=http://journals.royalsociety.org/openurl.asp?genre=article&doi=10.1098/rstb.2006.1914 |doi=10.1098/rstb.2006.1914}}</ref> However, a new approach was proposed in 1965,<ref>{{cite journal |author=Zuckerkandl E, Pauling L |title=Molecules as documents of evolutionary history |journal=J. Theor. Biol. |volume=8 |issue=2 |pages=357&ndash;66 |year=1965 |pmid=5876245 |doi=10.1016/0022-5193(65)90083-4}}</ref> using the sequences of the [[gene]]s in these organisms to work out which prokaryotes are genuinely related to each other.  This powerful approach, known as [[phylogenetics]], is the main method used today.
 [[Image:Grand prismatic spring.jpg|thumb|right|250px|Archaea were first detected in extreme environments, such as volcanic [[hot spring]]s.]]
-Archaea were identified as a separate group of prokaryotes in 1977 by [[Carl Woese]] and [[George E. Fox]] in [[phylogenetic tree]]s based on the sequences of [[ribosomal RNA]] (rRNA) genes.<ref>{{cite journal|author=Woese C, Fox G |title=Phylogenetic structure of the prokaryotic domain: the primary kingdoms |journal=Proc Natl Acad Sci USA |volume=74 |issue=11 |pages=5088&ndash;90 |year=1977 |pmid=270744 |url=http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=270744 |doi=10.1073/pnas.74.11.5088}}</ref> These two groups were originally named the Archaebacteria and Eubacteria and treated as [[kingdom (biology)|kingdom]]s or subkingdoms, which Woese and Fox termed ''Urkingdoms''. Woese argued that this group of prokaryotes represented a fundamentally different branch of living things. He later renamed the two groups of prokaryotes Archaea and [[Bacteria]] to emphasize this, and argued that together with [[Eukaryota|Eukarya]] they compose [[three-domain system|three domains]] of living organisms.<ref>{{cite journal |author=Woese CR, Kandler O, Wheelis ML |title=Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya |journal=Proc. Natl. Acad. Sci. U.S.A. |volume=87 |issue=12 |pages=4576&ndash;9 |year=1990 |pmid=2112744 |url=http://www.pnas.org/cgi/pmidlookup?view=long&pmid=2112744 |doi=10.1073/pnas.87.12.4576}}</ref>
+Archaea were identified as a separate group of prokaryotes in 1977 by [[Carl Woese]] and [[George E. Fox]] in [[phylogenetic tree]]s based on the sequences of [[ribosomal RNA]] (rRNA) genes.<ref>{{cite journal|author=Woese C, Fox G |title=Phylogenetic structure of the prokaryotic domain: the primary kingdoms |journal=Proc Natl Acad Sci USA |volume=74 |issue=11 |pages=5088&ndash;90 |year=1977 |pmid=270744 |url=http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=270744 |doi=10.1073/pnas.74.11.5088}}</ref> These two groups were originally named the Archaebacteria and Eubacteria and treated as [[kingdom (biology)|kingdom]]s or subkingdoms, which Woese and Fox termed ''Urkingdoms''. Woese argued that this group of prokaryotes is a fundamentally different sort of life. He later renamed the two groups of prokaryotes Archaea and [[Bacteria]] to emphasize this, and argued that together with [[Eukaryota|Eukarya]] they are [[three-domain system|three domains]] of living organisms.<ref>{{cite journal |author=Woese CR, Kandler O, Wheelis ML |title=Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya |journal=Proc. Natl. Acad. Sci. U.S.A. |volume=87 |issue=12 |pages=4576&ndash;9 |year=1990 |pmid=2112744 |url=http://www.pnas.org/cgi/pmidlookup?view=long&pmid=2112744 |doi=10.1073/pnas.87.12.4576}}</ref>
-At first, only the [[methanogen]]s were placed in this new domain, and the archaea were seen as extremophiles that existed only in apparently inhospitable habitats, such as [[hot spring]]s and [[salt lake]]s.  By the end of the 20th century, microbiologists realized that the archaea are a large and diverse group of organisms that are widely distributed in nature and are common in much less extreme habitats, such as soils and oceans.<ref name=DeLong>{{cite journal |author=DeLong EF |title=Everything in moderation: archaea as 'non-extremophiles' |journal=Curr. Opin. Genet. Dev. |volume=8 |issue=6 |pages=649&ndash;54 |year=1998 |pmid=9914204 |doi=10.1016/S0959-437X(98)80032-4}}</ref> This new appreciation of the importance and ubiquity of archaea came mostly from the use of [[molecular biology]] techniques to detect prokaryotes in samples of water or soil from their [[nucleic acid]]s alone.  Such techniques eliminate the need to [[microbiological culture|culture]] organisms in the laboratory, which is often difficult.<ref>{{cite journal |author=Theron J, Cloete TE |title=Molecular techniques for determining microbial diversity and community structure in natural environments |journal=Crit. Rev. Microbiol. |volume=26 |issue=1 |pages=37&ndash;57 |year=2000 |pmid=10782339 |doi=10.1080/10408410091154174}}</ref><ref>{{cite journal |author=Schmidt TM |title=The maturing of microbial ecology |journal=Int. Microbiol. |volume=9 |issue=3 |pages=217&ndash;23 |year=2006 |pmid=17061212 |url=http://www.im.microbios.org/0903/0903217.pdf}}</ref>
+At first, only the [[methanogen]]s were placed in this new domain, and the archaea were seen as extremophiles that exist only in habitats such as [[hot spring]]s and [[salt lake]]s.  By the end of the 20th century, microbiologists realized that the archaea are a large and diverse group of organisms that are widely distributed in nature and are common in much less extreme habitats, such as soils and oceans.<ref name=DeLong>{{cite journal |author=DeLong EF |title=Everything in moderation: archaea as 'non-extremophiles' |journal=Curr. Opin. Genet. Dev. |volume=8 |issue=6 |pages=649&ndash;54 |year=1998 |pmid=9914204 |doi=10.1016/S0959-437X(98)80032-4}}</ref> This new appreciation of the importance and ubiquity of archaea came mostly from the use of [[molecular biology]] techniques to detect prokaryotes in samples of water or soil from their [[nucleic acid]]s alone.  Such techniques eliminate the need to [[microbiological culture|culture]] organisms in the laboratory, which is often difficult.<ref>{{cite journal |author=Theron J, Cloete TE |title=Molecular techniques for determining microbial diversity and community structure in natural environments |journal=Crit. Rev. Microbiol. |volume=26 |issue=1 |pages=37&ndash;57 |year=2000 |pmid=10782339 |doi=10.1080/10408410091154174}}</ref><ref>{{cite journal |author=Schmidt TM |title=The maturing of microbial ecology |journal=Int. Microbiol. |volume=9 |issue=3 |pages=217&ndash;23 |year=2006 |pmid=17061212 |url=http://www.im.microbios.org/0903/0903217.pdf}}</ref>
 ==Morphology==
@@ Line 35: / Line 35: @@
 [[Image:Relative scale.svg|thumb|250px|left|The sizes of prokaryotic cells relative to other cells and biomolecules.]]
-Individual archaeans range from 0.1&nbsp;[[Micrometre|micrometer]]s (μm) to over 15&nbsp;μm in diameter, and occur in various shapes, commonly as spheres, rods, spirals or plates.<ref name=Bergey/> Other morphologies in the [[Crenarchaeota]] include irregularly-shaped lobed cells in ''[[Sulfolobus]]'', thin needle-like filaments that are less than half a micrometer in diameter in ''[[Thermofilum]]'', and almost perfectly rectangular rods in ''[[Thermoproteus]]'' and ''[[Pyrobaculum]]''.<ref>Barns, Sue and Burggraf, Siegfried. (1997) [http://tolweb.org/Crenarchaeota/9 Crenarchaeota]. Version 01 January 1997. in ''The Tree of Life Web Project''</ref> There is even a species of flat, square archaea called ''[[Haloquadra|Haloquadra walsbyi]]'' that lives in hypersaline pools.<ref name=Walsby1980>{{cite journal |author=Walsby, A.E. |year=1980 |title=A square bacterium |journal=Nature |volume=283 |issue=5742 |pages=69&ndash;71 |doi=10.1038/283069a0}}</ref> These unusual shapes are probably maintained both by their cell walls and a [[prokaryotic cytoskeleton]]. Proteins related to the cytoskeleton components of other organisms have been identified in the archaea,<ref>{{cite journal |author=Hara F, Yamashiro K, Nemoto N, ''et al'' |title=An actin homolog of the archaeon Thermoplasma acidophilum that retains the ancient characteristics of eukaryotic actin |journal=J. Bacteriol. |volume=189 |issue=5 |pages=2039&ndash;45 |year=2007 |pmid=17189356 |url=http://jb.asm.org/cgi/pmidlookup?view=long&pmid=17189356 |doi =10.1128/JB.01454-06}}</ref> and filaments have been observed within these cells,<ref>{{cite journal |author=Trent JD, Kagawa HK, Yaoi T, Olle E, Zaluzec NJ |title=Chaperonin filaments: the archaeal cytoskeleton? |journal=Proc. Natl. Acad. Sci. U.S.A. |volume=94 |issue=10 |pages=5383&ndash;8 |year=1997 |pmid=9144246 |url=http://www.pnas.org/cgi/pmidlookup?view=long&pmid=9144246 |doi=10.1073/pnas.94.10.5383}}</ref> but in contrast to bacteria, these cellular structures are poorly understood in archaea.<ref>{{cite journal |author=Hixon WG, Searcy DG |title=Cytoskeleton in the archaebacterium Thermoplasma acidophilum? Viscosity increase in soluble extracts |journal=BioSystems |volume=29 |issue=2–3 |pages=151&ndash;60 |year=1993 |pmid=8374067 |doi=10.1016/0303-2647(93)90091-P}}</ref>
+Individual archaeans range from 0.1&nbsp;[[Micrometre|micrometer]]s (μm) to over 15&nbsp;μm in diameter, and occur in various shapes, commonly as spheres, rods, spirals or plates.<ref name=Bergey/> Other morphologies in the [[Crenarchaeota]] include irregularly-shaped lobed cells in ''[[Sulfolobus]]'', thin needle-like filaments that are less than half a micrometer in diameter in ''[[Thermofilum]]'', and almost perfectly rectangular rods in ''[[Thermoproteus]]'' and ''[[Pyrobaculum]]''.<ref>Barns, Sue and Burggraf, Siegfried. (1997) [http://tolweb.org/Crenarchaeota/9 Crenarchaeota]. Version 01 January 1997. in ''The Tree of Life Web Project''</ref> There is even a species of flat, square archaea called ''[[Haloquadra|Haloquadra walsbyi]]'' that lives in hypersaline pools.<ref name=Walsby1980>{{cite journal |author=Walsby, A.E. |year=1980 |title=A square bacterium |journal=Nature |volume=283 |issue=5742 |pages=69&ndash;71 |doi=10.1038/283069a0}}</ref> These unusual shapes are probably maintained both by their cell walls and a [[prokaryotic cytoskeleton]]. Proteins related to the cytoskeleton components of other organisms exist in the archaea,<ref>{{cite journal |author=Hara F, Yamashiro K, Nemoto N, ''et al'' |title=An actin homolog of the archaeon Thermoplasma acidophilum that retains the ancient characteristics of eukaryotic actin |journal=J. Bacteriol. |volume=189 |issue=5 |pages=2039&ndash;45 |year=2007 |pmid=17189356 |url=http://jb.asm.org/cgi/pmidlookup?view=long&pmid=17189356 |doi =10.1128/JB.01454-06}}</ref> and filaments are formed within their cells,<ref>{{cite journal |author=Trent JD, Kagawa HK, Yaoi T, Olle E, Zaluzec NJ |title=Chaperonin filaments: the archaeal cytoskeleton? |journal=Proc. Natl. Acad. Sci. U.S.A. |volume=94 |issue=10 |pages=5383&ndash;8 |year=1997 |pmid=9144246 |url=http://www.pnas.org/cgi/pmidlookup?view=long&pmid=9144246 |doi=10.1073/pnas.94.10.5383}}</ref> but in contrast to bacteria, these cellular structures are poorly understood in archaea.<ref>{{cite journal |author=Hixon WG, Searcy DG |title=Cytoskeleton in the archaebacterium Thermoplasma acidophilum? Viscosity increase in soluble extracts |journal=BioSystems |volume=29 |issue=2–3 |pages=151&ndash;60 |year=1993 |pmid=8374067 |doi=10.1016/0303-2647(93)90091-P}}</ref>
 Some species of archaea form aggregates or filaments of cells up to 200&nbsp;μm in length,<ref name=Bergey/> and these organisms can be prominent members of the communities of microbes that make up [[biofilm]]s.<ref>{{cite journal |author=Hall-Stoodley L, Costerton JW, Stoodley P |title=Bacterial biofilms: from the natural environment to infectious diseases |journal=Nat. Rev. Microbiol. |volume=2 |issue=2 |pages=95&ndash;108 |year=2004 |pmid=15040259 |doi=10.1038/nrmicro821}}</ref> An extreme example is ''[[Thermococcus|Thermococcus coalescens]]'', as aggregates of these cells fuse together in culture, forming single giant cells.<ref>{{cite journal |author=Kuwabara T, Minaba M, Iwayama Y, ''et al'' |title=Thermococcus coalescens sp. nov., a cell-fusing hyperthermophilic archaeon from Suiyo Seamount |journal=Int. J. Syst. Evol. Microbiol. |volume=55 |issue=Pt 6 |pages=2507&ndash;14 |year=2005 |month=November |pmid=16280518 |doi=10.1099/ijs.0.63432-0 |url=http://ijs.sgmjournals.org/cgi/pmidlookup?view=long&pmid=16280518}}</ref> A particularly elaborate form of multicellular colony is produced by archaea in the genus ''[[Pyrodictium]]''. Here, the cells produce arrays of long, thin hollow tubes called ''cannulae'' that stick out from the cells' surfaces and connect them together into a dense bush-like colony.<ref>{{cite journal |author=Nickell S, Hegerl R, Baumeister W, Rachel R |title=Pyrodictium cannulae enter the periplasmic space but do not enter the cytoplasm, as revealed by cryo-electron tomography |journal=J. Struct. Biol. |volume=141 |issue=1 |pages=34&ndash;42 |year=2003 |pmid=12576018 |url=http://linkinghub.elsevier.com/retrieve/pii/S1047847702005816 |doi=10.1016/S1047-8477(02)00581-6}}</ref> The function of these cannulae is not known, but they may allow the cells to communicate or exchange nutrients with their neighbors.<ref>{{cite journal |author=Horn C, Paulmann B, Kerlen G, Junker N, Huber H |title=In vivo observation of cell division of anaerobic hyperthermophiles by using a high-intensity dark-field microscope |journal=J. Bacteriol. |volume=181 |issue=16 |pages=5114&ndash;8 |year=1999 |pmid=10438790 |url=http://jb.asm.org/cgi/pmidlookup?view=long&pmid=10438790 |doi=10.1073/pnas.241636498v1}}</ref> Colonies can also be produced by an association between different species.  For example, in the "string-of-pearls" community that was discovered in 2001 in a German swamp, round whitish colonies of a novel species of archaea in the phylum Euryarchaeota are spaced along thin filaments that can be up to {{convert|15|cm}} long; these filaments are made of a particular species of bacteria.<ref>{{cite journal |author=Rudolph C, Wanner G, Huber R |title=Natural communities of novel archaea and bacteria growing in cold sulfurous springs with a string-of-pearls-like morphology |journal=Appl. Environ. Microbiol. |volume=67 |issue=5 |pages=2336&ndash;44 |year=2001 |month=May |pmid=11319120 |pmc=92875 |doi=10.1128/AEM.67.5.2336-2344.2001 |url=http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=11319120}}</ref>
@@ Line 45: / Line 45: @@
 [[Image:Collapsed tree labels simplified.png|thumb|400px|right|[[Phylogenetic tree]] showing the relationship between the archaea and other forms of life. [[Eukaryote]]s are colored red, archaea green and [[bacteria]] blue. Adapted from Ciccarelli ''et al.''.<ref>{{cite journal |author=Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, Bork P |title=Toward automatic reconstruction of a highly resolved tree of life |journal=Science |volume=311 |issue=5765 |pages=1283&ndash;7 |year=2006 |pmid=16513982 |doi=10.1126/science.1123061}}</ref>]]
-Woese argued that the bacteria, archaea, and eukaryotes each represent a primary line of descent that diverged early on from an ancestral ''progenote'' or colony or organisms with poorly developed genetic machinery.<ref>{{cite journal |author=Woese CR, Gupta R |title=Are archaebacteria merely derived 'prokaryotes'? |journal=Nature |volume=289 |issue=5793 |pages=95&ndash;6 |year=1981 |pmid=6161309 |doi=10.1038/289095a0}}</ref><ref>{{cite journal |author=Woese C |title=The universal ancestor |journal=Proc. Natl. Acad. Sci. U.S.A. |volume=95 |issue=12 |pages=6854&ndash;9 |year=1998 |pmid=9618502 |url=http://www.pnas.org/cgi/pmidlookup?view=long&pmid=9618502 |doi=10.1073/pnas.95.12.6854}}</ref> A few biologists, however, have argued that the Archaea and Eukaryota arose from a group of bacteria.<ref>{{cite journal |author=Gupta RS |title=The natural evolutionary relationships among prokaryotes |journal=Crit. Rev. Microbiol. |volume=26 |issue=2 |pages=111&ndash;31 |year=2000 |pmid=10890353 |doi=10.1080/10408410091154219}}</ref> It is possible that the last common ancestor of the bacteria and archaea was a thermophile, which raises the possibility that lower temperatures are "extreme environments" in archaeal terms, and organisms that live in cooler environments appeared later in the history of life on Earth.<ref>{{cite journal |author=Gribaldo S, Brochier-Armanet C |title=The origin and evolution of Archaea: a state of the art |journal=Philos. Trans. R. Soc. Lond., B, Biol. Sci. |volume=361 |issue=1470 |pages=1007&ndash;22 |year=2006 |pmid=16754611 |url=http://www.journals.royalsoc.ac.uk/content/q74671t476444mq5/ |doi =10.1098/rstb.2006.1841}}</ref> The recognition that the Archaea and Bacteria are not significantly more related to each other than they are to eukaryotes has led to the argument that the term ''prokaryote'' has no real evolutionary meaning and should be discarded entirely.<ref name=PMID8177167>{{cite journal |author=Woese CR |title=There must be a prokaryote somewhere: microbiology's search for itself |journal=Microbiol. Rev. |volume=58 |issue=1 |pages=1&ndash;9 |year=1994 |month=March |pmid=8177167 |pmc=372949 |url=http://mmbr.asm.org/cgi/pmidlookup?view=long&pmid=8177167}}</ref>
+Woese argued that the bacteria, archaea, and eukaryotes each represent a separate line of descent that diverged early on from an ancestral colony of organisms.<ref>{{cite journal |author=Woese CR, Gupta R |title=Are archaebacteria merely derived 'prokaryotes'? |journal=Nature |volume=289 |issue=5793 |pages=95&ndash;6 |year=1981 |pmid=6161309 |doi=10.1038/289095a0}}</ref><ref>{{cite journal |author=Woese C |title=The universal ancestor |journal=Proc. Natl. Acad. Sci. U.S.A. |volume=95 |issue=12 |pages=6854&ndash;9 |year=1998 |pmid=9618502 |url=http://www.pnas.org/cgi/pmidlookup?view=long&pmid=9618502 |doi=10.1073/pnas.95.12.6854}}</ref> A few biologists, however, have argued that the Archaea and Eukaryota arose from a group of bacteria.<ref>{{cite journal |author=Gupta RS |title=The natural evolutionary relationships among prokaryotes |journal=Crit. Rev. Microbiol. |volume=26 |issue=2 |pages=111&ndash;31 |year=2000 |pmid=10890353 |doi=10.1080/10408410091154219}}</ref> It is possible that the last common ancestor of the bacteria and archaea was a thermophile, which raises the possibility that lower temperatures are "extreme environments" in archaeal terms, and organisms that live in cooler environments appeared later in the history of life on Earth.<ref>{{cite journal |author=Gribaldo S, Brochier-Armanet C |title=The origin and evolution of Archaea: a state of the art |journal=Philos. Trans. R. Soc. Lond., B, Biol. Sci. |volume=361 |issue=1470 |pages=1007&ndash;22 |year=2006 |pmid=16754611 |url=http://www.journals.royalsoc.ac.uk/content/q74671t476444mq5/ |doi =10.1098/rstb.2006.1841}}</ref> Since the Archaea and Bacteria are no more related to each other than they are to eukaryotes, this has led to the argument that the term ''prokaryote'' has no real evolutionary meaning and should be discarded entirely.<ref name=PMID8177167>{{cite journal |author=Woese CR |title=There must be a prokaryote somewhere: microbiology's search for itself |journal=Microbiol. Rev. |volume=58 |issue=1 |pages=1&ndash;9 |year=1994 |month=March |pmid=8177167 |pmc=372949 |url=http://mmbr.asm.org/cgi/pmidlookup?view=long&pmid=8177167}}</ref>
-The relationship between archaea and eukaryotes remains an important problem. Aside from the similarities in cell structure and function that are discussed below, many genetic trees group the two together, with some early analyses even suggesting that the relationship between eukaryotes and the archaeal phylum [[Euryarchaeota]] is closer than the relationship between the Euryarchaeota and the phylum [[Crenarchaeota]].<ref>{{cite journal |author=Lake JA |title=Origin of the eukaryotic nucleus determined by rate-invariant analysis of rRNA sequences |journal=Nature |volume=331 |issue=6152 |pages=184&ndash;6 |year=1988 |month=January |pmid=3340165 |doi=10.1038/331184a0}}</ref> However, it is now considered more likely that the ancestor of the eukaryotes diverged early from the main Archaeal lineage.<ref>{{cite journal |author=Gouy M, Li WH |title=Phylogenetic analysis based on rRNA sequences supports the archaebacterial rather than the eocyte tree |journal=Nature |volume=339 |issue=6220 |pages=145&ndash;7 |year=1989 |month=May |pmid=2497353 |doi=10.1038/339145a0}}</ref><ref>{{cite journal |author=Yutin N, Makarova KS, Mekhedov SL, Wolf YI, Koonin EV |title=The deep archaeal roots of eukaryotes |journal=Mol. Biol. Evol. |year=2008 |month=May |pmid=18463089 |doi=10.1093/molbev/msn108 |url=http://mbe.oxfordjournals.org/cgi/reprint/msn108v1}}</ref> The discovery of archaean-like genes in certain bacteria, such as ''[[Thermotogae|Thermotoga maritima]]'', makes these relationships difficult to determine, since [[horizontal gene transfer]] has occurred.<ref>{{cite journal |author=Nelson KE, Clayton RA, Gill SR, ''et al'' |title=Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima |journal=Nature |volume=399 |issue=6734 |pages=323&ndash;9 |year=1999 |pmid=10360571 |doi=10.1038/20601}}</ref> Some have suggested that eukaryotes arose through fusion of an archaean and eubacterium, which became the nucleus and [[cytoplasm]]; this accounts for various genetic similarities but runs into difficulties explaining cell structure.<ref>{{cite journal |author=Lake JA. |title=Origin of the eukaryotic nucleus determined by rate-invariant analysis of rRNA sequences |journal=Nature |volume=331 |issue=6152 |pages=184&ndash;6 |year=1988 |pmid=3340165 |doi=10.1038/331184a0}}</ref>
+The relationship between archaea and eukaryotes remains an important problem. Aside from the similarities in cell structure and function that are discussed below, many genetic trees group the two together. Some early analyses even suggested that the relationship between eukaryotes and the archaeal phylum [[Euryarchaeota]] is closer than the relationship between the Euryarchaeota and the phylum [[Crenarchaeota]].<ref>{{cite journal |author=Lake JA |title=Origin of the eukaryotic nucleus determined by rate-invariant analysis of rRNA sequences |journal=Nature |volume=331 |issue=6152 |pages=184&ndash;6 |year=1988 |month=January |pmid=3340165 |doi=10.1038/331184a0}}</ref> However, it is now considered more likely that the ancestor of the eukaryotes diverged early from the Archaea.<ref>{{cite journal |author=Gouy M, Li WH |title=Phylogenetic analysis based on rRNA sequences supports the archaebacterial rather than the eocyte tree |journal=Nature |volume=339 |issue=6220 |pages=145&ndash;7 |year=1989 |month=May |pmid=2497353 |doi=10.1038/339145a0}}</ref><ref>{{cite journal |author=Yutin N, Makarova KS, Mekhedov SL, Wolf YI, Koonin EV |title=The deep archaeal roots of eukaryotes |journal=Mol. Biol. Evol. |year=2008 |month=May |pmid=18463089 |doi=10.1093/molbev/msn108 |url=http://mbe.oxfordjournals.org/cgi/reprint/msn108v1}}</ref> The discovery of archaean-like genes in certain bacteria, such as ''[[Thermotogae|Thermotoga maritima]]'', makes these relationships difficult to determine, since [[horizontal gene transfer]] has occurred.<ref>{{cite journal |author=Nelson KE, Clayton RA, Gill SR, ''et al'' |title=Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima |journal=Nature |volume=399 |issue=6734 |pages=323&ndash;9 |year=1999 |pmid=10360571 |doi=10.1038/20601}}</ref> Some have suggested that eukaryotes arose through fusion of an archaean and eubacterium, which became the nucleus and [[cytoplasm]]; this accounts for various genetic similarities but runs into difficulties explaining cell structure.<ref>{{cite journal |author=Lake JA. |title=Origin of the eukaryotic nucleus determined by rate-invariant analysis of rRNA sequences |journal=Nature |volume=331 |issue=6152 |pages=184&ndash;6 |year=1988 |pmid=3340165 |doi=10.1038/331184a0}}</ref>
 ==Classification==
@@ Line 134: / Line 134: @@
 Archaea are genetically distinct from other organisms, with up to 15% of the proteins encoded by any one archaeal genome being unique to the Archaea, although most of these unique genes have no known function.<ref>{{cite journal |author=Graham DE, Overbeek R, Olsen GJ, Woese CR |title=An archaeal genomic signature |journal=Proc. Natl. Acad. Sci. U.S.A. |volume=97 |issue=7 |pages=3304&ndash;8 |year=2000 |pmid=10716711 |url=http://www.pnas.org/cgi/pmidlookup?view=long&pmid=10716711 |doi =10.1073/pnas.050564797}}</ref> Of the remainder of the genes that are unique to archaea and do have an identified function, most are involved in methanogenesis. The genes that are shared between archaea, bacteria and eukaryotes form a common core of cell function, relating mostly to [[Transcription (genetics)|transcription]], [[Translation (biology)|translation]], and [[nucleotide|nucleotide metabolism]].<ref name=Gaasterland/> Other characteristic features of archaean genomes are the organization of genes of related function—such as enzymes catalysing steps in the same [[metabolic pathway]]—into novel [[operon]]s, and large differences in [[tRNA]] genes and their [[aminoacyl tRNA synthetase]]s.<ref name=Gaasterland>{{cite journal |author=Gaasterland T |title=Archaeal genomics |journal=Curr. Opin. Microbiol. |volume=2 |issue=5 |pages=542&ndash;7 |year=1999 |pmid=10508726 |doi=10.1016/S1369-5274(99)00014-4}}</ref>
-Transcription and translation in archaea are more similar to those in eukaryotes than in bacteria, with archaean [[RNA polymerase II]] and [[ribosome]]s sharing both subunits and sequence similarity with their equivalents in eukaryotes.<ref name=Allers>{{cite journal |author=Allers T, Mevarech M |title=Archaeal genetics - the third way |journal=Nat. Rev. Genet. |volume=6 |issue=1 |pages=58&ndash;73 |year=2005 |pmid=15630422 |doi=10.1038/nrg1504}}</ref> The function and interactions of the archaeal RNA polymerase in transcription also seems to be related to that of eukaryotes, with similar assemblies of proteins (the [[general transcription factor]]s) directing the binding of the RNA polymerase to a gene's [[promoter]]. However, other archaean [[transcription factor]]s are similar to those found in bacteria.<ref>{{cite journal |author=Aravind L, Koonin EV |title=DNA-binding proteins and evolution of transcription regulation in the archaea |journal=Nucleic Acids Res. |volume=27 |issue=23 |pages=4658&ndash;70 |year=1999 |pmid=10556324 |url=http://nar.oxfordjournals.org/cgi/pmidlookup?view=long&pmid=10556324 |doi=10.1093/nar/27.23.4658}}</ref>
+Transcription and translation in archaea are more similar to those in eukaryotes than in bacteria, with archaean [[RNA polymerase II]] and [[ribosome]]s being very similar to their equivalents in eukaryotes.<ref name=Allers>{{cite journal |author=Allers T, Mevarech M |title=Archaeal genetics - the third way |journal=Nat. Rev. Genet. |volume=6 |issue=1 |pages=58&ndash;73 |year=2005 |pmid=15630422 |doi=10.1038/nrg1504}}</ref> The archaeal RNA polymerase in transcription also seems to function in a similar way to that of eukaryotes, with similar assemblies of proteins (the [[general transcription factor]]s) directing the binding of the RNA polymerase to a gene's [[promoter]]. However, other archaean [[transcription factor]]s are similar to those found in bacteria.<ref>{{cite journal |author=Aravind L, Koonin EV |title=DNA-binding proteins and evolution of transcription regulation in the archaea |journal=Nucleic Acids Res. |volume=27 |issue=23 |pages=4658&ndash;70 |year=1999 |pmid=10556324 |url=http://nar.oxfordjournals.org/cgi/pmidlookup?view=long&pmid=10556324 |doi=10.1093/nar/27.23.4658}}</ref>
 ==Reproduction==
 {{Further|[[Asexual reproduction]]}}
-Archaea reproduce asexually by binary or multiple fission, fragmentation, or budding; [[meiosis]] does not occur, so if a species of archaea exists in more than one form, these will all have the same number of chromosomes (they have the same [[karyotype]]).<ref name=Bergey>{{cite book |title=Bergey’s Manual® of Systematic Bacteriology |last=Krieg |first=Noel |year=2005 |publisher=Springer |location=USA |isbn=978-0-387-24143-2 |pages=21&ndash;6}}</ref> [[Cell division]] is controlled in the archaea as part of a complex [[cell cycle]]; after the cell's [[chromosome]] is replicated and the two daughter chromosomes are separated, the cell divides.<ref name=Bernander>{{cite journal |author=Bernander R |title=Archaea and the cell cycle |journal=Mol. Microbiol. |volume=29 |issue=4 |pages=955&ndash;61 |year=1998 |pmid=9767564 |doi=10.1046/j.1365-2958.1998.00956.x}}</ref> The details of the archaeal cell cycle have only been investigated in the genus ''[[Sulfolobus]]'', but here it has characters that are similar to both bacterial and eukaryotic systems: with the chromosomes being replicated from multiple starting-points ([[origin of replication|origins of replication]]) using [[DNA polymerase]]s that are similar to the equivalent eukaryotic enzymes.<ref>{{cite journal |author=Kelman LM, Kelman Z |title=Multiple origins of replication in archaea |journal=Trends Microbiol. |volume=12 |issue=9 |pages=399&ndash;401 |year=2004 |pmid=153371581 |doi=10.1016/j.tim.2004.07.001}}</ref> However, the proteins that direct cell division, such as the protein [[FtsZ]], which forms a contracting ring around the cell, and the components of the [[septum]] that is constructed across the center of the cell, are closer to their bacterial equivalents.<ref name=Bernander/>
+Archaea reproduce asexually by binary or multiple fission, fragmentation, or budding; [[meiosis]] does not occur, so if a species of archaea exists in more than one form, these will all have the same number of chromosomes (they have the same [[karyotype]]).<ref name=Bergey>{{cite book |title=Bergey’s Manual® of Systematic Bacteriology |last=Krieg |first=Noel |year=2005 |publisher=Springer |location=USA |isbn=978-0-387-24143-2 |pages=21&ndash;6}}</ref> [[Cell division]] is controlled in the archaea as part of a complex [[cell cycle]]; after the cell's [[chromosome]] is replicated and the two daughter chromosomes are separated, the cell divides.<ref name=Bernander>{{cite journal |author=Bernander R |title=Archaea and the cell cycle |journal=Mol. Microbiol. |volume=29 |issue=4 |pages=955&ndash;61 |year=1998 |pmid=9767564 |doi=10.1046/j.1365-2958.1998.00956.x}}</ref> The details of the archaeal cell cycle have only been investigated in the genus ''[[Sulfolobus]]'', but here it has characters that are similar to both bacterial and eukaryotic systems. In this archaean, the chromosomes are replicated from multiple starting-points ([[origin of replication|origins of replication]]) using [[DNA polymerase]]s that are similar to the equivalent eukaryotic enzymes.<ref>{{cite journal |author=Kelman LM, Kelman Z |title=Multiple origins of replication in archaea |journal=Trends Microbiol. |volume=12 |issue=9 |pages=399&ndash;401 |year=2004 |pmid=153371581 |doi=10.1016/j.tim.2004.07.001}}</ref> However, the proteins that direct cell division, such as the protein [[FtsZ]], which forms a contracting ring around the cell, and the components of the [[septum]] that is constructed across the center of the cell, are similar to their bacterial equivalents.<ref name=Bernander/>
 Spores, such as the [[endospore]]s made by some bacteria, are not formed in any of the known archaea.<ref>{{cite journal |author=Onyenwoke RU, Brill JA, Farahi K, Wiegel J |title=Sporulation genes in members of the low G+C Gram-type-positive phylogenetic branch ( Firmicutes) |journal=Arch. Microbiol. |volume=182 |issue=2–3 |pages=182&ndash;92 |year=2004 |pmid=15340788 |doi=10.1007/s00203-004-0696-y}}</ref> Some species of [[Haloarchaea]] undergo [[phenotypic switching]] and grow as several different types of cell, including thick-walled structures that are resistant to [[osmotic shock]] and allow the archaea to survive in water at low concentrations of salt, but these are not reproductive structures and may instead help them disperse to new habitats.<ref>{{cite journal |author=Kostrikina NA, Zvyagintseva IS, Duda VI. |title=Cytological peculiarities of some extremely halophilic soil archaeobacteria |journal=Arch. Microbiol. |volume=156 |issue=5 |pages=344&ndash;49 |year=1991 |doi=10.1007/BF00248708}}</ref>
@@ Line 147: / Line 147: @@
 Archaea exist in a broad range of [[habitat]]s, and are a major part of global [[ecosystem]]s,<ref name=DeLong/> and may contribute up to 20% of the total [[Biomass (ecology)|biomass]] on Earth.<ref>{{cite journal |author=DeLong EF, Pace NR |title=Environmental diversity of bacteria and archaea |journal=Syst. Biol. |volume=50 |issue=4 |pages=470&ndash;8 |year=2001 |pmid=12116647 |doi=10.1080/106351501750435040}}</ref> Multiple archaeans are [[extremophile]]s, and historically this was seen as their [[ecological niche]].<ref name=valentine/> Indeed, some archaea survive high temperatures, often above 100&nbsp;[[Celsius|°C]], as found in [[geyser]]s, [[black smoker]]s, and oil wells. Others are found in very cold habitats and others in highly [[salt|saline]], [[acid]]ic, or [[alkaline]] water. However, other archaea are [[mesophile]]s that grow in much milder conditions, in [[marsh]]land, [[sewage]], the [[ocean]]s, and [[soil]]s.<ref name=DeLong/>
 [[Image:Phytoplankton CZCS.jpg|thumb|left|300px|Image of [[plankton]] in the [[ocean]]s; archaea form a major part of oceanic life.]]
-Extremophile archaea are members of four main [[physiological]] groups. These are the [[halophile]]s, [[thermophile]]s, [[alkaliphile]]s, and [[Acidophile (organisms)|acidophile]]s.<ref name=Pikuta/> These groups are not comprehensive or [[monophyletic]], nor even mutually exclusive. Nonetheless, they are a useful starting point for classification. Halophiles, including the genus ''[[Halobacterium]]'', live in extremely saline environments such as [[salt lake]]s and start outnumbering their bacterial counterparts at salinities greater than 20–25%.<ref name=valentine/> Thermophiles live in places that have high temperatures, such as hot springs.  ''Hyperthermophilic'' archaea are defined as those that grow optimally at temperatures greater than 80&nbsp;°C; the archaeal [[Strain 121]] grows at 121&nbsp;°C, which is the highest recorded temperature at which any organism will grow.<ref>{{cite journal |author=Cowen DA |title=The upper temperature of life—where do we draw the line? |journal=Trends Microbiol. |volume=12 |issue=2 |pages=58&ndash;60 |year=2004 |month=February |pmid=15040324}}</ref> Other archaea exist in very acid or alkali conditions.<ref name=Pikuta>{{cite journal |author=Pikuta EV, Hoover RB, Tang J |title=Microbial extremophiles at the limits of life |journal=Crit. Rev. Microbiol. |volume=33 |issue=3 |pages=183&ndash;209 |year=2007 |pmid=17653987 |doi=10.1080/10408410701451948}}</ref> For example, one of the most extreme archaean acidophiles is ''Picrophilus torridus'', which grows at pH&nbsp;0, which is equivalent to thriving in 1.2&nbsp;[[Molar concentration|Molar]] [[sulfuric acid]].<ref>{{cite journal |author=Ciaramella M, Napoli A, Rossi M |title=Another extreme genome: how to live at pH 0 |journal=Trends Microbiol. |volume=13 |issue=2 |pages=49&ndash;51 |year=2005 |month=February |pmid=15680761 |doi=10.1016/j.tim.2004.12.001}}</ref>
+Extremophile archaea are members of four main [[physiological]] groups. These are the [[halophile]]s, [[thermophile]]s, [[alkaliphile]]s, and [[Acidophile (organisms)|acidophile]]s.<ref name=Pikuta/> These groups are not comprehensive or related to which phylum the organisms belong to, nor are they mutually exclusive, since some archaea belong to several of these groups. Nonetheless, they are a useful starting point for classification. Halophiles, including the genus ''[[Halobacterium]]'', live in extremely saline environments such as [[salt lake]]s and start outnumbering their bacterial counterparts at salinities greater than 20–25%.<ref name=valentine/> Thermophiles live in places that have high temperatures, such as hot springs.  ''Hyperthermophilic'' archaea are defined as those that grow optimally at temperatures greater than 80&nbsp;°C; the archaeal [[Strain 121]] grows at 121&nbsp;°C, which is the highest recorded temperature at which any organism will grow.<ref>{{cite journal |author=Cowen DA |title=The upper temperature of life—where do we draw the line? |journal=Trends Microbiol. |volume=12 |issue=2 |pages=58&ndash;60 |year=2004 |month=February |pmid=15040324}}</ref> Other archaea exist in very acid or alkali conditions.<ref name=Pikuta>{{cite journal |author=Pikuta EV, Hoover RB, Tang J |title=Microbial extremophiles at the limits of life |journal=Crit. Rev. Microbiol. |volume=33 |issue=3 |pages=183&ndash;209 |year=2007 |pmid=17653987 |doi=10.1080/10408410701451948}}</ref> For example, one of the most extreme archaean acidophiles is ''Picrophilus torridus'', which grows at pH&nbsp;0, which is equivalent to thriving in 1.2&nbsp;[[Molar concentration|Molar]] [[sulfuric acid]].<ref>{{cite journal |author=Ciaramella M, Napoli A, Rossi M |title=Another extreme genome: how to live at pH 0 |journal=Trends Microbiol. |volume=13 |issue=2 |pages=49&ndash;51 |year=2005 |month=February |pmid=15680761 |doi=10.1016/j.tim.2004.12.001}}</ref>
 This resistance to extreme environments has made archaea the focus of speculation about the possible properties of [[extraterrestrial life]].<ref>{{cite journal |author=Javaux EJ |title=Extreme life on Earth—past, present and possibly beyond |journal=Res. Microbiol. |volume=157 |issue=1 |pages=37&ndash;48 |year=2006 |pmid=16376523 |doi=10.1016/j.resmic.2005.07.008}}</ref> This has focused on the possibility that microbial life may exist on [[Mars]],<ref>{{cite journal |author=Nealson KH |title=Post-Viking microbiology: new approaches, new data, new insights |journal=Orig Life Evol Biosph |volume=29 |issue=1 |pages=73&ndash;93 |year=1999 |month=January |pmid=11536899 |url=http://www.kluweronline.com/art.pdf?issn=0169-6149&volume=29&page=73}}</ref> and has even led to the suggestion that viable microbes could be transferred between planets in [[meteorite]]s.<ref>{{cite journal |author=Davies PC |title=The transfer of viable microorganisms between planets |journal=Ciba Found. Symp. |volume=202 |pages=304&ndash;14; discussion 314–7 |year=1996 |pmid=9243022}}</ref>
@@ Line 170: / Line 170: @@
 The well-characterized interactions between archaea and other organisms are either [[mutualistic|mutualism]] or [[commensalism|commensal]]. As of 2007, no clear examples of archaeal [[pathogen]]s or [[parasite]]s are known.<ref>{{cite journal |author=Eckburg P, Lepp P, Relman D |title=Archaea and their potential role in human disease |journal=Infect Immun |volume=71 |issue=2 |pages=591&ndash;6 |year=2003 |pmid=12540534 |doi=10.1128/IAI.71.2.591-596.2003}}</ref><ref>{{cite journal |author=Cavicchioli R, Curmi P, Saunders N, Thomas T |title=Pathogenic archaea: do they exist? |journal=Bioessays |volume=25 |issue=11 |pages=1119&ndash;28 |year=2003 |pmid=14579252 |doi=10.1002/bies.10354}}</ref> However, a relationship has been proposed between the presence of some species of methanogens and [[periodontal disease|infections in the mouth]],<ref>{{cite journal |author=Lepp P, Brinig M, Ouverney C, Palm K, Armitage G, Relman D |title=Methanogenic Archaea and human periodontal disease |journal=Proc Natl Acad Sci U S A |volume=101 |issue=16 |pages=6176&ndash;81 |year=2004 |pmid=15067114 |doi=10.1073/pnas.0308766101}}</ref><ref>{{cite journal |author=Vianna ME, Conrads G, Gomes BP, Horz HP |title=Identification and quantification of archaea involved in primary endodontic infections |journal=J. Clin. Microbiol. |volume=44 |issue=4 |pages=1274&ndash;82 |year=2006 |month=April |pmid=16597851 |pmc=1448633 |doi=10.1128/JCM.44.4.1274-1282.2006 |url=http://jcm.asm.org/cgi/pmidlookup?view=long&pmid=16597851}}</ref> and ''[[Nanoarchaeum equitans]]'' may be parasitic, since it only survives and reproduces within the cells of the Crenarchaeon ''[[Ignicoccus|Ignicoccus hospitalis]]'',<ref>{{cite journal |author=Waters E, Hohn MJ, Ahel I, ''et al'' |title=The genome of Nanoarchaeum equitans: insights into early archaeal evolution and derived parasitism |journal=Proc. Natl. Acad. Sci. U.S.A. |volume=100 |issue=22 |pages=12984&ndash;8 |year=2003 |month=October |pmid=14566062 |pmc=240731 |doi=10.1073/pnas.1735403100 |url=http://www.pnas.org/cgi/pmidlookup?view=long&pmid=14566062}}</ref> and appears to offer no benefit to its [[host (biology)|host]].<ref>{{cite journal |author=Jahn U, Gallenberger M, Paper W, ''et al'' |title=Nanoarchaeum equitans and Ignicoccus hospitalis: new insights into a unique, intimate association of two archaea |journal=J. Bacteriol. |volume=190 |issue=5 |pages=1743&ndash;50 |year=2008 |month=March |pmid=18165302 |doi=10.1128/JB.01731-07 |url=http://jb.asm.org/cgi/pmidlookup?view=long&pmid=18165302}}</ref>
-The best-understood example of archaean mutualists are the [[methanogen]]ic archaea that are found in the digestive tracts of animals that digest [[cellulose]], such as [[ruminant]]s and [[termite]]s.<ref name=Chaban>{{cite journal |author=Chaban B, Ng SY, Jarrell KF |title=Archaeal habitats—from the extreme to the ordinary |journal=Can. J. Microbiol. |volume=52 |issue=2 |pages=73&ndash;116 |year=2006 |month=February |pmid=16541146 |doi=10.1139/w05-147}}</ref> In these environments, the archaea consume the hydrogen produced during cellulose digestion by anaerobic [[protozoa]],<ref>{{cite journal |author=Purdy KJ |title=The distribution and diversity of Euryarchaeota in termite guts |journal=Adv. Appl. Microbiol. |volume=62 |pages=63&ndash;80 |year=2007 |pmid=17869602 |doi=10.1016/S0065-2164(07)62003-6}}</ref> and in turn the archaea supply enzymes necessary for the digestion of cellulose as well as break down potentially dangerous hydrogen gas. These associations between methanogens and protozoa are taken a step further in several species of anaerobic protozoa, such as ''Plagiopyla frontata''; here the archaea actually reside inside the protozoa and consume the hydrogen produced in their [[hydrogenosome]]s.<ref name=Lange2005>{{cite journal |author=Lange, M.; Westermann, P.; Ahring, B.K. |year=2005 |title=Archaea in protozoa and metazoa |journal=Applied Microbiology and Biotechnology |volume=66 |issue=5 |pages=465–474}}</ref><ref>{{cite journal |author=van Hoek AH, van Alen TA, Sprakel VS, ''et al'' |title=Multiple acquisition of methanogenic archaeal symbionts by anaerobic ciliates |journal=Mol. Biol. Evol. |volume=17 |issue=2 |pages=251&ndash;8 |year=2000 |month=February |pmid=10677847 |url=http://mbe.oxfordjournals.org/cgi/pmidlookup?view=long&pmid=10677847}}</ref> Similar associations with multicellular organisms are now being found, with the discovery that the marine archaean ''[[Cenarchaeum|Cenarchaeum symbiosum]]'' lives within (it is an [[endosymbiont]] of) the [[sponge]] ''Axinella mexicana''.<ref name=Preston1996>{{cite journal |year=1996 |title=A psychrophilic crenarchaeon inhabits a marine sponge: Cenarchaeum symbiosum gen. nov., sp. nov. |journal=Proc Natl Acad Sci USA |volume=93 |issue=13 |pages=6241&ndash;6246 |url=http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=39006 |author=Preston, C.M.; Wu, K.Y.; Molinski, T.F.; Delong, E.F. |doi =10.1073/pnas.93.13.6241 |pmid =8692799}}</ref>
+The best-understood example of archaean mutualists are the [[methanogen]]ic archaea that are found in the digestive tracts of animals that digest [[cellulose]], such as [[ruminant]]s and [[termite]]s.<ref name=Chaban>{{cite journal |author=Chaban B, Ng SY, Jarrell KF |title=Archaeal habitats—from the extreme to the ordinary |journal=Can. J. Microbiol. |volume=52 |issue=2 |pages=73&ndash;116 |year=2006 |month=February |pmid=16541146 |doi=10.1139/w05-147}}</ref> In these environments, the archaea consume the hydrogen produced during cellulose digestion by anaerobic [[protozoa]], helping the protozoa gain energy from this process.<ref>{{cite journal |author=Purdy KJ |title=The distribution and diversity of Euryarchaeota in termite guts |journal=Adv. Appl. Microbiol. |volume=62 |pages=63&ndash;80 |year=2007 |pmid=17869602 |doi=10.1016/S0065-2164(07)62003-6}}</ref> These associations between methanogens and protozoa are taken a step further in several species of anaerobic protozoa, such as ''Plagiopyla frontata''; here the archaea actually reside inside the protozoa and consume the hydrogen produced in their [[hydrogenosome]]s.<ref name=Lange2005>{{cite journal |author=Lange, M.; Westermann, P.; Ahring, B.K. |year=2005 |title=Archaea in protozoa and metazoa |journal=Applied Microbiology and Biotechnology |volume=66 |issue=5 |pages=465–474}}</ref><ref>{{cite journal |author=van Hoek AH, van Alen TA, Sprakel VS, ''et al'' |title=Multiple acquisition of methanogenic archaeal symbionts by anaerobic ciliates |journal=Mol. Biol. Evol. |volume=17 |issue=2 |pages=251&ndash;8 |year=2000 |month=February |pmid=10677847 |url=http://mbe.oxfordjournals.org/cgi/pmidlookup?view=long&pmid=10677847}}</ref> Similar associations with larger organisms are now being found, with the discovery that the marine archaean ''[[Cenarchaeum|Cenarchaeum symbiosum]]'' lives within (it is an [[endosymbiont]] of) the [[sponge]] ''Axinella mexicana''.<ref name=Preston1996>{{cite journal |year=1996 |title=A psychrophilic crenarchaeon inhabits a marine sponge: Cenarchaeum symbiosum gen. nov., sp. nov. |journal=Proc Natl Acad Sci USA |volume=93 |issue=13 |pages=6241&ndash;6246 |url=http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=39006 |author=Preston, C.M.; Wu, K.Y.; Molinski, T.F.; Delong, E.F. |doi =10.1073/pnas.93.13.6241 |pmid =8692799}}</ref>
-Archaea can also be commensals, benefitting from an association without helping or harming the other organism. For example, the formate-consuming methanogen ''[[Methanobrevibacter smithii]]'' is by far the most common archaean in the [[human flora]], with this species making up about one in ten of all the prokaryotes in the human gut.<ref>{{cite journal |author=Eckburg PB, Bik EM, Bernstein CN, ''et al'' |title=Diversity of the human intestinal microbial flora |journal=Science (journal) |volume=308 |issue=5728 |pages=1635&ndash;8 |year=2005 |month=June |pmid=15831718 |pmc=1395357 |doi=10.1126/science.1110591 |url=http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=15831718}}</ref> As in termites, these methanogens may in fact be mutualists in humans, interacting with other microbes in the gut to aid the digestion of food.<ref>{{cite journal |author=Samuel BS, Gordon JI |title=A humanized gnotobiotic mouse model of host-archaeal-bacterial mutualism |journal=Proc. Natl. Acad. Sci. U.S.A. |volume=103 |issue=26 |pages=10011&ndash;6 |year=2006 |month=June |pmid=16782812 |pmc=1479766 |doi=10.1073/pnas.0602187103}}</ref> Communities of archaea are also associated with a range of other organisms, such as on the surface of [[coral]]s,<ref>{{cite journal |author=Wegley, L.; Yu, Y.; Breitbart, M.; Casas, V.; Kline, D.I.; Rohwer, F. |year =2004 |title =Coral-associated Archaea |journal =Marine Ecology Progress Series |volume =273 |pages =89–96 |url =http://www.marine.usf.edu/genomics/PDFs%20of%20papers/wegleyetal2004.pdf}}</ref> and in the region of soil that surrounds plant roots (the [[Rhizosphere (ecology)|rhizosphere]]).<ref>{{cite journal |author=Chelius MK, Triplett EW |title=The Diversity of Archaea and Bacteria in Association with the Roots of Zea mays L |journal=Microb. Ecol. |volume=41 |issue=3 |pages=252&ndash;63 |year=2001 |month=April |pmid=11391463 |doi=10.1007/s002480000087}}</ref><ref>{{cite journal |author=Simon HM, Dodsworth JA, Goodman RM |title=Crenarchaeota colonize terrestrial plant roots |journal=Environ. Microbiol. |volume=2 |issue=5 |pages=495&ndash;505 |year=2000 |month=October |pmid=11233158}}</ref>
+Archaea can also be commensals, benefiting from an association without helping or harming the other organism. For example, the formate-consuming methanogen ''[[Methanobrevibacter smithii]]'' is by far the most common archaean in the [[human flora]], with this species making up about one in ten of all the prokaryotes in the human gut.<ref>{{cite journal |author=Eckburg PB, Bik EM, Bernstein CN, ''et al'' |title=Diversity of the human intestinal microbial flora |journal=Science (journal) |volume=308 |issue=5728 |pages=1635&ndash;8 |year=2005 |month=June |pmid=15831718 |pmc=1395357 |doi=10.1126/science.1110591 |url=http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=15831718}}</ref> As in termites, these methanogens may in fact be mutualists in humans, interacting with other microbes in the gut to aid the digestion of food.<ref>{{cite journal |author=Samuel BS, Gordon JI |title=A humanized gnotobiotic mouse model of host-archaeal-bacterial mutualism |journal=Proc. Natl. Acad. Sci. U.S.A. |volume=103 |issue=26 |pages=10011&ndash;6 |year=2006 |month=June |pmid=16782812 |pmc=1479766 |doi=10.1073/pnas.0602187103}}</ref> Communities of archaea are also associated with a range of other organisms, such as on the surface of [[coral]]s,<ref>{{cite journal |author=Wegley, L.; Yu, Y.; Breitbart, M.; Casas, V.; Kline, D.I.; Rohwer, F. |year =2004 |title =Coral-associated Archaea |journal =Marine Ecology Progress Series |volume =273 |pages =89–96 |url =http://www.marine.usf.edu/genomics/PDFs%20of%20papers/wegleyetal2004.pdf}}</ref> and in the region of soil that surrounds plant roots (the [[Rhizosphere (ecology)|rhizosphere]]).<ref>{{cite journal |author=Chelius MK, Triplett EW |title=The Diversity of Archaea and Bacteria in Association with the Roots of Zea mays L |journal=Microb. Ecol. |volume=41 |issue=3 |pages=252&ndash;63 |year=2001 |month=April |pmid=11391463 |doi=10.1007/s002480000087}}</ref><ref>{{cite journal |author=Simon HM, Dodsworth JA, Goodman RM |title=Crenarchaeota colonize terrestrial plant roots |journal=Environ. Microbiol. |volume=2 |issue=5 |pages=495&ndash;505 |year=2000 |month=October |pmid=11233158}}</ref>
 ==Significance in technology and industry==