archaea
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Archaea ( ; singular archaeon ) is a domain of single-celled organisms. These microorganisms lack cell nuclei and are therefore prokaryotes. Archaea were initially classified as
bacteria Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were a ...
, receiving the name archaebacteria (in the Archaebacteria kingdom), but this term has fallen out of use. Archaeal cells have unique properties separating them from the other two domains,
Bacteria Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were a ...
and Eukaryota. Archaea are further divided into multiple recognized phyla. Classification is difficult because most have not been isolated in a laboratory and have been detected only by their gene sequences in environmental samples. Archaea and bacteria are generally similar in size and shape, although a few archaea have very different shapes, such as the flat, square cells of '' Haloquadratum walsbyi''. Despite this morphological similarity to bacteria, archaea possess
gene In biology, the word gene (from , ; "... Wilhelm Johannsen coined the word gene to describe the Mendelian units of heredity..." meaning ''generation'' or ''birth'' or ''gender'') can have several different meanings. The Mendelian gene is a ...
s and several metabolic pathways that are more closely related to those of eukaryotes, notably for the
enzyme Enzymes () are protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic rea ...
s involved in transcription and translation. Other aspects of archaeal biochemistry are unique, such as their reliance on ether lipids in their
cell membrane The cell membrane (also known as the plasma membrane (PM) or cytoplasmic membrane, and historically referred to as the plasmalemma) is a biological membrane that separates and protects the interior of all cells from the outside environment ( ...
s, including archaeols. Archaea use more diverse energy sources than eukaryotes, ranging from organic compounds such as sugars, to
ammonia Ammonia is an inorganic compound of nitrogen and hydrogen with the formula . A stable binary hydride, and the simplest pnictogen hydride, ammonia is a colourless gas with a distinct pungent smell. Biologically, it is a common nitrogen ...
, metal ions or even hydrogen gas. The salt-tolerant Haloarchaea use sunlight as an energy source, and other species of archaea fix carbon (autotrophy), but unlike plants and cyanobacteria, no known species of archaea does both. Archaea reproduce asexually by binary fission, fragmentation, or budding; unlike bacteria, no known species of Archaea form endospores. The first observed archaea were extremophiles, living in extreme environments such as hot springs and salt lakes with no other organisms. Improved molecular detection tools led to the discovery of archaea in almost every
habitat In ecology, the term habitat summarises the array of resources, physical and biotic factors that are present in an area, such as to support the survival and reproduction of a particular species. A species habitat can be seen as the physical ...
, including soil, oceans, and marshlands. Archaea are particularly numerous in the oceans, and the archaea in
plankton Plankton are the diverse collection of organisms found in water (or air) that are unable to propel themselves against a current (or wind Wind is the natural movement of air or other gases relative to a planet's surface. Winds occu ...
may be one of the most abundant groups of organisms on the planet. Archaea are a major part of Earth's life. They are part of the microbiota of all organisms. In the human microbiome, they are important in the gut, mouth, and on the skin. Their morphological, metabolic, and geographical diversity permits them to play multiple ecological roles: carbon fixation; nitrogen cycling; organic compound turnover; and maintaining microbial symbiotic and syntrophic communities, for example. No clear examples of archaeal pathogens or
parasite Parasitism is a close relationship between species, where one organism, the parasite, lives on or inside another organism, the host, causing it some harm, and is adapted structurally to this way of life. The entomologist E. O. Wilson ...
s are known. Instead they are often mutualists or commensals, such as the methanogens (methane-producing strains) that inhabit the gastrointestinal tract in humans and ruminants, where their vast numbers facilitate digestion. Methanogens are also used in biogas production and sewage treatment, and biotechnology exploits enzymes from extremophile archaea that can endure high temperatures and organic solvents.


Classification


Early concept

For much of the 20th century, prokaryotes were regarded as a single group of organisms and classified based on their
biochemistry Biochemistry or biological chemistry is the study of chemical processes within and relating to living organisms. A sub-discipline of both chemistry Chemistry is the scientific study of the properties and behavior of matter. It is a ...
, morphology and
metabolism Metabolism (, from el, μεταβολή ''metabolē'', "change") is the set of life-sustaining chemical reactions in organisms. The three main functions of metabolism are: the conversion of the energy in food to energy available to run ...
. Microbiologists tried to classify microorganisms based on the structures of their
cell wall A cell wall is a structural layer surrounding some types of cells, just outside the cell membrane The cell membrane (also known as the plasma membrane (PM) or cytoplasmic membrane, and historically referred to as the plasmalemma) is a biolo ...
s, their shapes, and the substances they consume. In 1965, Emile Zuckerkandl and
Linus Pauling Linus Carl Pauling (; February 28, 1901August 19, 1994) was an American chemist, biochemist, chemical engineer, peace activist, author, and educator. He published more than 1,200 papers and books, of which about 850 dealt with scientific ...
instead proposed using the sequences of the
gene In biology, the word gene (from , ; "... Wilhelm Johannsen coined the word gene to describe the Mendelian units of heredity..." meaning ''generation'' or ''birth'' or ''gender'') can have several different meanings. The Mendelian gene is a ...
s in different prokaryotes to work out how they are related to each other. This phylogenetic approach is the main method used today. Archaea – at that time only the methanogens were known – were first classified separately from bacteria in 1977 by Carl Woese and George E. Fox based on their
ribosomal RNA Ribosomal ribonucleic acid (rRNA) is a type of non-coding RNA which is the primary component of ribosomes, essential to all cells. rRNA is a ribozyme which carries out protein synthesis Protein biosynthesis (or protein synthesis) is a cor ...
(rRNA) genes. They called these groups the ''Urkingdoms'' of Archaebacteria and Eubacteria, though other researchers treated them as kingdoms or subkingdoms. Woese and Fox gave the first evidence for Archaebacteria as a separate "line of descent": 1. lack of peptidoglycan in their cell walls, 2. two unusual coenzymes, 3. results of 16S ribosomal RNA gene sequencing. To emphasize this difference, Woese, Otto Kandler and Mark Wheelis later proposed reclassifying organisms into three natural domains known as the three-domain system: the
Eukarya Eukaryotes () are organisms whose cells have a nucleus. All animals, plants, fungi, and many unicellular organisms, are Eukaryotes. They belong to the group of organisms Eukaryota or Eukarya, which is one of the three domains of life. Bac ...
, the
Bacteria Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were a ...
and the Archaea, in what is now known as the Woesian Revolution. The word ''archaea'' comes from the
Ancient Greek Ancient Greek includes the forms of the Greek language used in ancient Greece and the ancient world Ancient history is a time period from the beginning of writing and recorded human history to as far as late antiquity. The s ...
, meaning "ancient things", as the first representatives of the domain Archaea were methanogens and it was assumed that their metabolism reflected Earth's primitive atmosphere and the organisms' antiquity, but as new habitats were studied, more organisms were discovered. Extreme halophilic and hyperthermophilic microbes were also included in Archaea. For a long time, archaea were seen as extremophiles that exist only in extreme habitats such as hot springs and salt lakes, but by the end of the 20th century, archaea had been identified in non-extreme environments as well. Today, they are known to be a large and diverse group of organisms abundantly distributed throughout nature. This new appreciation of the importance and ubiquity of archaea came from using
polymerase chain reaction The polymerase chain reaction (PCR) is a method widely used to rapidly make millions to billions of copies (complete or partial) of a specific DNA sample, allowing scientists to take a very small sample of DNA and amplify it (or a part of it) ...
(PCR) to detect prokaryotes from environmental samples (such as water or soil) by multiplying their ribosomal genes. This allows the detection and identification of organisms that have not been cultured in the laboratory.


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. These classifications rely heavily on the use of the sequence of
ribosomal RNA Ribosomal ribonucleic acid (rRNA) is a type of non-coding RNA which is the primary component of ribosomes, essential to all cells. rRNA is a ribozyme which carries out protein synthesis Protein biosynthesis (or protein synthesis) is a cor ...
genes to reveal relationships among organisms ( molecular phylogenetics). Most of the culturable and well-investigated species of archaea are members of two main phyla, the " Euryarchaeota" and the Thermoproteota (formerly Crenarchaeota). Other groups have been tentatively created, like the peculiar species '' Nanoarchaeum equitans'', which was discovered in 2003 and has been given its own phylum, the " Nanoarchaeota". A new phylum " Korarchaeota" has also been proposed. It contains a small group of unusual thermophilic species that shares features of both of the main phyla, but is most closely related to the Thermoproteota. Other recently detected species of archaea are only distantly related to any of these groups, such as the Archaeal Richmond Mine acidophilic nanoorganisms (ARMAN, comprising Micrarchaeota and Parvarchaeota), which were discovered in 2006 and are some of the smallest organisms known. A superphylum – TACK – which includes the Thaumarchaeota (now Nitrososphaerota), " Aigarchaeota", Crenarchaeota (now Thermoproteota), and " Korarchaeota" was proposed in 2011 to be related to the origin of eukaryotes. In 2017, the newly discovered and newly named Asgard superphylum was proposed to be more closely related to the original eukaryote and a sister group to TACK. In 2013 the superphylum DPANN was proposed to group " Nanoarchaeota", " Nanohaloarchaeota", Archaeal Richmond Mine acidophilic nanoorganisms (ARMAN, comprising " Micrarchaeota" and " Parvarchaeota"), and other similar archaea. This archaeal superphylum encompasses at least 10 different lineages and includes organisms with extremely small cell and genome sizes and limited metabolic capabilities. Therefore, many members of DPANN may be obligately dependent on symbiotic interactions with other organisms and may even include novel parasites. However, in other phylogenetic analyses it was found that DPANN does not form a monophyletic group and that it is caused by the long branch attraction (LBA), suggesting that all these lineages belong to "Euryarchaeota".


Cladogram

According to Tom A. Williams ''et al.'' (2017), Castelle & Banfield (2018) and GTDB release 07-RS207 (8th April 2022):


Concept of species

The classification of archaea into species is also controversial. Biology defines a
species In biology Biology is the scientific study of life. It is a natural science with a broad scope but has several unifying themes that tie it together as a single, coherent field. For instance, all organisms are made up of cells that ...
as a group of related organisms. The familiar exclusive breeding criterion (organisms that can breed with each other but not with others) is of no help since archaea only reproduce asexually. Archaea show high levels of horizontal gene transfer between lineages. Some researchers suggest that individuals can be grouped into species-like populations given highly similar genomes and infrequent gene transfer to/from cells with less-related genomes, as in the genus '' Ferroplasma''. On the other hand, studies in '' Halorubrum'' found significant genetic transfer to/from less-related populations, limiting the criterion's applicability. Some researchers question whether such species designations have practical meaning. Current knowledge on genetic diversity is fragmentary and the total number of archaeal species cannot be estimated with any accuracy. Estimates of the number of phyla range from 18 to 23, of which only 8 have representatives that have been cultured and studied directly. Many of these hypothesized groups are known from a single rRNA sequence, indicating that the diversity among these organisms remains obscure. The Bacteria also include many uncultured microbes with similar implications for characterization.


Phyla


Valid Phyla

The following phyla have been validly published according to the Bacteriological Code: * Nitrososphaerota * Thermoproteota


Provisional Phyla

The following phyla have been proposed, but have not been validly published according to the Bacteriological Code (including those that have '' candidatus'' status): * "''Candidatus'' Aenigmarchaeota" * "''Candidatus'' Aigarchaeota" * "''Candidatus'' Altiarchaeota" * "''Candidatus'' Asgardaeota" * "''Candidatus'' Bathyarchaeota" * "''Candidatus'' Brockarchaeota" * "''Candidatus'' Diapherotrites" * "'' Euryarchaeota''" * "''Candidatus'' Geoarchaeota" * "''Candidatus'' Hadarchaeota" * "''Candidatus'' Hadesarchaeota" * "''Candidatus'' Halobacterota" * "''Candidatus'' Heimdallarchaeota" * "''Candidatus'' Helarchaeota" * "''Candidatus'' Huberarchaeota" * "''Candidatus'' Hydrothermarchaeota" * "''Candidatus'' Korarchaeota" * "''Candidatus'' Lokiarchaeia" * "''Candidatus'' Lokiarchaeota" * "''Candidatus'' Mamarchaeota" * "''Candidatus'' Marsarchaeota" * "''Candidatus'' Methanobacteriota" * "''Candidatus'' Micrarchaeota" * "''Candidatus'' Nanoarchaeota" * "''Candidatus'' Nanohaloarchaeota" * "''Candidatus'' Nezhaarchaeota" * "''Candidatus'' Odinarchaeota" * "''Candidatus'' Pacearchaeota" * "''Candidatus'' Parvarchaeota" * "''Candidatus'' Thermoplasmatota" * "''Candidatus'' Thorarchaeota" * "''Candidatus'' Undinarchaeota" * "''Candidatus'' Verstraetearchaeota" * "''Candidatus'' Woesearchaeota"


Origin and evolution

The age of the Earth is about 4.54 billion years. Scientific evidence suggests that life began on Earth at least 3.5  billion years ago. The earliest evidence for life on Earth is graphite found to be biogenic in 3.7-billion-year-old metasedimentary rocks discovered in Western Greenland and microbial mat fossils found in 3.48-billion-year-old
sandstone Sandstone is a clastic sedimentary rock composed mainly of sand-sized (0.0625 to 2 mm) silicate grains. Sandstones comprise about 20–25% of all sedimentary rock Sedimentary rocks are types of rock that are formed by the accu ...
discovered in
Western Australia Western Australia (commonly abbreviated as WA) is a state of Australia occupying the western percent of the land area of Australia excluding external territories. It is bounded by the Indian Ocean to the north and west, the Southern Ocean to th ...
. In 2015, possible remains of biotic matter were found in 4.1-billion-year-old rocks in Western Australia. Although probable prokaryotic cell fossils date to almost 3.5  billion years ago, most prokaryotes do not have distinctive morphologies, and fossil shapes cannot be used to identify them as archaea. Instead, chemical fossils of unique
lipid Lipids are a broad group of naturally-occurring molecules which includes fats, waxes, sterols, fat-soluble vitamins (such as vitamins A, D, E and K), monoglycerides, diglycerides, phospholipids, and others. The functions of lipids in ...
s are more informative because such compounds do not occur in other organisms. Some publications suggest that archaeal or eukaryotic lipid remains are present in shales dating from 2.7 billion years ago, though such data have since been questioned. These lipids have also been detected in even older rocks from west
Greenland Greenland ( kl, Kalaallit Nunaat, ; da, Grønland, ) is an island country in North America North America is a continent in the Northern Hemisphere and almost entirely within the Western Hemisphere. It is bordered to the nort ...
. The oldest such traces come from the Isua district, which includes Earth's oldest known sediments, formed 3.8 billion years ago. The archaeal lineage may be the most ancient that exists on Earth. Woese argued that the Bacteria, Archaea, and Eukaryotes represent separate lines of descent that diverged early on from an ancestral colony of organisms. One possibility is that this occurred before the evolution of cells, when the lack of a typical cell membrane allowed unrestricted lateral gene transfer, and that the common ancestors of the three domains arose by fixation of specific subsets of genes. It is possible that the last common ancestor of bacteria and archaea was a thermophile, which raises the possibility that lower temperatures are "extreme environments" for archaea, and organisms that live in cooler environments appeared only later. Since archaea and bacteria are no more related to each other than they are to eukaryotes, the term ''prokaryote'' may suggest a false similarity between them. However, structural and functional similarities between lineages often occur because of shared ancestral traits or evolutionary convergence. These similarities are known as a ''grade'', and prokaryotes are best thought of as a grade of life, characterized by such features as an absence of membrane-bound organelles.


Comparison with other domains

The following table compares some major characteristics of the three domains, to illustrate their similarities and differences. Archaea were split off as a third domain because of the large differences in their ribosomal RNA structure. The particular molecule 16S rRNA is key to the production of proteins in all organisms. Because this function is so central to life, organisms with mutations in their 16S rRNA are unlikely to survive, leading to great (but not absolute) stability in the structure of this polynucleotide over generations. 16S rRNA is large enough to show organism-specific variations, but still small enough to be compared quickly. In 1977, Carl Woese, a microbiologist studying the genetic sequences of organisms, developed a new comparison method that involved splitting the RNA into fragments that could be sorted and compared with other fragments from other organisms. The more similar the patterns between species, the more closely they are related. Woese used his new rRNA comparison method to categorize and contrast different organisms. He compared a variety of species and happened upon a group of methanogens with rRNA vastly different from any known prokaryotes or eukaryotes. These methanogens were much more similar to each other than to other organisms, leading Woese to propose the new domain of Archaea. His experiments showed that the archaea were genetically more similar to eukaryotes than prokaryotes, even though they were more similar to prokaryotes in structure. This led to the conclusion that Archaea and Eukarya shared a common ancestor more recent than Eukarya and Bacteria. The development of the nucleus occurred after the split between Bacteria and this common ancestor. One property unique to archaea is the abundant use of ether-linked lipids in their cell membranes. Ether linkages are more chemically stable than the ester linkages found in bacteria and eukarya, which may be a contributing factor to the ability of many archaea to survive in extreme environments that place heavy stress on cell membranes, such as extreme heat and
salinity Salinity () is the saltiness or amount of salt dissolved in a body of water, called saline water (see also soil salinity). It is usually measured in g/L or g/kg (grams of salt per liter/kilogram of water; the latter is dimensionless and equa ...
. Comparative analysis of archaeal genomes has also identified several molecular conserved signature indels and signature proteins uniquely present in either all archaea or different main groups within archaea. Another unique feature of archaea, found in no other organisms, is methanogenesis (the metabolic production of methane). Methanogenic archaea play a pivotal role in ecosystems with organisms that derive energy from oxidation of methane, many of which are bacteria, as they are often a major source of methane in such environments and can play a role as primary producers. Methanogens also play a critical role in the carbon cycle, breaking down organic carbon into methane, which is also a major greenhouse gas. This difference in biochemical structure of Bacteria and Archaea has been explained by researchers that they originated at deep sea alkaline hydrothermal vents, where they independently developed lipid biosynthesis and cell wall biochemistry during their transition to Archaea and Bacteria. It has been suggested that the last universal common ancestor was a not free-living organism. However this view has been challenged by other researchers and is currently in dispute.


Relationship to bacteria

The relationships among the three domains are of central importance for understanding the origin of life. Most of the metabolic pathways, which are the object of the majority of an organism's genes, are common between Archaea and Bacteria, while most genes involved in genome expression are common between Archaea and Eukarya. Within prokaryotes, archaeal cell structure is most similar to that of gram-positive bacteria, largely because both have a single lipid bilayer and usually contain a thick sacculus (exoskeleton) of varying chemical composition. In some phylogenetic trees based upon different gene/protein sequences of prokaryotic homologs, the archaeal homologs are more closely related to those of gram-positive bacteria. Archaea and gram-positive bacteria also share conserved indels in a number of important proteins, such as Hsp70 and glutamine synthetase I; but the phylogeny of these genes was interpreted to reveal interdomain gene transfer, and might not reflect the organismal relationship(s). It has been proposed that the archaea evolved from gram-positive bacteria in response to antibiotic selection pressure. This is suggested by the observation that archaea are resistant to a wide variety of antibiotics that are produced primarily by gram-positive bacteria, and that these antibiotics act primarily on the genes that distinguish archaea from bacteria. The proposal is that the selective pressure towards resistance generated by the gram-positive antibiotics was eventually sufficient to cause extensive changes in many of the antibiotics' target genes, and that these strains represented the common ancestors of present-day Archaea. The evolution of Archaea in response to antibiotic selection, or any other competitive selective pressure, could also explain their adaptation to extreme environments (such as high temperature or acidity) as the result of a search for unoccupied niches to escape from antibiotic-producing organisms; Cavalier-Smith has made a similar suggestion. This proposal is also supported by other work investigating protein structural relationships and studies that suggest that gram-positive bacteria may constitute the earliest branching lineages within the prokaryotes.


Relation to eukaryotes

The evolutionary relationship between archaea and
eukaryote Eukaryotes () are organisms whose cells have a nucleus. All animals, plants, fungi, and many unicellular organisms, are Eukaryotes. They belong to the group of organisms Eukaryota or Eukarya, which is one of the three domains of life. Bac ...
s remains unclear. Aside from the similarities in cell structure and function that are discussed below, many genetic trees group the two. Complicating factors include claims that the relationship between eukaryotes and the archaeal phylum Thermoproteota is closer than the relationship between the " Euryarchaeota" and the phylum Thermoproteota and the presence of archaea-like genes in certain bacteria, such as '' Thermotoga maritima'', from horizontal gene transfer. The standard hypothesis states that the ancestor of the eukaryotes diverged early from the Archaea, and that eukaryotes arose through fusion of an archaean and eubacterium, which became the nucleus and
cytoplasm In cell biology, the cytoplasm is all of the material within a eukaryotic cell, enclosed by the cell membrane, except for the cell nucleus. The material inside the nucleus and contained within the nuclear membrane is termed the nucleoplas ...
; this hypothesis explains the genetic similarities between the groups. The eocyte hypothesis instead posits that Eukaryota emerged relatively late from the Archaea. A lineage of archaea discovered in 2015, '' Lokiarchaeum'' (of proposed new Phylum " Lokiarchaeota"), named for a
hydrothermal vent A hydrothermal vent is a fissure on the seabed from which geothermally heated water discharges. They are commonly found near volcanically active places, areas where tectonic plates are moving apart at mid-ocean ridges, ocean basins, and ho ...
called Loki's Castle in the Arctic Ocean, was found to be the most closely related to eukaryotes known at that time. It has been called a transitional organism between prokaryotes and eukaryotes. Several sister phyla of "Lokiarchaeota" have since been found (" Thorarchaeota", " Odinarchaeota", " Heimdallarchaeota"), all together comprising a newly proposed supergroup Asgard, which may appear as a sister taxon to Proteoarchaeota. Details of the relation of Asgard members and eukaryotes are still under consideration, although, in January 2020, scientists reported that '' Candidatus Prometheoarchaeum syntrophicum'', a type of Asgard archaea, may be a possible link between simple prokaryotic and complex eukaryotic microorganisms about two billion years ago.


Morphology

Individual archaea range from 0.1  micrometers (μm) to over 15 μm in diameter, and occur in various shapes, commonly as spheres, rods, spirals or plates. Other morphologies in the Thermoproteota include irregularly shaped lobed cells in '' Sulfolobus'', needle-like filaments that are less than half a micrometer in diameter in '' Thermofilum'', and almost perfectly rectangular rods in '' Thermoproteus'' and '' Pyrobaculum''. Archaea in the genus '' Haloquadratum'' such as '' Haloquadratum walsbyi'' are flat, square specimens that live in hypersaline pools. These unusual shapes are probably maintained by both their cell walls and a prokaryotic cytoskeleton. Proteins related to the cytoskeleton components of other organisms exist in archaea, and filaments form within their cells, but in contrast with other organisms, these cellular structures are poorly understood. In '' Thermoplasma'' and '' Ferroplasma'' the lack of a
cell wall A cell wall is a structural layer surrounding some types of cells, just outside the cell membrane The cell membrane (also known as the plasma membrane (PM) or cytoplasmic membrane, and historically referred to as the plasmalemma) is a biolo ...
means that the cells have irregular shapes, and can resemble amoebae. Some species form aggregates or filaments of cells up to 200 μm long. These organisms can be prominent in biofilms. Notably, aggregates of '' Thermococcus coalescens'' cells fuse together in culture, forming single giant cells. Archaea in the genus '' Pyrodictium'' produce an elaborate multicell colony involving arrays of long, thin hollow tubes called ''cannulae'' that stick out from the cells' surfaces and connect them into a dense bush-like agglomeration. The function of these cannulae is not settled, but they may allow communication or nutrient exchange with neighbors. Multi-species colonies exist, such as the "string-of-pearls" community that was discovered in 2001 in a German swamp. Round whitish colonies of a novel Euryarchaeota species are spaced along thin filaments that can range up to long; these filaments are made of a particular bacteria species.


Structure, composition development, and operation

Archaea and bacteria have generally similar cell structure, but cell composition and organization set the archaea apart. Like bacteria, archaea lack interior membranes and organelles. Like bacteria, the
cell membrane The cell membrane (also known as the plasma membrane (PM) or cytoplasmic membrane, and historically referred to as the plasmalemma) is a biological membrane that separates and protects the interior of all cells from the outside environment ( ...
s of archaea are usually bounded by a
cell wall A cell wall is a structural layer surrounding some types of cells, just outside the cell membrane The cell membrane (also known as the plasma membrane (PM) or cytoplasmic membrane, and historically referred to as the plasmalemma) is a biolo ...
and they swim using one or more flagella. Structurally, archaea are most similar to gram-positive bacteria. Most have a single plasma membrane and cell wall, and lack a periplasmic space; the exception to this general rule is '' Ignicoccus'', which possess a particularly large periplasm that contains membrane-bound vesicles and is enclosed by an outer membrane.


Cell wall and archaella

Most archaea (but not '' Thermoplasma'' and '' Ferroplasma'') possess a cell wall. In most archaea the wall is assembled from surface-layer proteins, which form an S-layer. An S-layer is a rigid array of protein molecules that cover the outside of the cell (like chain mail). This layer provides both chemical and physical protection, and can prevent macromolecules from contacting the cell membrane. Unlike bacteria, archaea lack peptidoglycan in their cell walls. Methanobacteriales do have cell walls containing pseudopeptidoglycan, which resembles eubacterial peptidoglycan in morphology, function, and physical structure, but pseudopeptidoglycan is distinct in chemical structure; it lacks D-amino acids and N-acetylmuramic acid, substituting the latter with N-Acetyltalosaminuronic acid. Archaeal flagella are known as archaella, that operate like bacterial flagella – their long stalks are driven by rotatory motors at the base. These motors are powered by a proton gradient across the membrane, but archaella are notably different in composition and development. The two types of flagella evolved from different ancestors. The bacterial flagellum shares a common ancestor with the type III secretion system, while archaeal flagella appear to have evolved from bacterial type IV pili. In contrast with the bacterial flagellum, which is hollow and assembled by subunits moving up the central pore to the tip of the flagella, archaeal flagella are synthesized by adding subunits at the base.


Membranes

Archaeal membranes are made of molecules that are distinctly different from those in all other life forms, showing that archaea are related only distantly to bacteria and eukaryotes. In all organisms,
cell membrane The cell membrane (also known as the plasma membrane (PM) or cytoplasmic membrane, and historically referred to as the plasmalemma) is a biological membrane that separates and protects the interior of all cells from the outside environment ( ...
s are made of molecules known as phospholipids. These molecules possess both a polar part that dissolves in water (the phosphate "head"), and a "greasy" non-polar part that does not (the lipid tail). These dissimilar parts are connected by a glycerol moiety. In water, phospholipids cluster, with the heads facing the water and the tails facing away from it. The major structure in cell membranes is a double layer of these phospholipids, which is called a lipid bilayer. The phospholipids of archaea are unusual in four ways: * They have membranes composed of glycerol- ether lipids, whereas bacteria and eukaryotes have membranes composed mainly of glycerol-
ester In chemistry Chemistry is the scientific study of the properties and behavior of matter. It is a natural science that covers the elements that make up matter to the compounds made of atoms, molecules and ions: their composition, ...
lipid Lipids are a broad group of naturally-occurring molecules which includes fats, waxes, sterols, fat-soluble vitamins (such as vitamins A, D, E and K), monoglycerides, diglycerides, phospholipids, and others. The functions of lipids in ...
s. The difference is the type of bond that joins the lipids to the glycerol moiety; the two types are shown in yellow in the figure at the right. In ester lipids this is an ester bond, whereas in ether lipids this is an ether bond. * The stereochemistry of the archaeal glycerol moiety is the mirror image of that found in other organisms. The glycerol moiety can occur in two forms that are mirror images of one another, called '' enantiomers''. Just as a right hand does not fit easily into a left-handed glove, enantiomers of one type generally cannot be used or made by
enzyme Enzymes () are protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic rea ...
s adapted for the other. The archaeal phospholipids are built on a backbone of ''sn''-glycerol-1-phosphate, which is an enantiomer of ''sn''-glycerol-3-phosphate, the phospholipid backbone found in bacteria and eukaryotes. This suggests that archaea use entirely different enzymes for synthesizing phospholipids as compared to bacteria and eukaryotes. Such enzymes developed very early in life's history, indicating an early split from the other two domains. * Archaeal lipid tails differ from those of other organisms in that they are based upon long isoprenoid chains with multiple side-branches, sometimes with cyclopropane or cyclohexane rings. By contrast, the
fatty acid In chemistry, particularly in biochemistry, a fatty acid is a carboxylic acid with an aliphatic chain, which is either saturated or unsaturated. Most naturally occurring fatty acids have an unbranched chain of an even number of carbon atoms ...
s in the membranes of other organisms have straight chains without side 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 archaeal membranes from leaking at high temperatures. * In some archaea, the lipid bilayer is replaced by a monolayer. In effect, the archaea fuse the tails of two phospholipid molecules into a single molecule with two polar heads (a bolaamphiphile); this fusion may make their membranes more rigid and better able to resist harsh environments. For example, the lipids in '' Ferroplasma'' are of this type, which is thought to aid this organism's survival in its highly acidic habitat.


Metabolism

Archaea exhibit a great variety of chemical reactions in their
metabolism Metabolism (, from el, μεταβολή ''metabolē'', "change") is the set of life-sustaining chemical reactions in organisms. The three main functions of metabolism are: the conversion of the energy in food to energy available to run ...
and use many sources of energy. These reactions are classified into nutritional groups, depending on energy and carbon sources. Some archaea obtain energy from inorganic compounds such as
sulfur Sulfur (or sulphur in British English) is a chemical element with the Symbol (chemistry), symbol S and atomic number 16. It is abundance of the chemical elements, abundant, Polyvalency (chemistry), multivalent and nonmetallic. Under standard c ...
or
ammonia Ammonia is an inorganic compound of nitrogen and hydrogen with the formula . A stable binary hydride, and the simplest pnictogen hydride, ammonia is a colourless gas with a distinct pungent smell. Biologically, it is a common nitrogen ...
(they are chemotrophs). These include nitrifiers, methanogens and anaerobic methane oxidisers. In these reactions one compound passes electrons to another (in a
redox Redox (reduction–oxidation, , ) is a type of chemical reaction in which the oxidation states of substrate change. Oxidation is the loss of electrons or an increase in the oxidation state, while reduction is the gain of electrons or ...
reaction), releasing energy to fuel the cell's activities. One compound acts as an electron donor and one as an
electron acceptor An electron acceptor is a chemical entity that accepts electrons transferred to it from another compound. It is an oxidizing agent An oxidizing agent (also known as an oxidant, oxidizer, electron recipient, or electron acceptor) is a substa ...
. The energy released is used to generate
adenosine triphosphate Adenosine triphosphate (ATP) is an organic compound In chemistry, organic compounds are generally any chemical compounds that contain carbon- hydrogen or carbon-carbon bonds. Due to carbon's ability to catenate (form chains with other c ...
(ATP) through chemiosmosis, the same basic process that happens in the
mitochondrion A mitochondrion (; ) is an organelle found in the cells of most Eukaryotes, such as animals, plants and fungi. Mitochondria have a double membrane structure and use aerobic respiration to generate adenosine triphosphate (ATP), which i ...
of eukaryotic cells. Other groups of archaea use sunlight as a source of energy (they are phototrophs), but oxygen–generating
photosynthesis Photosynthesis is a process used by plant Plants are predominantly photosynthetic eukaryote Eukaryotes () are organisms whose cells have a nucleus. All animals, plants, fungi, and many unicellular organisms, are Eukaryotes. Th ...
does not occur in any of these organisms. Many basic metabolic pathways are shared among all forms of life; for example, archaea use a modified form of
glycolysis Glycolysis is the metabolic pathway that converts glucose Glucose is a simple sugar with the molecular formula . Glucose is overall the most abundant monosaccharide, a subcategory of carbohydrates. Glucose is mainly made by plants and mo ...
(the Entner–Doudoroff pathway) and either a complete or partial
citric acid cycle The citric acid cycle (CAC)—also known as the Krebs cycle or the TCA cycle (tricarboxylic acid cycle)—is a series of chemical reactions to release stored energy through the oxidation Redox (reduction–oxidation, , ) is a type of ...
. These similarities to other organisms probably reflect both early origins in the history of life and their high level of efficiency. Some Euryarchaeota are methanogens (archaea that produce methane as a result of metabolism) living in anaerobic environments, such as swamps. This form of metabolism evolved early, and it is even possible that the first free-living organism was a methanogen. A common reaction involves the use of
carbon dioxide Carbon dioxide ( chemical formula ) is a chemical compound made up of molecules that each have one carbon atom covalently double bonded to two oxygen atoms. It is found in the gas state at room temperature. In the air, carbon dioxide is t ...
as an electron acceptor to oxidize
hydrogen Hydrogen is the chemical element A chemical element is a species of atoms that have a given number of protons in their nuclei, including the pure substance consisting only of that species. Unlike chemical compounds, chemical element ...
. Methanogenesis involves a range of coenzymes that are unique to these archaea, such as coenzyme M and methanofuran. Other organic compounds such as
alcohol Alcohol most commonly refers to: * Alcohol (chemistry) In chemistry, an alcohol is a type of organic compound that carries at least one hydroxyl () functional group bound to a Saturated and unsaturated compounds, saturated carbon atom. The ...
s, acetic acid or formic acid are used as alternative
electron acceptor An electron acceptor is a chemical entity that accepts electrons transferred to it from another compound. It is an oxidizing agent An oxidizing agent (also known as an oxidant, oxidizer, electron recipient, or electron acceptor) is a substa ...
s by methanogens. These reactions are common in gut-dwelling archaea. Acetic acid is also broken down into methane and carbon dioxide directly, by ''acetotrophic'' archaea. These acetotrophs are archaea in the order Methanosarcinales, and are a major part of the communities of microorganisms that produce biogas. Other archaea use in the atmosphere as a source of carbon, in a process called carbon fixation (they are autotrophs). This process involves either a highly modified form of the Calvin cycle or another metabolic pathway called the 3-hydroxypropionate/ 4-hydroxybutyrate cycle. The Thermoproteota also use the reverse Krebs cycle while the "Euryarchaeota" also use the reductive acetyl-CoA pathway. Carbon fixation is powered by inorganic energy sources. No known archaea carry out
photosynthesis Photosynthesis is a process used by plant Plants are predominantly photosynthetic eukaryote Eukaryotes () are organisms whose cells have a nucleus. All animals, plants, fungi, and many unicellular organisms, are Eukaryotes. Th ...
( Halobacterium is the only known phototroph archeon but it uses an alternative process to photosynthesis). Archaeal energy sources are extremely diverse, and range from the oxidation of
ammonia Ammonia is an inorganic compound of nitrogen and hydrogen with the formula . A stable binary hydride, and the simplest pnictogen hydride, ammonia is a colourless gas with a distinct pungent smell. Biologically, it is a common nitrogen ...
by the Nitrosopumilales to the oxidation of
hydrogen sulfide Hydrogen sulfide is a chemical compound with the formula . It is a colorless chalcogen-hydride gas, and is poisonous, corrosive, and flammable, with trace amounts in ambient atmosphere having a characteristic foul odor of rotten eggs. The un ...
or elemental
sulfur Sulfur (or sulphur in British English) is a chemical element with the Symbol (chemistry), symbol S and atomic number 16. It is abundance of the chemical elements, abundant, Polyvalency (chemistry), multivalent and nonmetallic. Under standard c ...
by species of '' Sulfolobus'', using either oxygen or metal ions as electron acceptors. Phototrophic archaea use light to produce chemical energy in the form of ATP. In the Halobacteria, light-activated ion pumps like bacteriorhodopsin and halorhodopsin generate ion gradients by pumping ions out of and into the cell across the
plasma membrane The cell membrane (also known as the plasma membrane (PM) or cytoplasmic membrane, and historically referred to as the plasmalemma) is a biological membrane that separates and protects the interior of all cells from the outside environment ( ...
. The energy stored in these electrochemical gradients is then converted into ATP by ATP synthase. This process is a form of photophosphorylation. The ability of these light-driven pumps to move ions across membranes depends on light-driven changes in the structure of a retinol cofactor buried in the center of the protein.


Genetics

Archaea usually have a single circular chromosome, with as many as 5,751,492 
base pair A base pair (bp) is a fundamental unit of double-stranded nucleic acids consisting of two nucleobases bound to each other by hydrogen bonds. They form the building blocks of the DNA double helix and contribute to the folded structure of both ...
s in '' Methanosarcina acetivorans'', the largest known archaeal genome. The tiny 490,885 base-pair genome of '' Nanoarchaeum equitans'' is one-tenth of this size and the smallest archaeal genome known; it is estimated to contain only 537 protein-encoding genes. Smaller independent pieces of DNA, called ''
plasmid A plasmid is a small, extrachromosomal DNA molecule within a cell that is physically separated from chromosomal DNA and can replicate independently. They are most commonly found as small circular, double-stranded DNA molecules in bacteria ...
s'', are also found in archaea. Plasmids may be transferred between cells by physical contact, in a process that may be similar to bacterial conjugation. Archaea are genetically distinct from bacteria and eukaryotes, with up to 15% of the proteins encoded by any one archaeal genome being unique to the domain, although most of these unique genes have no known function. Of the remainder of the unique proteins that have an identified function, most belong to the Euryarchaeota and are involved in methanogenesis. The proteins that archaea, bacteria and eukaryotes share form a common core of cell function, relating mostly to transcription, translation, and nucleotide metabolism. Other characteristic archaeal features are the organization of genes of related function – such as enzymes that catalyze steps in the same metabolic pathway into novel operons, and large differences in tRNA genes and their aminoacyl tRNA synthetases. Transcription in archaea more closely resembles eukaryotic than bacterial transcription, with the archaeal RNA polymerase being very close to its equivalent in eukaryotes, while archaeal translation shows signs of both bacterial and eukaryotic equivalents. Although archaea have only one type of RNA polymerase, its structure and function in transcription seems to be close to that of the eukaryotic
RNA polymerase II RNA polymerase II (RNAP II and Pol II) is a multiprotein complex that transcribes DNA into precursors of messenger RNA (mRNA) and most small nuclear RNA (snRNA) and microRNA MicroRNA (miRNA) are small, single-stranded, non-coding RNA m ...
, with similar protein assemblies (the general transcription factors) directing the binding of the RNA polymerase to a gene's promoter, but other archaeal
transcription factor In molecular biology, a transcription factor (TF) (or sequence-specific DNA-binding factor) is a protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perfor ...
s are closer to those found in bacteria. Post-transcriptional modification is simpler than in eukaryotes, since most archaeal genes lack
intron An intron is any nucleotide sequence within a gene In biology, the word gene (from , ; "... Wilhelm Johannsen coined the word gene to describe the Mendelian units of heredity..." meaning ''generation'' or ''birth'' or ''gender'') can ha ...
s, although there are many introns in their transfer RNA and
ribosomal RNA Ribosomal ribonucleic acid (rRNA) is a type of non-coding RNA which is the primary component of ribosomes, essential to all cells. rRNA is a ribozyme which carries out protein synthesis Protein biosynthesis (or protein synthesis) is a cor ...
genes, and introns may occur in a few protein-encoding genes.


Gene transfer and genetic exchange

'' Haloferax volcanii'', an extreme halophilic archaeon, forms cytoplasmic bridges between cells that appear to be used for transfer of DNA from one cell to another in either direction. When the hyperthermophilic archaea '' Sulfolobus solfataricus'' and '' Sulfolobus acidocaldarius'' are exposed to DNA-damaging UV irradiation or to the agents bleomycin or mitomycin C, species-specific cellular aggregation is induced. Aggregation in ''S. solfataricus'' could not be induced by other physical stressors, such as pH or temperature shift, suggesting that aggregation is induced specifically by DNA damage. Ajon et al. showed that UV-induced cellular aggregation mediates chromosomal marker exchange with high frequency in ''S. acidocaldarius''. Recombination rates exceeded those of uninduced cultures by up to three orders of magnitude. Frols et al. and Ajon et al. hypothesized that cellular aggregation enhances species-specific DNA transfer between ''Sulfolobus'' cells in order to provide increased repair of damaged DNA by means of
homologous recombination Homologous recombination is a type of genetic recombination in which genetic information is exchanged between two similar or identical molecules of double-stranded or single-stranded nucleic acid Nucleic acids are biopolymers, macromolecules, ...
. This response may be a primitive form of sexual interaction similar to the more well-studied bacterial transformation systems that are also associated with species-specific DNA transfer between cells leading to homologous recombinational repair of DNA damage.


Archaeal viruses

Archaea are the target of a number of
virus A virus is a submicroscopic infectious agent that replicates only inside the living cells of an organism. Viruses infect all life forms, from animals and plants to microorganisms, including bacteria Bacteria (; singular: bacte ...
es in a diverse virosphere distinct from bacterial and eukaryotic viruses. They have been organized into 15-18 DNA-based families so far, but multiple species remain un-isolated and await classification. These families can be informally divided into two groups: archaea-specific and cosmopolitan. Archaeal-specific viruses target only archaean species and currently include 12 families. Numerous unique, previously unidentified viral structures have been observed in this group, including: bottle-shaped, spindle-shaped, coil-shaped, and droplet-shaped viruses. While the reproductive cycles and genomic mechanisms of archaea-specific species may be similar to other viruses, they bear unique characteristics that were specifically developed due to the morphology of host cells they infect. Their virus release mechanisms differ from that of other phages.
Bacteriophage A bacteriophage (), also known informally as a ''phage'' (), is a duplodnaviria virus that infects and replicates within bacteria and archaea. The term was derived from "bacteria" and the Greek language, Greek φαγεῖν ('), meaning "to d ...
s generally undergo either lytic pathways, lysogenic pathways, or (rarely) a mix of the two. Most archaea-specific viral strains maintain a stable, somewhat lysogenic, relationship with their hosts – appearing as a chronic infection. This involves the gradual, and continuous, production and release of virions without killing the host cell. Prangishyili (2013) noted that it has been hypothesized that tailed archaeal phages originated from bacteriophages capable of infecting haloarchaeal species. If the hypothesis is correct, it can be concluded that other double-stranded DNA viruses that make up the rest of the archaea-specific group are their own unique group in the global viral community. Krupovic et al. (2018) states that the high levels of horizontal gene transfer, rapid mutation rates in viral genomes, and lack of universal gene sequences have led researchers to perceive the evolutionary pathway of archaeal viruses as a network. The lack of similarities among phylogenetic markers in this network and the global virosphere, as well as external linkages to non-viral elements, may suggest that some species of archaea specific viruses evolved from non-viral mobile genetic elements (MGE). These viruses have been studied in most detail in thermophilics, particularly the orders Sulfolobales and Thermoproteales. Two groups of single-stranded DNA viruses that infect archaea have been recently isolated. One group is exemplified by the '' Halorubrum pleomorphic virus 1'' ('' Pleolipoviridae'') infecting halophilic archaea, and the other one by the '' Aeropyrum coil-shaped virus'' ('' Spiraviridae'') infecting a hyperthermophilic (optimal growth at 90–95 °C) host. Notably, the latter virus has the largest currently reported ssDNA genome. Defenses against these viruses may involve RNA interference from repetitive DNA sequences that are related to the genes of the viruses.


Reproduction

Archaea reproduce asexually by binary or multiple fission, fragmentation, or budding;
mitosis In cell biology, mitosis () is a part of the cell cycle The cell cycle, or cell-division cycle, is the series of events that take place in a cell that cause it to divide into two daughter cells. These events include the duplication ...
and meiosis do not occur, so if a species of archaea exists in more than one form, all have the same genetic material.
Cell division Cell division is the process by which a parent cell divides into two daughter cells. Cell division usually occurs as part of a larger cell cycle The cell cycle, or cell-division cycle, is the series of events that take place in a cell ...
is controlled in a
cell cycle The cell cycle, or cell-division cycle, is the series of events that take place in a cell that cause it to divide into two daughter cells. These events include the duplication of its DNA (DNA replication In molecular biology, DNA replicat ...
; after the cell's chromosome is replicated and the two daughter chromosomes separate, the cell divides. In the genus '' Sulfolobus'', the cycle has characteristics that are similar to both bacterial and eukaryotic systems. The chromosomes replicate from multiple starting points ( origins of replication) using DNA polymerases that resemble the equivalent eukaryotic enzymes. In Euryarchaeota the cell division 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. In cren- and thaumarchaea, the cell division machinery Cdv fulfills a similar role. This machinery is related to the eukaryotic ESCRT-III machinery which, while best known for its role in cell sorting, also has been seen to fulfill a role in separation between divided cell, suggesting an ancestral role in cell division. Both bacteria and eukaryotes, but not archaea, make
spore In biology Biology is the scientific study of life. It is a natural science with a broad scope but has several unifying themes that tie it together as a single, coherent field. For instance, all organisms are made up of cells tha ...
s. Some species of Haloarchaea undergo phenotypic switching and grow as several different cell types, including thick-walled structures that are resistant to osmotic shock and allow the archaea to survive in water at low salt concentrations, but these are not reproductive structures and may instead help them reach new habitats.


Behavior


Communication

Quorum sensing was originally thought to not exist in Archaea, but recent studies have shown evidence of some species being able to perform cross-talk through quorum sensing. Other studies have shown syntrophic interactions between archaea and bacteria during biofilm growth. Although research is limited in archaeal quorum sensing, some studies have uncovered LuxR proteins in archaeal species, displaying similarities with bacteria LuxR, and ultimately allowing for the detection of small molecules that are used in high density communication. Similarly to bacteria, Archaea LuxR solos have shown to bind to AHLs (lactones) and non-AHLs ligans, which is a large part in performing intraspecies, interspecies, and interkingdom communication through quorum sensing.


Ecology


Habitats

Archaea exist in a broad range of
habitat In ecology, the term habitat summarises the array of resources, physical and biotic factors that are present in an area, such as to support the survival and reproduction of a particular species. A species habitat can be seen as the physical ...
s, and are now recognized as a major part of global ecosystems, and may represent about 20% of microbial cells in the oceans. However, the first-discovered archaeans were extremophiles. Indeed, some archaea survive high temperatures, often above , as found in geysers, black smokers, and oil wells. Other common habitats include very cold habitats and highly saline,
acid In computer science Computer science is the study of computation, automation, and information. Computer science spans theoretical disciplines (such as algorithms, theory of computation, information theory, and automation) to pract ...
ic, or
alkaline In chemistry Chemistry is the scientific study of the properties and behavior of matter. It is a natural science that covers the elements that make up matter to the compounds made of atoms, molecules and ions: their compositi ...
water, but archaea include mesophiles that grow in mild conditions, in swamps and marshland, sewage, the oceans, the intestinal tract of animals, and
soil Soil, also commonly referred to as earth or dirt, is a mixture of organic matter, minerals, gases, liquid A liquid is a nearly incompressible fluid that conforms to the shape of its container but retains a (nearly) constant volume ...
s. Similar to PGPR, Archaea are now considered as a source of plant growth promotion as well. Extremophile archaea are members of four main physiological groups. These are the halophiles, thermophiles, alkaliphiles, and acidophiles. These groups are not comprehensive or phylum-specific, nor are they mutually exclusive, since some archaea belong to several 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 outnumber their bacterial counterparts at salinities greater than 20–25%. Thermophiles grow best at temperatures above , in places such as hot springs; ''hyperthermophilic'' archaea grow optimally at temperatures greater than . The archaeal '' Methanopyrus kandleri'' Strain 116 can even reproduce at , the highest recorded temperature of any organism. Other archaea exist in very acidic or alkaline conditions. 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 Sulfuric acid ( American spelling and the preferred IUPAC name) or sulphuric acid ( Commonwealth spelling), known in antiquity as oil of vitriol, is a mineral acid composed of the elements sulfur, oxygen Oxygen is the chemical ele ...
. This resistance to extreme environments has made archaea the focus of speculation about the possible properties of extraterrestrial life. Some extremophile habitats are not dissimilar to those on Mars, leading to the suggestion that viable microbes could be transferred between planets in meteorites. 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 polar seas. Even more significant are the large numbers of archaea found throughout the world's oceans in non-extreme habitats among the
plankton Plankton are the diverse collection of organisms found in water (or air) that are unable to propel themselves against a current (or wind Wind is the natural movement of air or other gases relative to a planet's surface. Winds occu ...
community (as part of the picoplankton). 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. Consequently, our understanding of the role of archaea in ocean ecology is rudimentary, so their full influence on global biogeochemical cycles remains largely unexplored. Some marine Thermoproteota are capable of nitrification, suggesting these organisms may affect the oceanic nitrogen cycle, although these oceanic Thermoproteota may also use other sources of energy. Vast numbers of archaea are also found in the sediments that cover the sea floor, with these organisms making up the majority of living cells at depths over 1 meter below the ocean bottom. It has been demonstrated that in all oceanic surface sediments (from 1000- to 10,000-m water depth), the impact of viral infection is higher on archaea than on bacteria and virus-induced lysis of archaea accounts for up to one-third of the total microbial biomass killed, resulting in the release of ~0.3 to 0.5 gigatons of carbon per year globally.


Role in chemical cycling

Archaea recycle elements such as
carbon Carbon () is a chemical element with the symbol C and atomic number 6. It is nonmetal In chemistry, a nonmetal is a chemical element that generally lacks a predominance of metallic properties; they range from colorless gases (like ...
, nitrogen, and
sulfur Sulfur (or sulphur in British English) is a chemical element with the Symbol (chemistry), symbol S and atomic number 16. It is abundance of the chemical elements, abundant, Polyvalency (chemistry), multivalent and nonmetallic. Under standard c ...
through their various habitats. Archaea carry out many steps in the nitrogen cycle. This includes both reactions that remove nitrogen from ecosystems (such as
nitrate Nitrate is a polyatomic ion with the chemical formula . Salts containing this ion are called nitrates. Nitrates are common components of fertilizers and explosives. Almost all inorganic nitrates are soluble in water. An example of an ins ...
-based respiration and denitrification) as well as processes that introduce nitrogen (such as nitrate assimilation and nitrogen fixation). Researchers recently discovered archaeal involvement in
ammonia Ammonia is an inorganic compound of nitrogen and hydrogen with the formula . A stable binary hydride, and the simplest pnictogen hydride, ammonia is a colourless gas with a distinct pungent smell. Biologically, it is a common nitrogen ...
oxidation reactions. These reactions are particularly important in the oceans. The archaea also appear crucial for ammonia oxidation in soils. They produce nitrite, which other microbes then oxidize to
nitrate Nitrate is a polyatomic ion with the chemical formula . Salts containing this ion are called nitrates. Nitrates are common components of fertilizers and explosives. Almost all inorganic nitrates are soluble in water. An example of an ins ...
. Plants and other organisms consume the latter. In the sulfur cycle, archaea that grow by oxidizing
sulfur Sulfur (or sulphur in British English) is a chemical element with the Symbol (chemistry), symbol S and atomic number 16. It is abundance of the chemical elements, abundant, Polyvalency (chemistry), multivalent and nonmetallic. Under standard c ...
compounds release this element from rocks, making it available to other organisms, but the archaea that do this, such as ''Sulfolobus'', produce
sulfuric acid Sulfuric acid ( American spelling and the preferred IUPAC name) or sulphuric acid ( Commonwealth spelling), known in antiquity as oil of vitriol, is a mineral acid composed of the elements sulfur, oxygen Oxygen is the chemical ele ...
as a waste product, and the growth of these organisms in abandoned mines can contribute to acid mine drainage and other environmental damage. In the carbon cycle, methanogen archaea remove hydrogen and play an important role in the decay of organic matter by the populations of microorganisms that act as decomposers in anaerobic ecosystems, such as sediments, marshes, and sewage-treatment works.


Interactions with other organisms

The well-characterized interactions between archaea and other organisms are either mutual or commensal. There are no clear examples of known archaeal pathogens or
parasite Parasitism is a close relationship between species, where one organism, the parasite, lives on or inside another organism, the host, causing it some harm, and is adapted structurally to this way of life. The entomologist E. O. Wilson ...
s, but some species of methanogens have been suggested to be involved in infections in the mouth, and '' Nanoarchaeum equitans'' may be a parasite of another species of archaea, since it only survives and reproduces within the cells of the Crenarchaeon '' Ignicoccus hospitalis'', and appears to offer no benefit to its host.


Mutualism

Mutualism is an interaction between individuals of different species that results in positive (beneficial) effects on per capita reproduction and/or survival of the interacting populations. One well-understood example of mutualism is the interaction between protozoa and methanogenic archaea in the digestive tracts of animals that digest cellulose, such as ruminants and termites. In these anaerobic environments, protozoa break down plant cellulose to obtain energy. This process releases hydrogen as a waste product, but high levels of hydrogen reduce energy production. When methanogens convert hydrogen to methane, protozoa benefit from more energy. In anaerobic protozoa, such as ''Plagiopyla frontata'', archaea reside inside the protozoa and consume hydrogen produced in their hydrogenosomes. Archaea also associate with larger organisms. For example, the marine archaean '' Cenarchaeum symbiosum'' lives within (is an endosymbiont of) the sponge '' Axinella mexicana''.


Commensalism

Archaea can also be commensals, benefiting from an association without helping or harming the other organism. For example, the methanogen '' Methanobrevibacter smithii'' is by far the most common archaean in the human flora, making up about one in ten of all the prokaryotes in the human gut. In termites and in humans, these methanogens may in fact be mutualists, interacting with other microbes in the gut to aid digestion. Archaean communities also associate with a range of other organisms, such as on the surface of corals, and in the region of soil that surrounds plant roots (the rhizosphere).


Parasitism

Although Archaea do not have a historical reputation of being pathogens, Archaea are often found with similar genomes to more common pathogen like ''E. coli,'' showing metabolic links and evolutionary history with today's pathogens. Archaea also has inconsistent detection within clinical studies because of the lack of categorization of Archaea into more specific species.


Significance in technology and industry

Extremophile archaea, particularly those resistant either to heat or to extremes of acidity and alkalinity, are a source of
enzyme Enzymes () are protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic rea ...
s that function under these harsh conditions. These enzymes have found many uses. For example, thermostable DNA polymerases, such as the Pfu DNA polymerase from '' Pyrococcus furiosus'', revolutionized
molecular biology Molecular biology is the branch of biology Biology is the scientific study of life. It is a natural science with a broad scope but has several unifying themes that tie it together as a single, coherent field. For instance, all organ ...
by allowing the
polymerase chain reaction The polymerase chain reaction (PCR) is a method widely used to rapidly make millions to billions of copies (complete or partial) of a specific DNA sample, allowing scientists to take a very small sample of DNA and amplify it (or a part of it) ...
to be used in research as a simple and rapid technique for cloning DNA. In industry, amylases, galactosidases and pullulanases in other species of '' Pyrococcus'' that function at over allow food processing at high temperatures, such as the production of low
lactose Lactose is a disaccharide sugar Sugar is the generic name for sweet-tasting, soluble carbohydrates, many of which are used in food. Simple sugars, also called monosaccharides, include glucose Glucose is a simple sugar with the mol ...
milk and whey. 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. This stability 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. In contrast with the range of applications of archaean enzymes, the use of the organisms themselves in biotechnology is less developed. 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. In
mineral processing In the field of extractive metallurgy, mineral processing, also known as ore dressing, is the process of separating commercially valuable minerals from their ores. History Before the advent of heavy machinery the raw ore was broken up usi ...
, acidophilic archaea display promise for the extraction of metals from ores, including
gold Gold is a chemical element with the Symbol (chemistry), symbol Au (from la, aurum) and atomic number 79. This makes it one of the higher atomic number elements that occur naturally. It is a Brightness, bright, slightly orange-yellow, dense, s ...
, cobalt and
copper Copper is a chemical element with the Symbol (chemistry), symbol Cu (from la, cuprum) and atomic number 29. It is a soft, malleable, and ductility, ductile metal with very high thermal conductivity, thermal and electrical conductivity. A fre ...
. Archaea host a new class of potentially useful antibiotics. A few of these archaeocins have been characterized, but hundreds more are believed to exist, especially within '' Haloarchaea'' and '' Sulfolobus''. These compounds differ in structure from 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.


See also

* Aerobic methane production * Earliest known life forms * List of Archaea genera * List of sequenced archaeal genomes * Nuclear localization sequence * '' The Surprising Archaea'' (book) * Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya * Unique properties of hyperthermophilic archaea * Branching order of bacterial phyla (Genome Taxonomy Database, 2018)


References


Further reading

* * * * * * * *


External links


General


Introduction to the Archaea, ecology, systematics and morphology

Oceans of Archaea
nbsp;– E.F. DeLong, ''ASM News'', 2003


Classification


NCBI taxonomy page on Archaea


nbsp;– list of Prokaryotic names with Standing in Nomenclature
Shotgun sequencing finds nanoorganisms
nbsp;– discovery of the ARMAN group of archaea


Genomics


Browse any completed archaeal genome at UCSC

Comparative Analysis of Archaeal Genomes
(at DOE's IMG system) {{Authority control Extremophiles Domains (biology) Systems of bacterial taxonomy