Last updated

Temporal range: 3.5–0 Ga
Halobacterium sp. strain NRC-1,
each cell about 5  μm long
Scientific classification Red Pencil Icon.png
Domain: Archaea
Woese, Kandler & Wheelis, 1990 [1]
Subkingdoms [2] and phyla [3]
  • Archaebacteria Woese & Fox, 1977
  • Mendosicutes Gibbons & Murray, 1978
  • Metabacteria Hori and Osawa 1979

Archaea ( /ɑːrˈkə/ ( Loudspeaker.svg listen ) or /ɑːrˈkə/ ar-KEE or ar-KAY) (singular archaeon) constitute a domain of single-celled organisms. These microorganisms lack cell nuclei and are therefore prokaryotes. Archaea were initially classified as bacteria, receiving the name archaebacteria (in the Archaebacteria kingdom), but this classification is obsolete. [6]


Archaeal cells have unique properties separating them from the other two domains, Bacteria and Eukaryota. Archaea are further divided into multiple recognized phyla. Classification is difficult because most have not been isolated in the laboratory and have been detected only by analysis of their nucleic acids in samples from their environment.

Archaea and bacteria are generally similar in size and shape, although a few archaea have very different shapes, such as the flat and square cells of Haloquadratum walsbyi . [7] Despite this morphological similarity to bacteria, archaea possess genes and several metabolic pathways that are more closely related to those of eukaryotes, notably for the enzymes involved in transcription and translation. Other aspects of archaeal biochemistry are unique, such as their reliance on ether lipids in their cell membranes, [8] including archaeols. Archaea use more energy sources than eukaryotes: these range from organic compounds, such as sugars, to ammonia, metal ions or even hydrogen gas. Salt-tolerant archaea (the Haloarchaea) use sunlight as an energy source, and other species of archaea fix carbon, 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 forms endospores.

The first observed archaea were extremophiles, living in extreme environments, such as hot springs and salt lakes with no other organisms. Improved detection tools led to the discovery of archaea in almost every habitat, including soil, 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.

Archaea are a major part of Earth's life. They are part of the microbiota of all organisms. In the human microbiota, they are important in the gut, mouth, and on the skin. [9] 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. [10]

No clear examples of archaeal pathogens or parasites 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 aid 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.


Early concept

Archaea were found in volcanic hot springs. Pictured here is Grand Prismatic Spring of Yellowstone National Park. Grand prismatic spring.jpg
Archaea were found in volcanic hot springs. Pictured here is Grand Prismatic Spring of Yellowstone National Park.

For much of the 20th century, prokaryotes were regarded as a single group of organisms and classified based on their biochemistry, morphology and metabolism. Microbiologists tried to classify microorganisms based on the structures of their cell walls, their shapes, and the substances they consume. [11] In 1965, Emile Zuckerkandl and Linus Pauling [12] instead proposed using the sequences of the genes in different prokaryotes to work out how they are related to each other. This phylogenetic approach is the main method used today. [13]

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 (rRNA) genes. [14] 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, the Bacteria and the Archaea, [1] in what is now known as "The Woesian Revolution". [15]

The word archaea comes from the Ancient Greek ἀρχαῖα , meaning "ancient things", [16] 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 [17] and hyperthermophilic microbes [18] 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. [19] This new appreciation of the importance and ubiquity of archaea came from using polymerase chain reaction (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. [20] [21]


The ARMAN are a group of archaea recently discovered in acid mine drainage. Rio tinto river CarolStoker NASA Ames Research Center.jpg
The ARMAN are a group of archaea recently discovered in acid mine drainage.

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. [22] These classifications rely heavily on the use of the sequence of ribosomal RNA genes to reveal relationships among organisms (molecular phylogenetics). [23] 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, like the peculiar species Nanoarchaeum equitans , which was discovered in 2003 and has been given its own phylum, the Nanoarchaeota. [24] 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 Crenarchaeota. [25] [26] 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 [27] and are some of the smallest organisms known. [28]

A superphylum – TACK – which includes the Thaumarchaeota, Aigarchaeota, Crenarchaeota, and Korarchaeota was proposed in 2011 to be related to the origin of eukaryotes. [29] 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. [30]


According to Tom A. Williams et al. (2017) [31] and Castelle & Banfield (2018) [32] (DPANN):

























Aciduliprofundum boonei

Thermoplasma volcanium












Helarchaeota [33]


(+α─Proteobacteria )



Concept of species

The classification of archaea into species is also controversial. Biology defines a species 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 reproduce asexually. [34]

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 . [35] On the other hand, studies in Halorubrum found significant genetic transfer to/from less-related populations, limiting the criterion's applicability. [36] Some researchers question whether such species designations have practical meaning. [37]

Current knowledge on genetic diversity is fragmentary and the total number of archaeal species cannot be estimated with any accuracy. [23] 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. [38] The Bacteria also include many uncultured microbes with similar implications for characterization. [39]

Origin and evolution

The age of the Earth is about 4.54 billion years. [40] [41] [42] Scientific evidence suggests that life began on Earth at least 3.5  billion years ago. [43] [44] 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 [45] and microbial mat fossils found in 3.48-billion-year-old sandstone discovered in Western Australia. [46] [47] In 2015, possible remains of biotic matter were found in 4.1-billion-year-old rocks in Western Australia. [48] [49]

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. [50] Instead, chemical fossils of unique lipids are more informative because such compounds do not occur in other organisms. [51] Some publications suggest that archaeal or eukaryotic lipid remains are present in shales dating from 2.7 billion years ago; [52] though such data have since been questioned. [53] These lipids have also been detected in even older rocks from west Greenland. The oldest such traces come from the Isua district, which includes Earth's oldest known sediments, formed 3.8 billion years ago. [54] The archaeal lineage may be the most ancient that exists on Earth. [55]

Woese argued that the Bacteria, Archaea, and Eukaryotes represent separate lines of descent that diverged early on from an ancestral colony of organisms. [56] [57] One possibility [57] [58] 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. [57] [58] 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. [59] Since archaea and bacteria are no more related to each other than they are to eukaryotes, the term prokaryote suggests a false similarity between them. [60]

Comparison with other domains

The following table compares some major characteristics of the three domains, to illustrate their similarities and differences. [61]

Cell membrane Ether-linked lipids Ester-linked lipidsEster-linked lipids
Cell wall Pseudopeptidoglycan, glycoprotein, or S-layer Peptidoglycan, S-layer, or no cell wallVarious structures
Gene structureCircular chromosomes, similar translation and transcription to EukaryaCircular chromosomes, unique translation and transcriptionMultiple, linear chromosomes, but translation and transcription similar to Archaea
Internal cell structureNo membrane-bound organelles (? [62] ) or nucleus No membrane-bound organelles or nucleusMembrane-bound organelles and nucleus
Metabolism [63] Various, including diazotrophy, with methanogenesis unique to ArchaeaVarious, including photosynthesis, aerobic and anaerobic respiration, fermentation, diazotrophy, and autotrophy Photosynthesis, cellular respiration, and fermentation; no diazotrophy
Reproduction Asexual reproduction, horizontal gene transfer Asexual reproduction, horizontal gene transfer Sexual and asexual reproduction
Protein synthesis initiationMethionineFormylmethionineMethionine
RNA polymeraseManyOneMany
ToxinSensitive to diphtheria toxinResistant to diphtheria toxinSensitive to diphtheria toxin

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 nucleotide 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. [14] The more similar the patterns between species, the more closely they are related. [64]

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. [14] These methanogens were much more similar to each other than to other organisms, leading Woese to propose the new domain of Archaea. [14] His experiments showed that the archaea were genetically more similar to eukaryotes than prokaryotes, even though they were more similar to prokaryotes in structure. [65] This led to the conclusion that Archaea and Eukarya shared a common ancestor more recent than Eukarya and Bacteria. [65] The development of the nucleus occurred after the split between Bacteria and this common ancestor. [65] [1]

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. 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. [66] [67] [68] 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. [69]

Relationship to bacteria

EuryarchaeotaNanoarchaeotaCrenarchaeotaProtozoaAlgaePlantSlime moldsAnimalFungusGram-positive bacteriaChlamydiaeChloroflexiActinobacteriaPlanctomycetesSpirochaetesFusobacteriaCyanobacteriaThermophilesAcidobacteriaProteobacteriaArchaea
Phylogenetic tree showing the relationship between the Archaea and other domains of life. Eukaryotes are colored red, archaea green and bacteria blue. Adapted from Ciccarelli et al. (2006) [1]
  1. ^ Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, Bork P (March 2006). "Toward automatic reconstruction of a highly resolved tree of life". Science. 311 (5765): 1283–87. Bibcode:2006Sci...311.1283C. CiteSeerX . doi:10.1126/science.1123061. PMID 16513982.

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. [70] Within prokaryotes, archaeal cell structure is most similar to that of gram-positive bacteria, largely because both have a single lipid bilayer [71] and usually contain a thick sacculus (exoskeleton) of varying chemical composition. [72] 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. [71] Archaea and gram-positive bacteria also share conserved indels in a number of important proteins, such as Hsp70 and glutamine synthetase  I; [71] [73] but the phylogeny of these genes was interpreted to reveal interdomain gene transfer, [74] [75] and might not reflect the organismal relationship(s). [76]

It has been proposed that the archaea evolved from gram-positive bacteria in response to antibiotic selection pressure. [71] [73] [77] This is suggested by the observation that archaea are resistant to a wide variety of antibiotics that are produced primarily by gram-positive bacteria, [71] [73] 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. [77] 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; [77] [78] Cavalier-Smith has made a similar suggestion. [79] This proposal is also supported by other work investigating protein structural relationships [80] and studies that suggest that gram-positive bacteria may constitute the earliest branching lineages within the prokaryotes. [81]

Relation to eukaryotes

The evolutionary relationship between archaea and eukaryotes remains unclear. Aside from the similarities in cell structure and function that are discussed below, many genetic trees group the two. [82]

Complicating factors include claims that the relationship between eukaryotes and the archaeal phylum Crenarchaeota is closer than the relationship between the Euryarchaeota and the phylum Crenarchaeota [83] and the presence of archaea-like genes in certain bacteria, such as Thermotoga maritima , from horizontal gene transfer. [84] The standard hypothesis states that the ancestor of the eukaryotes diverged early from the Archaea, [85] [86] and that eukaryotes arose through fusion of an archaean and eubacterium, which became the nucleus and cytoplasm; this hypothesis explains various genetic similarities but runs into difficulties explaining cell structure. [83] An alternative hypothesis, the eocyte hypothesis, posits that Eukaryota emerged relatively late from the Archaea. [87]

A lineage of archaea discovered in 2015, Lokiarchaeum (of proposed new Phylum "Lokiarchaeota"), named for a hydrothermal vent 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. [88] [89]

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. [30] [3] [90]

Details of the relation of Asgard members and eukaryotes are still under consideration, [91] 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. [92] [93]


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. [94] Other morphologies in the Crenarchaeota 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 . [95] Archaea in the genus Haloquadratum such as Haloquadratum walsbyi are flat, square specimens that live in hypersaline pools. [96] 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, [97] and filaments form within their cells, [98] but in contrast with other organisms, these cellular structures are poorly understood. [99] In Thermoplasma and Ferroplasma the lack of a cell wall means that the cells have irregular shapes, and can resemble amoebae. [100]

Some species form aggregates or filaments of cells up to 200 μm long. [94] These organisms can be prominent in biofilms. [101] Notably, aggregates of Thermococcus coalescens cells fuse together in culture, forming single giant cells. [102] 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. [103] The function of these cannulae is not settled, but they may allow communication or nutrient exchange with neighbors. [104] 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 15 centimetres (5.9 in) long; these filaments are made of a particular bacteria species. [105]

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. [60] Like bacteria, the cell membranes of archaea are usually bounded by a cell wall and they swim using one or more flagella. [106] 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. [107]

Cell wall and flagella

Most archaea (but not Thermoplasma and Ferroplasma ) possess a cell wall. [100] In most archaea the wall is assembled from surface-layer proteins, which form an S-layer. [108] An S-layer is a rigid array of protein molecules that cover the outside of the cell (like chain mail). [109] This layer provides both chemical and physical protection, and can prevent macromolecules from contacting the cell membrane. [110] Unlike bacteria, archaea lack peptidoglycan in their cell walls. [111] 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. [110]

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. [106] The two types of flagella evolved from different ancestors. The bacterial flagellum shares a common ancestor with the type III secretion system, [112] [113] while archaeal flagella appear to have evolved from bacterial type IV pili. [114] 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. [115]


Membrane structures. Top, an archaeal phospholipid: 1, isoprene chains; 2, ether linkages; 3, L-glycerol moiety; 4, phosphate group. Middle, a bacterial or eukaryotic phospholipid: 5, fatty acid chains; 6, ester linkages; 7, D-glycerol moiety; 8, phosphate group. Bottom: 9, lipid bilayer of bacteria and eukaryotes; 10, lipid monolayer of some archaea. Archaea membrane.svg
Membrane structures. Top, an archaeal phospholipid: 1, isoprene chains; 2, ether linkages; 3,  L-glycerol moiety; 4, phosphate group. Middle, a bacterial or eukaryotic phospholipid: 5, fatty acid chains; 6, ester linkages; 7,  D-glycerol moiety; 8, phosphate group. Bottom: 9, lipid bilayer of bacteria and eukaryotes; 10, lipid monolayer of some archaea.

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. [116] In all organisms, cell membranes 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. [117]

The phospholipids of archaea are unusual in four ways:


Archaea exhibit a great variety of chemical reactions in their metabolism 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 or ammonia (they are chemotrophs). These include nitrifiers, methanogens and anaerobic methane oxidisers. [124] In these reactions one compound passes electrons to another (in a redox reaction), releasing energy to fuel the cell's activities. One compound acts as an electron donor and one as an electron acceptor. The energy released is used to generate adenosine triphosphate (ATP) through chemiosmosis, the same basic process that happens in the mitochondrion of eukaryotic cells. [125]

Other groups of archaea use sunlight as a source of energy (they are phototrophs), but oxygen–generating photosynthesis does not occur in any of these organisms. [125] Many basic metabolic pathways are shared among all forms of life; for example, archaea use a modified form of glycolysis (the Entner–Doudoroff pathway) and either a complete or partial citric acid cycle. [126] These similarities to other organisms probably reflect both early origins in the history of life and their high level of efficiency. [127]

Nutritional types in archaeal metabolism
Nutritional typeSource of energySource of carbonExamples
  Phototrophs   Sunlight  Organic compounds   Halobacterium  
  Lithotrophs  Inorganic compounds Organic compounds or carbon fixation   Ferroglobus , Methanobacteria or Pyrolobus  
  Organotrophs  Organic compounds  Organic compounds or carbon fixation    Pyrococcus , Sulfolobus or Methanosarcinales  

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. [128] A common reaction involves the use of carbon dioxide as an electron acceptor to oxidize hydrogen. Methanogenesis involves a range of coenzymes that are unique to these archaea, such as coenzyme M and methanofuran. [129] Other organic compounds such as alcohols, acetic acid or formic acid are used as alternative electron acceptors 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. [130]

Bacteriorhodopsin from Halobacterium salinarum. The retinol cofactor and residues involved in proton transfer are shown as ball-and-stick models. Bacteriorhodopsin.png
Bacteriorhodopsin from Halobacterium salinarum . The retinol cofactor and residues involved in proton transfer are shown as ball-and-stick models.

Other archaea use CO
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 [132] or another metabolic pathway called the 3-hydroxypropionate/4-hydroxybutyrate cycle. [133] The Crenarchaeota also use the reverse Krebs cycle while the Euryarchaeota also use the reductive acetyl-CoA pathway. [134] Carbon fixation is powered by inorganic energy sources. No known archaea carry out photosynthesis. [135] Archaeal energy sources are extremely diverse, and range from the oxidation of ammonia by the Nitrosopumilales [136] [137] to the oxidation of hydrogen sulfide or elemental sulfur by species of Sulfolobus , using either oxygen or metal ions as electron acceptors. [125]

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 energy stored in these electrochemical gradients is then converted into ATP by ATP synthase. [94] 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. [138]


Archaea usually have a single circular chromosome, [139] with as many as 5,751,492  base pairs in Methanosarcina acetivorans , [140] 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. [141] 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. [142] [143]

Sulfolobus infected with the DNA virus STSV1. Bar is 1 micrometer. RT8-4.jpg
Sulfolobus infected with the DNA virus STSV1. Bar is 1  micrometer.

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. [145] Of the remainder of the unique proteins that have an identified function, most belong to the Euryarchaea 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. [146] 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. [146]

Transcription in archaea more closely resembles eukaryotic than bacterial transcription, with the archaeal RNA polymerase being very close to its equivalent in eukaryotes, [139] while archaeal translation shows signs of both bacterial and eukaryotic equivalents. [147] 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, with similar protein assemblies (the general transcription factors) directing the binding of the RNA polymerase to a gene's promoter, [148] but other archaeal transcription factors are closer to those found in bacteria. [149] Post-transcriptional modification is simpler than in eukaryotes, since most archaeal genes lack introns, although there are many introns in their transfer RNA and ribosomal RNA genes, [150] and introns may occur in a few protein-encoding genes. [151] [152]

Gene transfer and genetic exchange

Halobacterium 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. [153]

When the hyperthermophilic archaea Sulfolobus solfataricus [154] and Sulfolobus acidocaldarius [155] 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, [154] suggesting that aggregation is induced specifically by DNA damage. Ajon et al. [155] 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. [154] [156] and Ajon et al. [155] 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. 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. [157]

Archaeal viruses

Archaea are the target of a number of viruses 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. [158] [159] [160] 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. [159] 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. [158] Their virus release mechanisms differ from that of other phages. Bacteriophages generally undergo either lytic pathways, lysogenic pathways, or (rarely) a mix of the two. [161] 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. [162] 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 (dsDNA) 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). [159]

These viruses have been studied in most detail in thermophilics, particularly the orders Sulfolobales and Thermoproteales. [163] 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, [164] and the other one by the Aeropyrum coil-shaped virus ("Spiraviridae") infecting a hyperthermophilic (optimal growth at 90–95 °C) host. [165] 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. [166] [167]


Archaea reproduce asexually by binary or multiple fission, fragmentation, or budding; mitosis and meiosis do not occur, so if a species of archaea exists in more than one form, all have the same genetic material. [94] Cell division is controlled in a cell cycle; after the cell's chromosome is replicated and the two daughter chromosomes separate, the cell divides. [168] 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. [169]

In euryarchaea 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. [168] In cren- [170] [171] and thaumarchaea, [172] 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. [173]

Both bacteria and eukaryotes, but not archaea, make spores. [174] 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. [175]



Archaea that grow in the hot water of the Morning Glory Hot Spring in Yellowstone National Park produce a bright colour Morning-Glory Hotspring.jpg
Archaea that grow in the hot water of the Morning Glory Hot Spring in Yellowstone National Park produce a bright colour

Archaea exist in a broad range of habitats, and are now recognized as a major part of global ecosystems, [19] and may represent about 20% of microbial cells in the oceans. [176] However, the first-discovered archaeans were extremophiles. [124] Indeed, some archaea survive high temperatures, often above 100 °C (212 °F), as found in geysers, black smokers, and oil wells. Other common habitats include very cold habitats and highly saline, acidic, or alkaline water, but archaea include mesophiles that grow in mild conditions, in swamps and marshland, sewage, the oceans, the intestinal tract of animals, and soils. [19]

Extremophile archaea are members of four main physiological groups. These are the halophiles, thermophiles, alkaliphiles, and acidophiles. [177] 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. [178]

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%. [124] Thermophiles grow best at temperatures above 45 °C (113 °F), in places such as hot springs; hyperthermophilic archaea grow optimally at temperatures greater than 80 °C (176 °F). [179] The archaeal Methanopyrus kandleri Strain 116 can even reproduce at 122 °C (252 °F), the highest recorded temperature of any organism. [180]

Other archaea exist in very acidic or alkaline conditions. [177] 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. [181]

This resistance to extreme environments has made archaea the focus of speculation about the possible properties of extraterrestrial life. [182] Some extremophile habitats are not dissimilar to those on Mars, [183] leading to the suggestion that viable microbes could be transferred between planets in meteorites. [184]

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. [185] Even more significant are the large numbers of archaea found throughout the world's oceans in non-extreme habitats among the plankton community (as part of the picoplankton). [186] 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. [187] Consequently, our understanding of the role of archaea in ocean ecology is rudimentary, so their full influence on global biogeochemical cycles remains largely unexplored. [188] Some marine Crenarchaeota are capable of nitrification, suggesting these organisms may affect the oceanic nitrogen cycle, [136] although these oceanic Crenarchaeota may also use other sources of energy. [189]

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. [190] [191] 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. [192]

Role in chemical cycling

Archaea recycle elements such as carbon, nitrogen, and sulfur through their various habitats. [193] Archaea carry out many steps in the nitrogen cycle. This includes both reactions that remove nitrogen from ecosystems (such as nitrate-based respiration and denitrification) as well as processes that introduce nitrogen (such as nitrate assimilation and nitrogen fixation). [194] [195] Researchers recently discovered archaeal involvement in ammonia oxidation reactions. These reactions are particularly important in the oceans. [137] [196] The archaea also appear crucial for ammonia oxidation in soils. They produce nitrite, which other microbes then oxidize to nitrate. Plants and other organisms consume the latter. [197]

In the sulfur cycle, archaea that grow by oxidizing sulfur compounds release this element from rocks, making it available to other organisms, but the archaea that do this, such as Sulfolobus, produce sulfuric acid as a waste product, and the growth of these organisms in abandoned mines can contribute to acid mine drainage and other environmental damage. [198]

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. [199]

Interactions with other organisms

Methanogenic archaea form a symbiosis with termites. Coptotermes formosanus shiraki USGov k8204-7.jpg
Methanogenic archaea form a symbiosis with termites.

The well-characterized interactions between archaea and other organisms are either mutual or commensal. There are no clear examples of known archaeal pathogens or parasites, [200] [201] but some species of methanogens have been suggested to be involved in infections in the mouth, [202] [203] 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 , [141] and appears to offer no benefit to its host. [204]


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. [205] 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. [206]

In anaerobic protozoa, such as Plagiopyla frontata, archaea reside inside the protozoa and consume hydrogen produced in their hydrogenosomes. [207] [208] Archaea also associate with larger organisms. For example, the marine archaean Cenarchaeum symbiosum lives within (is an endosymbiont of) the sponge Axinella mexicana . [209]


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. [210] In termites and in humans, these methanogens may in fact be mutualists, interacting with other microbes in the gut to aid digestion. [211] Archaean communities also associate with a range of other organisms, such as on the surface of corals, [212] and in the region of soil that surrounds plant roots (the rhizosphere). [213] [214]

Significance in technology and industry

Extremophile archaea, particularly those resistant either to heat or to extremes of acidity and alkalinity, are a source of enzymes that function under these harsh conditions. [215] [216] These enzymes have found many uses. For example, thermostable DNA polymerases, such as the Pfu DNA polymerase from Pyrococcus furiosus , revolutionized molecular biology by allowing the polymerase chain reaction 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 100 °C (212 °F) allow food processing at high temperatures, such as the production of low lactose milk and whey. [217] 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. [216] 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. [218]

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. [219] In mineral processing, acidophilic archaea display promise for the extraction of metals from ores, including gold, cobalt and copper. [220]

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. [221]

See also

Related Research Articles

Microorganism Microscopic living organism

A microorganism, or microbe, is a microscopic organism, which may exist in its single-celled form or in a colony of cells.

Carl Woese American microbiologist and biophysicist

Carl Richard Woese was an American microbiologist and biophysicist. Woese is famous for defining the Archaea in 1977 by phylogenetic taxonomy of 16S ribosomal RNA, a technique he pioneered that revolutionized microbiology. He also originated the RNA world hypothesis in 1967, although not by that name. Woese held the Stanley O. Ikenberry Chair and was professor of microbiology at the University of Illinois at Urbana–Champaign.

Symbiogenesis An evolutionary theory holding that eukaryotic organelles evolved through symbiosis with prokaryotes

Symbiogenesis, or endosymbiotic theory, is an evolutionary theory of the origin of eukaryotic cells from prokaryotic organisms, first articulated in 1905 and 1910 by the Russian botanist Konstantin Mereschkowski, and advanced and substantiated with microbiological evidence by Lynn Margulis in 1967. It holds that the organelles distinguishing eukaryote cells evolved through symbiosis of individual single-celled prokaryotes . The theory holds that mitochondria, plastids such as chloroplasts, and possibly other organelles of eukaryotic cells are descended from formerly free-living prokaryotes taken one inside the other in endosymbiosis. Mitochondria appear to be phylogenetically related to Rickettsiales proteobacteria, and chloroplasts to nitrogen-fixing filamentous cyanobacteria. Among the many lines of evidence supporting symbiogenesis are that new mitochondria and plastids are formed only through binary fission, and that cells cannot create new ones otherwise; that the transport proteins called porins are found in the outer membranes of mitochondria, chloroplasts and bacterial cell membranes; that cardiolipin is found only in the inner mitochondrial membrane and bacterial cell membranes; and that some mitochondria and plastids contain single circular DNA molecules similar to the chromosomes of bacteria.

Domain (biology) Taxonomic rank

In biological taxonomy, a domain, also superkingdom, realm, or empire, is the highest taxonomic rank of organisms in the three-domain system of taxonomy devised by Carl Woese in 1990.

Three-domain system Hypothesis for classification of life

The three-domain system is a biological classification introduced by Carl Woese et al. in 1990 that divides cellular life forms into archaea, bacteria, and eukaryote domains. The key difference from earlier classifications is the splitting of archaea from bacteria.

Unicellular organism Organism that consists of only one cell

A unicellular organism, also known as a single-celled organism, is an organism that consists of a single cell, unlike a multicellular organism that consists of multiple cells. Unicellular organisms fall into two general categories: prokaryotic organisms and eukaryotic organisms. All prokaryotes are unicellular and are classified into bacteria and archaea. Many eukaryotes are multicellular, but many are unicellular such as protozoa, unicellular algae, and unicellular fungi. Unicellular organisms are thought to be the oldest form of life, with early protocells possibly emerging 3.8–4 billion years ago.

Last universal common ancestor Last recent common ancestor of all current life

The last universal common ancestor (LUCA), also called the last universal ancestor (LUA), or concestor, is the most recent population of organisms from which all organisms now living on Earth have a common descent, the most recent common ancestor of all current life on Earth. LUCA is not thought to be the first life on Earth, but rather the only organism of its time to still have living descendants.

Viral eukaryogenesis is the hypothesis that the cell nucleus of eukaryotic life forms evolved from a large DNA virus in a form of endosymbiosis within a methanogenic archaeon. The virus later evolved into the eukaryotic nucleus by acquiring genes from the host genome and eventually usurping its role. The hypothesis was proposed by Philip Bell in 2001 and gained support as large, complex DNA viruses capable of protein biosynthesis were discovered. Recent supporting evidence includes the discovery that, upon the infection of a bacterial cell, the giant bacteriophage 201Phi2-1 assembles a nucleus-like structure that segregates proteins according to function. This nucleus-like structure and its key properties have been found conserved in the related phages.

Microbial genetics is a subject area within microbiology and genetic engineering. Microbial genetics studies microorganisms for different purposes. The microorganisms that are observed are bacteria, and archaea. Some fungi and protozoa are also subjects used to study in this field. The studies of microorganisms involve studies of genotype and expression system. Genotypes are the inherited compositions of an organism. Genetic Engineering is a field of work and study within microbial genetics. The usage of recombinant DNA technology is a process of this work. The process involves creating recombinant DNA molecules through manipulating a DNA sequence. That DNA created is then in contact with a host organism. Cloning is also an example of genetic engineering.

Bacteria Domain of prokaryotes

Bacteria are a type of biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a number of shapes, ranging from spheres to rods and spirals. Bacteria were among the first life forms to appear on Earth, and are present in most of its habitats. Bacteria inhabit soil, water, acidic hot springs, radioactive waste, and the deep biosphere of the earth's crust. Bacteria also live in symbiotic and parasitic relationships with plants and animals. Most bacteria have not been characterised, and only about 27 percent of the bacterial phyla have species that can be grown in the laboratory. The study of bacteria is known as bacteriology, a branch of microbiology.

Prokaryote Unicellular organism that lacks a membrane-bound nucleus

A prokaryote is a unicellular organism that lacks a membrane-bound nucleus, mitochondria, or any other membrane-bound organelle. The word prokaryote comes from the Greek πρό and κάρυον. Prokaryotes are divided into two domains, Archaea and Bacteria. Organisms with nuclei and other organelles are placed in a third domain, Eukaryota. Prokaryotes are asexual, reproducing without fusion of gametes. The first organisms are thought to have been prokaryotes.

Organism Any individual living physical entity

In biology, an organism is any individual entity that embodies the properties of life. It is a synonym for "life form".

Horizontal gene transfer in evolution The evolutionary consequences of transfer of genetic material between organisms of different taxa

Scientists trying to reconstruct evolutionary history have been challenged by the fact that genes can sometimes transfer between distant branches on the tree of life. This movement of genes can occur through horizontal gene transfer (HGT), scrambling the information on which biologists relied to reconstruct the phylogeny of organisms. Conversely, HGT can also help scientists to reconstruct and date the tree of life. Indeed, a gene transfer can be used as a phylogenetic marker, or as the proof of contemporaneity of the donor and recipient organisms, and as a trace of extinct biodiversity.

Eukaryote Organism whose cells have a nucleus enclosed within membranes

Eukaryotes are organisms whose cells have a nucleus enclosed within membranes, unlike prokaryotes, which have no membrane-bound organelles. Eukaryotes belong to the domain Eukaryota or Eukarya. Their name comes from the Greek εὖ and κάρυον. Eukaryotic cells typically contain other membrane-bound organelles such as mitochondria and the Golgi apparatus, and in addition, some cells of plants and algae contain chloroplasts. Unlike unicellular archaea and bacteria, eukaryotes may also be multicellular and include organisms consisting of many cell types forming different kinds of tissue. Animals and plants are the most familiar eukaryotes.

Evolution of cells The evolutionary origin and subsequent development of cells

Evolution of cells refers to the evolutionary origin and subsequent evolutionary development of cells. Cells first emerged at least 3.8 billion years ago. This was approximately 750 million years after the earth was formed.

Marine microorganisms Any life form too small for the naked human eye to see that lives in a marine environment

Marine microorganisms are defined by their habitat as the microorganisms living in a marine environment, that is, in the saltwater of a sea or ocean or the brackish water of a coastal estuary. A microorganism is any microscopic living organism, that is, any life form too small for the naked human eye to really see, needing a microscope. Microorganisms are very diverse. They can be single-celled or multicellular and include all bacteria and archaea and most protozoa, as well as some species of fungi, algae, and certain microscopic animals, such as rotifers and copepods. Many macroscopic animals and plants have microscopic juvenile stages. Some microbiologists also classify biologically active entities such as viruses and viroids as microorganisms, but others consider these as nonliving.

Eocyte hypothesis

The Eocyte hypothesis is a biological classification that indicates eukaryotes emerged within the prokaryotic Crenarchaeota, a phylum within the archaea. This hypothesis was originally proposed by James A. Lake and colleagues in 1984 based on the discovery that the shapes of ribosomes in the Crenarchaeota and eukaryotes are more similar to each other than to either bacteria or the second major kingdom of archaea, the Euryarchaeota.

Lokiarchaeota is a proposed phylum of the Archaea. The phylum includes all members of the group previously named Deep Sea Archaeal Group (DSAG), also known as Marine Benthic Group B (MBG-B). A phylogenetic analysis disclosed a monophyletic grouping of the Lokiarchaeota with the eukaryotes. The analysis revealed several genes with cell membrane-related functions. The presence of such genes support the hypothesis of an archaeal host for the emergence of the eukaryotes; the eocyte-like scenarios.

Marine viruses

Marine viruses are defined by their habitat as viruses that live in marine environments, that is, in the saltwater of seas or oceans or the brackish water of coastal estuaries. A virus is a small infectious agent that replicates only inside the living cells of another organism. This means the goal of a virus is to infect another organism so it can replicate. Viruses can infect all types of life forms, from animals and plants to microorganisms, including bacteria and archaea as well as other viruses.

Marine prokaryotes

Marine prokaryotes are marine bacteria and marine archaea. They are defined by their habitat as prokaryotes that live in marine environments, that is, in the saltwater of seas or oceans or the brackish water of coastal estuaries. All cellular life forms can be divided into prokaryotes and eukaryotes. Eukaryotes are organisms whose cells have a nucleus enclosed within membranes, whereas prokaryotes are the organisms that do not have a nucleus enclosed within a membrane. The three-domain system of classifying life adds another division: the prokaryotes are divided into two domains of life, the microscopic bacteria and archaea, while the eukaryotes become the third domain.


  1. 1 2 3 Woese CR, Kandler O, Wheelis ML (June 1990). "Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya". Proceedings of the National Academy of Sciences of the United States of America. 87 (12): 4576–9. Bibcode:1990PNAS...87.4576W. doi:10.1073/pnas.87.12.4576. PMC   54159 . PMID   2112744.
  2. Petitjean C, Deschamps P, López-García P, Moreira D (December 2014). "Rooting the domain archaea by phylogenomic analysis supports the foundation of the new kingdom Proteoarchaeota". Genome Biology and Evolution. 7 (1): 191–204. doi:10.1093/gbe/evu274. PMC   4316627 . PMID   25527841.
  3. 1 2 "NCBI taxonomy page on Archaea".
  4. 1 2 "Taxa above the rank of class". List of Prokaryotic names with Standing in Nomenclature . Retrieved 8 August 2017.
  5. Cavalier-Smith T (2014). "The neomuran revolution and phagotrophic origin of eukaryotes and cilia in the light of intracellular coevolution and a revised tree of life". Cold Spring Harb. Perspect. Biol. 6 (9): a016006. doi:10.1101/cshperspect.a016006. PMC   4142966 . PMID   25183828.
  6. Pace NR (May 2006). "Time for a change". Nature. 441 (7091): 289. Bibcode:2006Natur.441..289P. doi:10.1038/441289a. PMID   16710401.
  7. Stoeckenius W (October 1981). "Walsby's square bacterium: fine structure of an orthogonal procaryote". Journal of Bacteriology. 148 (1): 352–60. doi:10.1128/JB.148.1.352-360.1981. PMC   216199 . PMID   7287626.
  8. "Archaea Basic Biology". March 2018.
  9. Bang C, Schmitz RA (September 2015). "Archaea associated with human surfaces: not to be underestimated". FEMS Microbiology Reviews. 39 (5): 631–48. doi: 10.1093/femsre/fuv010 . PMID   25907112.
  10. Moissl-Eichinger C, Pausan M, Taffner J, Berg G, Bang C, Schmitz RA (January 2018). "Archaea Are Interactive Components of Complex Microbiomes". Trends in Microbiology. 26 (1): 70–85. doi:10.1016/j.tim.2017.07.004. PMID   28826642.
  11. Staley JT (November 2006). "The bacterial species dilemma and the genomic-phylogenetic species concept". Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 361 (1475): 1899–909. doi:10.1098/rstb.2006.1914. PMC   1857736 . PMID   17062409.
  12. Zuckerkandl E, Pauling L (March 1965). "Molecules as documents of evolutionary history". Journal of Theoretical Biology. 8 (2): 357–66. doi:10.1016/0022-5193(65)90083-4. PMID   5876245.
  13. Parks DH, Chuvochina M, Waite DW, Rinke C, Skarshewski A, Chaumeil PA, Hugenholtz P (November 2018). "A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life". Nature Biotechnology. 36 (10): 996–1004. doi:10.1038/nbt.4229. PMID   30148503.
  14. 1 2 3 4 Woese CR, Fox GE (November 1977). "Phylogenetic structure of the prokaryotic domain: the primary kingdoms". Proceedings of the National Academy of Sciences of the United States of America. 74 (11): 5088–90. Bibcode:1977PNAS...74.5088W. doi:10.1073/pnas.74.11.5088. PMC   432104 . PMID   270744.
  15. Sapp J (2009). The new foundations of evolution: on the tree of life. New York: Oxford University Press. ISBN   978-0-19-973438-2.
  16. Archaea. (2008). In Merriam-Webster Online Dictionary. Retrieved July 1, 2008
  17. Magrum LJ, Luehrsen KR, Woese CR (May 1978). "Are extreme halophiles actually "bacteria"?". Journal of Molecular Evolution. 11 (1): 1–8. Bibcode:1978JMolE..11....1M. doi:10.1007/bf01768019. PMID   660662.
  18. Stetter KO (1996). "Hyperthermophiles in the history of life". Ciba Foundation Symposium. 202: 1–10, discussion 11–8. PMID   9243007.
  19. 1 2 3 DeLong EF (December 1998). "Everything in moderation: archaea as 'non-extremophiles'". Current Opinion in Genetics & Development. 8 (6): 649–54. doi:10.1016/S0959-437X(98)80032-4. PMID   9914204.
  20. Theron J, Cloete TE (2000). "Molecular techniques for determining microbial diversity and community structure in natural environments". Critical Reviews in Microbiology. 26 (1): 37–57. doi:10.1080/10408410091154174. PMID   10782339.
  21. Schmidt TM (September 2006). "The maturing of microbial ecology" (PDF). International Microbiology. 9 (3): 217–23. PMID   17061212. Archived from the original (PDF) on 11 September 2008.
  22. Gevers D, Dawyndt P, Vandamme P, Willems A, Vancanneyt M, Swings J, et al. (November 2006). "Stepping stones towards a new prokaryotic taxonomy". Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 361 (1475): 1911–16. doi:10.1098/rstb.2006.1915. PMC   1764938 . PMID   17062410.
  23. 1 2 Robertson CE, Harris JK, Spear JR, Pace NR (December 2005). "Phylogenetic diversity and ecology of environmental Archaea". Current Opinion in Microbiology. 8 (6): 638–42. doi:10.1016/j.mib.2005.10.003. PMID   16236543.
  24. Huber H, Hohn MJ, Rachel R, Fuchs T, Wimmer VC, Stetter KO (May 2002). "A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont". Nature. 417 (6884): 63–67. Bibcode:2002Natur.417...63H. doi:10.1038/417063a. PMID   11986665.
  25. Barns SM, Delwiche CF, Palmer JD, Pace NR (August 1996). "Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences". Proceedings of the National Academy of Sciences of the United States of America. 93 (17): 9188–93. Bibcode:1996PNAS...93.9188B. doi:10.1073/pnas.93.17.9188. PMC   38617 . PMID   8799176.
  26. Elkins JG, Podar M, Graham DE, Makarova KS, Wolf Y, Randau L, et al. (June 2008). "A korarchaeal genome reveals insights into the evolution of the Archaea". Proceedings of the National Academy of Sciences of the United States of America. 105 (23): 8102–07. Bibcode:2008PNAS..105.8102E. doi:10.1073/pnas.0801980105. PMC   2430366 . PMID   18535141.
  27. Baker BJ, Tyson GW, Webb RI, Flanagan J, Hugenholtz P, Allen EE, Banfield JF (December 2006). "Lineages of acidophilic archaea revealed by community genomic analysis". Science. 314 (5807): 1933–35. Bibcode:2006Sci...314.1933B. doi:10.1126/science.1132690. PMID   17185602.
  28. Baker BJ, Comolli LR, Dick GJ, Hauser LJ, Hyatt D, Dill BD, et al. (May 2010). "Enigmatic, ultrasmall, uncultivated Archaea". Proceedings of the National Academy of Sciences of the United States of America. 107 (19): 8806–11. Bibcode:2010PNAS..107.8806B. doi:10.1073/pnas.0914470107. PMC   2889320 . PMID   20421484.
  29. Guy L, Ettema TJ (December 2011). "The archaeal 'TACK' superphylum and the origin of eukaryotes". Trends in Microbiology. 19 (12): 580–87. doi:10.1016/j.tim.2011.09.002. PMID   22018741.
  30. 1 2 Zaremba-Niedzwiedzka K, Caceres EF, Saw JH, Bäckström D, Juzokaite L, Vancaester E, et al. (January 2017). "Asgard archaea illuminate the origin of eukaryotic cellular complexity" (PDF). Nature. 541 (7637): 353–58. Bibcode:2017Natur.541..353Z. doi:10.1038/nature21031. PMID   28077874.
  31. Williams TA, Szöllősi GJ, Spang A, Foster PG, Heaps SE, Boussau B, et al. (June 2017). "Integrative modeling of gene and genome evolution roots the archaeal tree of life". Proceedings of the National Academy of Sciences of the United States of America. 114 (23): E4602–E4611. doi:10.1073/pnas.1618463114. PMID   28533395.
  32. Castelle CJ, Banfield JF (2018). "Major New Microbial Groups Expand Diversity and Alter our Understanding of the Tree of Life". Cell. 172: 1181–1197. doi:10.1016/j.cell.2018.02.016. PMID   29522741.
  33. Seitz KW, Dombrowski N, Eme L, Spang A, Lombard J, Sieber JR, et al. (April 2019). "Asgard archaea capable of anaerobic hydrocarbon cycling". Nature Communications. 10 (1): 1822. doi:10.1038/s41467-019-09364-x. PMID   31015394.
  34. de Queiroz K (May 2005). "Ernst Mayr and the modern concept of species". Proceedings of the National Academy of Sciences of the United States of America. 102 (Suppl 1): 6600–07. Bibcode:2005PNAS..102.6600D. doi:10.1073/pnas.0502030102. PMC   1131873 . PMID   15851674.
  35. Eppley JM, Tyson GW, Getz WM, Banfield JF (September 2007). "Genetic exchange across a species boundary in the archaeal genus ferroplasma". Genetics. 177 (1): 407–16. doi:10.1534/genetics.107.072892. PMC   2013692 . PMID   17603112.
  36. Papke RT, Zhaxybayeva O, Feil EJ, Sommerfeld K, Muise D, Doolittle WF (August 2007). "Searching for species in haloarchaea". Proceedings of the National Academy of Sciences of the United States of America. 104 (35): 14092–97. Bibcode:2007PNAS..10414092P. doi:10.1073/pnas.0706358104. PMC   1955782 . PMID   17715057.
  37. Kunin V, Goldovsky L, Darzentas N, Ouzounis CA (July 2005). "The net of life: reconstructing the microbial phylogenetic network". Genome Research. 15 (7): 954–59. doi:10.1101/gr.3666505. PMC   1172039 . PMID   15965028.
  38. Hugenholtz P (2002). "Exploring prokaryotic diversity in the genomic era". Genome Biology. 3 (2): REVIEWS0003. doi:10.1186/gb-2002-3-2-reviews0003. PMC   139013 . PMID   11864374.
  39. Rappé MS, Giovannoni SJ (2003). "The uncultured microbial majority". Annual Review of Microbiology. 57: 369–94. doi:10.1146/annurev.micro.57.030502.090759. PMID   14527284.
  40. "Age of the Earth". U.S. Geological Survey. 1997. Archived from the original on 23 December 2005. Retrieved 10 January 2006.
  41. Dalrymple GB (2001). "The age of the Earth in the twentieth century: a problem (mostly) solved". Special Publications, Geological Society of London. 190 (1): 205–21. Bibcode:2001GSLSP.190..205D. doi:10.1144/GSL.SP.2001.190.01.14.
  42. Manhesa G, Allègre CJ, Dupréa B, Hamelin B (1980). "Lead isotope study of basic-ultrabasic layered complexes: Speculations about the age of the earth and primitive mantle characteristics". Earth and Planetary Science Letters . 47 (3): 370–82. Bibcode:1980E&PSL..47..370M. doi:10.1016/0012-821X(80)90024-2.
  43. de Duve C (October 1995). "The Beginnings of Life on Earth". American Scientist . Retrieved 15 January 2014.
  44. Timmer J (4 September 2012). "3.5 billion year old organic deposits show signs of life". Ars Technica . Retrieved 15 January 2014.
  45. Ohtomo Y, Kakegawa T, Ishida A, Nagase T, Rosingm MT (8 December 2013). "Evidence for biogenic graphite in early Archaean Isua metasedimentary rocks". Nature Geoscience . 7 (1): 25. Bibcode:2014NatGe...7...25O. doi:10.1038/ngeo2025.
  46. Borenstein S (13 November 2013). "Oldest fossil found: Meet your microbial mom". Associated Press. Retrieved 15 November 2013.
  47. Noffke N, Christian D, Wacey D, Hazen RM (December 2013). "Microbially induced sedimentary structures recording an ancient ecosystem in the ca. 3.48 billion-year-old Dresser Formation, Pilbara, Western Australia". Astrobiology. 13 (12): 1103–24. Bibcode:2013AsBio..13.1103N. doi:10.1089/ast.2013.1030. PMC   3870916 . PMID   24205812.
  48. Borenstein S (19 October 2015). "Hints of life on what was thought to be desolate early Earth". Excite . Yonkers, NY: Mindspark Interactive Network. Associated Press . Retrieved 20 October 2015.
  49. Bell EA, Boehnke P, Harrison TM, Mao WL (November 2015). "Potentially biogenic carbon preserved in a 4.1 billion-year-old zircon" (PDF). Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. 112 (47): 14518–21. Bibcode:2015PNAS..11214518B. doi:10.1073/pnas.1517557112. PMC   4664351 . PMID   26483481.
  50. Schopf JW (June 2006). "Fossil evidence of Archaean life". Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 361 (1470): 869–85. doi:10.1098/rstb.2006.1834. PMC   1578735 . PMID   16754604.
  51. Chappe B, Albrecht P, Michaelis W (July 1982). "Polar lipids of archaebacteria in sediments and petroleums". Science. 217 (4554): 65–66. Bibcode:1982Sci...217...65C. doi:10.1126/science.217.4554.65. PMID   17739984.
  52. Brocks JJ, Logan GA, Buick R, Summons RE (August 1999). "Archean molecular fossils and the early rise of eukaryotes". Science. 285 (5430): 1033–36. CiteSeerX . doi:10.1126/science.285.5430.1033. PMID   10446042.
  53. Rasmussen B, Fletcher IR, Brocks JJ, Kilburn MR (October 2008). "Reassessing the first appearance of eukaryotes and cyanobacteria". Nature. 455 (7216): 1101–4. Bibcode:2008Natur.455.1101R. doi:10.1038/nature07381. PMID   18948954.
  54. Hahn J, Haug P (1986). "Traces of Archaebacteria in ancient sediments". System Applied Microbiology. 7 (Archaebacteria '85 Proceedings): 178–83. doi:10.1016/S0723-2020(86)80002-9.
  55. Wang M, Yafremava LS, Caetano-Anollés D, Mittenthal JE, Caetano-Anollés G (November 2007). "Reductive evolution of architectural repertoires in proteomes and the birth of the tripartite world". Genome Research. 17 (11): 1572–85. doi:10.1101/gr.6454307. PMC   2045140 . PMID   17908824.
  56. Woese CR, Gupta R (January 1981). "Are archaebacteria merely derived 'prokaryotes'?". Nature. 289 (5793): 95–96. Bibcode:1981Natur.289...95W. doi:10.1038/289095a0. PMID   6161309.
  57. 1 2 3 Woese C (June 1998). "The universal ancestor". Proceedings of the National Academy of Sciences of the United States of America. 95 (12): 6854–59. Bibcode:1998PNAS...95.6854W. doi:10.1073/pnas.95.12.6854. PMC   22660 . PMID   9618502.
  58. 1 2 Kandler O. The early diversification of life and the origin of the three domains: A proposal. In: Wiegel J, Adams WW, editors. Thermophiles: The keys to molecular evolution and the origin of life? Athens: Taylor and Francis, 1998: 19-31.
  59. Gribaldo S, Brochier-Armanet C (June 2006). "The origin and evolution of Archaea: a state of the art". Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 361 (1470): 1007–22. doi:10.1098/rstb.2006.1841. PMC   1578729 . PMID   16754611.
  60. 1 2 Woese CR (March 1994). "There must be a prokaryote somewhere: microbiology's search for itself". Microbiological Reviews. 58 (1): 1–9. doi:10.1128/MMBR.58.1.1-9.1994. PMC   372949 . PMID   8177167.
  61. Information is from Willey JM, Sherwood LM, Woolverton CJ. Microbiology 7th ed. (2008), Ch. 19 pp. 474–475, except where noted.
  62. Heimerl T, Flechsler J, Pickl C, Heinz V, Salecker B, Zweck J, Wanner G, Geimer S, Samson RY, Bell SD, Huber H, Wirth R, Wurch L, Podar M, Rachel R (13 June 2017). "Nanoarchaeum equitans". Frontiers in Microbiology. 8: 1072. doi:10.3389/fmicb.2017.01072. PMC   5468417 . PMID   28659892.
  63. Jurtshuk P (1996). "Bacterial Metabolism". Medical Microbiology (4th ed.). Galveston (TX): University of Texas Medical Branch at Galveston. ISBN   9780963117212 . Retrieved 5 November 2014.
  64. Howland JL (2000). The Surprising Archaea: Discovering Another Domain of Life. Oxford: Oxford University Press. pp. 25–30. ISBN   978-0-19-511183-5.
  65. 1 2 3 Cavicchioli R (January 2011). "Archaea--timeline of the third domain". Nature Reviews. Microbiology. 9 (1): 51–61. doi:10.1038/nrmicro2482. PMID   21132019.
  66. Gupta RS, Shami A (February 2011). "Molecular signatures for the Crenarchaeota and the Thaumarchaeota". Antonie van Leeuwenhoek. 99 (2): 133–57. doi:10.1007/s10482-010-9488-3. PMID   20711675.
  67. Gao B, Gupta RS (March 2007). "Phylogenomic analysis of proteins that are distinctive of Archaea and its main subgroups and the origin of methanogenesis". BMC Genomics. 8: 86. doi:10.1186/1471-2164-8-86. PMC   1852104 . PMID   17394648.
  68. Gupta RS, Naushad S, Baker S (March 2015). "Phylogenomic analyses and molecular signatures for the class Halobacteria and its two major clades: a proposal for division of the class Halobacteria into an emended order Halobacteriales and two new orders, Haloferacales ord. nov. and Natrialbales ord. nov., containing the novel families Haloferacaceae fam. nov. and Natrialbaceae fam. nov". International Journal of Systematic and Evolutionary Microbiology. 65 (Pt 3): 1050–69. doi: 10.1099/ijs.0.070136-0 . PMID   25428416.
  69. Deppenmeier U (2002). The unique biochemistry of methanogenesis. Progress in Nucleic Acid Research and Molecular Biology. 71. pp. 223–83. doi:10.1016/s0079-6603(02)71045-3. ISBN   978-0-12-540071-8. PMID   12102556.
  70. Koonin EV, Mushegian AR, Galperin MY, Walker DR (August 1997). "Comparison of archaeal and bacterial genomes: computer analysis of protein sequences predicts novel functions and suggests a chimeric origin for the archaea". Molecular Microbiology. 25 (4): 619–37. doi:10.1046/j.1365-2958.1997.4821861.x. PMID   9379893.
  71. 1 2 3 4 5 Gupta RS (December 1998). "Protein phylogenies and signature sequences: A reappraisal of evolutionary relationships among archaebacteria, eubacteria, and eukaryotes". Microbiology and Molecular Biology Reviews. 62 (4): 1435–91. doi:10.1128/MMBR.62.4.1435-1491.1998. PMC   98952 . PMID   9841678.
  72. Koch AL (April 2003). "Were Gram-positive rods the first bacteria?". Trends in Microbiology. 11 (4): 166–70. doi:10.1016/S0966-842X(03)00063-5. PMID   12706994.
  73. 1 2 3 Gupta RS (August 1998). "What are archaebacteria: life's third domain or monoderm prokaryotes related to gram-positive bacteria? A new proposal for the classification of prokaryotic organisms". Molecular Microbiology. 29 (3): 695–707. doi:10.1046/j.1365-2958.1998.00978.x. PMID   9723910.
  74. Gogarten JP (November 1994). "Which is the most conserved group of proteins? Homology-orthology, paralogy, xenology, and the fusion of independent lineages". Journal of Molecular Evolution. 39 (5): 541–43. Bibcode:1994JMolE..39..541G. doi:10.1007/bf00173425. PMID   7807544.
  75. Brown JR, Masuchi Y, Robb FT, Doolittle WF (June 1994). "Evolutionary relationships of bacterial and archaeal glutamine synthetase genes". Journal of Molecular Evolution. 38 (6): 566–76. Bibcode:1994JMolE..38..566B. doi:10.1007/BF00175876. PMID   7916055.
  76. Katz LA (September 2015). "Recent events dominate interdomain lateral gene transfers between prokaryotes and eukaryotes and, with the exception of endosymbiotic gene transfers, few ancient transfer events persist". Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 370 (1678): 20140324. doi:10.1098/rstb.2014.0324. PMC   4571564 . PMID   26323756.
  77. 1 2 3 Gupta RS (2000). "The natural evolutionary relationships among prokaryotes". Critical Reviews in Microbiology. 26 (2): 111–31. CiteSeerX . doi:10.1080/10408410091154219. PMID   10890353.
  78. Gupta RS (2005). "Molecular Sequences and the Early History of Life". In Sapp J (ed.). Microbial Phylogeny and Evolution: Concepts and Controversies. New York: Oxford University Press. pp. 160–183.
  79. Cavalier-Smith T (January 2002). "The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification". International Journal of Systematic and Evolutionary Microbiology. 52 (Pt 1): 7–76. doi: 10.1099/00207713-52-1-7 . PMID   11837318.
  80. Valas RE, Bourne PE (February 2011). "The origin of a derived superkingdom: how a gram-positive bacterium crossed the desert to become an archaeon". Biology Direct. 6: 16. doi:10.1186/1745-6150-6-16. PMC   3056875 . PMID   21356104.
  81. Skophammer RG, Herbold CW, Rivera MC, Servin JA, Lake JA (September 2006). "Evidence that the root of the tree of life is not within the Archaea". Molecular Biology and Evolution. 23 (9): 1648–51. doi: 10.1093/molbev/msl046 . PMID   16801395.
  82. Eme L, Spang A, Lombard J, Stairs CW, Ettema TJG (November 2017). "Archaea and the origin of eukaryotes". Nature Reviews. Microbiology. 15 (12): 711–723. doi:10.1038/nrmicro.2017.133. PMID   29123225.
  83. 1 2 Lake JA (January 1988). "Origin of the eukaryotic nucleus determined by rate-invariant analysis of rRNA sequences". Nature. 331 (6152): 184–86. Bibcode:1988Natur.331..184L. doi:10.1038/331184a0. PMID   3340165.
  84. Nelson KE, Clayton RA, Gill SR, Gwinn ML, Dodson RJ, Haft DH, et al. (May 1999). "Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima". Nature. 399 (6734): 323–29. Bibcode:1999Natur.399..323N. doi:10.1038/20601. PMID   10360571.
  85. Gouy M, Li WH (May 1989). "Phylogenetic analysis based on rRNA sequences supports the archaebacterial rather than the eocyte tree". Nature. 339 (6220): 145–47. Bibcode:1989Natur.339..145G. doi:10.1038/339145a0. PMID   2497353.
  86. Yutin N, Makarova KS, Mekhedov SL, Wolf YI, Koonin EV (August 2008). "The deep archaeal roots of eukaryotes". Molecular Biology and Evolution. 25 (8): 1619–30. doi:10.1093/molbev/msn108. PMC   2464739 . PMID   18463089. Archived from the original on 3 May 2009. Retrieved 24 June 2008.
  87. Williams TA, Foster PG, Cox CJ, Embley TM (December 2013). "An archaeal origin of eukaryotes supports only two primary domains of life". Nature. 504 (7479): 231–36. Bibcode:2013Natur.504..231W. doi:10.1038/nature12779. PMID   24336283.
  88. Zimmer C (6 May 2015). "Under the Sea, a Missing Link in the Evolution of Complex Cells". The New York Times . Retrieved 6 May 2015.
  89. Spang A, Saw JH, Jørgensen SL, Zaremba-Niedzwiedzka K, Martijn J, Lind AE, van Eijk R, Schleper C, Guy L, Ettema TJ (May 2015). "Complex archaea that bridge the gap between prokaryotes and eukaryotes". Nature. 521 (7551): 173–179. Bibcode:2015Natur.521..173S. doi:10.1038/nature14447. PMC   4444528 . PMID   25945739.
  90. Seitz KW, Lazar CS, Hinrichs KU, Teske AP, Baker BJ (July 2016). "Genomic reconstruction of a novel, deeply branched sediment archaeal phylum with pathways for acetogenesis and sulfur reduction". The ISME Journal. 10 (7): 1696–705. doi:10.1038/ismej.2015.233. PMC   4918440 . PMID   26824177.
  91. MacLeod F, Kindler GS, Wong HL, Chen R, Burns BP (2019). "Asgard archaea: Diversity, function, and evolutionary implications in a range of microbiomes". AIMS Microbiology. 5 (1): 48–61. doi:10.3934/microbiol.2019.1.48. PMC   6646929 . PMID   31384702.
  92. Zimmer C (15 January 2020). "This Strange Microbe May Mark One of Life's Great Leaps - A organism living in ocean muck offers clues to the origins of the complex cells of all animals and plants". The New York Times . Retrieved 16 January 2020.
  93. Imachi H, Nobu MK, Nakahara N, Morono Y, Ogawara M, Takaki Y, et al. (January 2020). "Isolation of an archaeon at the prokaryote-eukaryote interface". Nature. 577 (7791): 519–525. doi: 10.1038/s41586-019-1916-6 . PMC   7015854 . PMID   31942073.
  94. 1 2 3 4 Krieg N (2005). Bergey's Manual of Systematic Bacteriology. US: Springer. pp. 21–26. ISBN   978-0-387-24143-2.
  95. Barns S, Burggraf S (1997). "Crenarchaeota". The Tree of Life Web Project. Version 01 January 1997.
  96. Walsby AE (1980). "A square bacterium". Nature. 283 (5742): 69–71. Bibcode:1980Natur.283...69W. doi:10.1038/283069a0.
  97. Hara F, Yamashiro K, Nemoto N, Ohta Y, Yokobori S, Yasunaga T, et al. (March 2007). "An actin homolog of the archaeon Thermoplasma acidophilum that retains the ancient characteristics of eukaryotic actin". Journal of Bacteriology. 189 (5): 2039–45. doi:10.1128/JB.01454-06. PMC   1855749 . PMID   17189356.
  98. Trent JD, Kagawa HK, Yaoi T, Olle E, Zaluzec NJ (May 1997). "Chaperonin filaments: the archaeal cytoskeleton?". Proceedings of the National Academy of Sciences of the United States of America. 94 (10): 5383–88. Bibcode:1997PNAS...94.5383T. doi:10.1073/pnas.94.10.5383. PMC   24687 . PMID   9144246.
  99. Hixon WG, Searcy DG (1993). "Cytoskeleton in the archaebacterium Thermoplasma acidophilum? Viscosity increase in soluble extracts". Bio Systems. 29 (2–3): 151–60. doi:10.1016/0303-2647(93)90091-P. PMID   8374067.
  100. 1 2 Golyshina OV, Pivovarova TA, Karavaiko GI, Kondratéva TF, Moore ER, Abraham WR, et al. (May 2000). "Ferroplasma acidiphilum gen. nov., sp. nov., an acidophilic, autotrophic, ferrous-iron-oxidizing, cell-wall-lacking, mesophilic member of the Ferroplasmaceae fam. nov., comprising a distinct lineage of the Archaea". International Journal of Systematic and Evolutionary Microbiology. 50 (3): 997–1006. doi: 10.1099/00207713-50-3-997 . PMID   10843038.
  101. Hall-Stoodley L, Costerton JW, Stoodley P (February 2004). "Bacterial biofilms: from the natural environment to infectious diseases". Nature Reviews. Microbiology. 2 (2): 95–108. doi:10.1038/nrmicro821. PMID   15040259.
  102. Kuwabara T, Minaba M, Iwayama Y, Inouye I, Nakashima M, Marumo K, et al. (November 2005). "Thermococcus coalescens sp. nov., a cell-fusing hyperthermophilic archaeon from Suiyo Seamount". International Journal of Systematic and Evolutionary Microbiology. 55 (Pt 6): 2507–14. doi: 10.1099/ijs.0.63432-0 . PMID   16280518.
  103. Nickell S, Hegerl R, Baumeister W, Rachel R (January 2003). "Pyrodictium cannulae enter the periplasmic space but do not enter the cytoplasm, as revealed by cryo-electron tomography". Journal of Structural Biology. 141 (1): 34–42. doi:10.1016/S1047-8477(02)00581-6. PMID   12576018.
  104. Horn C, Paulmann B, Kerlen G, Junker N, Huber H (August 1999). "In vivo observation of cell division of anaerobic hyperthermophiles by using a high-intensity dark-field microscope". Journal of Bacteriology. 181 (16): 5114–18. doi:10.1128/JB.181.16.5114-5118.1999. PMC   94007 . PMID   10438790.
  105. Rudolph C, Wanner G, Huber R (May 2001). "Natural communities of novel archaea and bacteria growing in cold sulfurous springs with a string-of-pearls-like morphology". Applied and Environmental Microbiology. 67 (5): 2336–44. doi:10.1128/AEM.67.5.2336-2344.2001. PMC   92875 . PMID   11319120.
  106. 1 2 Thomas NA, Bardy SL, Jarrell KF (April 2001). "The archaeal flagellum: a different kind of prokaryotic motility structure". FEMS Microbiology Reviews. 25 (2): 147–74. doi: 10.1111/j.1574-6976.2001.tb00575.x . PMID   11250034.
  107. Rachel R, Wyschkony I, Riehl S, Huber H (March 2002). "The ultrastructure of Ignicoccus: evidence for a novel outer membrane and for intracellular vesicle budding in an archaeon". Archaea. 1 (1): 9–18. doi:10.1155/2002/307480. PMC   2685547 . PMID   15803654.
  108. Sára M, Sleytr UB (February 2000). "S-Layer proteins". Journal of Bacteriology. 182 (4): 859–68. doi:10.1128/JB.182.4.859-868.2000. PMC   94357 . PMID   10648507.
  109. Engelhardt H, Peters J (December 1998). "Structural research on surface layers: a focus on stability, surface layer homology domains, and surface layer-cell wall interactions". Journal of Structural Biology. 124 (2–3): 276–302. doi:10.1006/jsbi.1998.4070. PMID   10049812.
  110. 1 2 Kandler O, König H (April 1998). "Cell wall polymers in Archaea (Archaebacteria)". Cellular and Molecular Life Sciences. 54 (4): 305–08. doi:10.1007/s000180050156. PMID   9614965.
  111. Howland JL (2000). The Surprising Archaea: Discovering Another Domain of Life. Oxford: Oxford University Press. p. 32. ISBN   978-0-19-511183-5.
  112. Gophna U, Ron EZ, Graur D (July 2003). "Bacterial type III secretion systems are ancient and evolved by multiple horizontal-transfer events". Gene. 312: 151–63. doi:10.1016/S0378-1119(03)00612-7. PMID   12909351.
  113. Nguyen L, Paulsen IT, Tchieu J, Hueck CJ, Saier MH (April 2000). "Phylogenetic analyses of the constituents of Type III protein secretion systems". Journal of Molecular Microbiology and Biotechnology. 2 (2): 125–44. PMID   10939240.
  114. Ng SY, Chaban B, Jarrell KF (2006). "Archaeal flagella, bacterial flagella and type IV pili: a comparison of genes and posttranslational modifications". Journal of Molecular Microbiology and Biotechnology. 11 (3–5): 167–91. doi:10.1159/000094053. PMID   16983194.
  115. Bardy SL, Ng SY, Jarrell KF (February 2003). "Prokaryotic motility structures". Microbiology. 149 (Pt 2): 295–304. doi:10.1099/mic.0.25948-0. PMID   12624192.
  116. 1 2 Koga Y, Morii H (March 2007). "Biosynthesis of ether-type polar lipids in archaea and evolutionary considerations". Microbiology and Molecular Biology Reviews. 71 (1): 97–120. doi:10.1128/MMBR.00033-06. PMC   1847378 . PMID   17347520.
  117. Youssefian S, Rahbar N, Van Dessel S (May 2018). "Thermal conductivity and rectification in asymmetric archaeal lipid membranes". The Journal of Chemical Physics. 148 (17): 174901. doi:10.1063/1.5018589. PMID   29739208.
  118. De Rosa M, Gambacorta A, Gliozzi A (March 1986). "Structure, biosynthesis, and physicochemical properties of archaebacterial lipids". Microbiological Reviews. 50 (1): 70–80. doi:10.1128/MMBR.50.1.70-80.1986. PMC   373054 . PMID   3083222.
  119. Balleza D, Garcia-Arribas AB, Sot J, Ruiz-Mirazo K, Goñi FM (September 2014). "Ether- versus ester-linked phospholipid bilayers containing either linear or branched apolar chains". Biophysical Journal. 107 (6): 1364–74. doi:10.1016/j.bpj.2014.07.036. PMC   4167531 . PMID   25229144.
  120. Damsté JS, Schouten S, Hopmans EC, van Duin AC, Geenevasen JA (October 2002). "Crenarchaeol: the characteristic core glycerol dibiphytanyl glycerol tetraether membrane lipid of cosmopolitan pelagic crenarchaeota". Journal of Lipid Research. 43 (10): 1641–51. doi: 10.1194/jlr.M200148-JLR200 . PMID   12364548.
  121. Koga Y, Morii H (November 2005). "Recent advances in structural research on ether lipids from archaea including comparative and physiological aspects". Bioscience, Biotechnology, and Biochemistry. 69 (11): 2019–34. doi:10.1271/bbb.69.2019. PMID   16306681.
  122. Hanford MJ, Peeples TL (January 2002). "Archaeal tetraether lipids: unique structures and applications". Applied Biochemistry and Biotechnology. 97 (1): 45–62. doi:10.1385/ABAB:97:1:45. PMID   11900115.
  123. Macalady JL, Vestling MM, Baumler D, Boekelheide N, Kaspar CW, Banfield JF (October 2004). "Tetraether-linked membrane monolayers in Ferroplasma spp: a key to survival in acid". Extremophiles. 8 (5): 411–19. doi:10.1007/s00792-004-0404-5. PMID   15258835.
  124. 1 2 3 Valentine DL (April 2007). "Adaptations to energy stress dictate the ecology and evolution of the Archaea". Nature Reviews. Microbiology. 5 (4): 316–23. doi:10.1038/nrmicro1619. PMID   17334387.
  125. 1 2 3 Schäfer G, Engelhard M, Müller V (September 1999). "Bioenergetics of the Archaea". Microbiology and Molecular Biology Reviews. 63 (3): 570–620. doi:10.1128/MMBR.63.3.570-620.1999. PMC   103747 . PMID   10477309.
  126. Zillig W (December 1991). "Comparative biochemistry of Archaea and Bacteria". Current Opinion in Genetics & Development. 1 (4): 544–51. doi:10.1016/S0959-437X(05)80206-0. PMID   1822288.
  127. Romano AH, Conway T (1996). "Evolution of carbohydrate metabolic pathways". Research in Microbiology. 147 (6–7): 448–55. doi:10.1016/0923-2508(96)83998-2. PMID   9084754.
  128. Koch AL (1998). How did bacteria come to be?. Advances in Microbial Physiology. 40. pp. 353–99. doi:10.1016/S0065-2911(08)60135-6. ISBN   978-0-12-027740-7. PMID   9889982.
  129. DiMarco AA, Bobik TA, Wolfe RS (1990). "Unusual coenzymes of methanogenesis". Annual Review of Biochemistry. 59: 355–94. doi:10.1146/ PMID   2115763.
  130. Klocke M, Nettmann E, Bergmann I, Mundt K, Souidi K, Mumme J, et al. (August 2008). "Characterization of the methanogenic Archaea within two-phase biogas reactor systems operated with plant biomass". Systematic and Applied Microbiology. 31 (3): 190–205. doi:10.1016/j.syapm.2008.02.003. PMID   18501543.
  131. Based on PDB 1FBB. Data published in Subramaniam S, Henderson R (August 2000). "Molecular mechanism of vectorial proton translocation by bacteriorhodopsin". Nature. 406 (6796): 653–57. Bibcode:2000Natur.406..653S. doi:10.1038/35020614. PMID   10949309.
  132. Mueller-Cajar O, Badger MR (August 2007). "New roads lead to Rubisco in archaebacteria". BioEssays. 29 (8): 722–24. doi:10.1002/bies.20616. PMID   17621634.
  133. Berg IA, Kockelkorn D, Buckel W, Fuchs G (December 2007). "A 3-hydroxypropionate/4-hydroxybutyrate autotrophic carbon dioxide assimilation pathway in Archaea". Science. 318 (5857): 1782–86. Bibcode:2007Sci...318.1782B. doi:10.1126/science.1149976. PMID   18079405.
  134. Thauer RK (December 2007). "Microbiology. A fifth pathway of carbon fixation". Science. 318 (5857): 1732–33. doi:10.1126/science.1152209. PMID   18079388.
  135. Bryant DA, Frigaard NU (November 2006). "Prokaryotic photosynthesis and phototrophy illuminated". Trends in Microbiology. 14 (11): 488–96. doi:10.1016/j.tim.2006.09.001. PMID   16997562.
  136. 1 2 Könneke M, Bernhard AE, de la Torre JR, Walker CB, Waterbury JB, Stahl DA (September 2005). "Isolation of an autotrophic ammonia-oxidizing marine archaeon". Nature. 437 (7058): 543–46. Bibcode:2005Natur.437..543K. doi:10.1038/nature03911. PMID   16177789.
  137. 1 2 Francis CA, Beman JM, Kuypers MM (May 2007). "New processes and players in the nitrogen cycle: the microbial ecology of anaerobic and archaeal ammonia oxidation". The ISME Journal. 1 (1): 19–27. doi: 10.1038/ismej.2007.8 . PMID   18043610.
  138. Lanyi JK (2004). "Bacteriorhodopsin". Annual Review of Physiology. 66: 665–88. doi:10.1146/annurev.physiol.66.032102.150049. PMID   14977418.
  139. 1 2 Allers T, Mevarech M (January 2005). "Archaeal genetics – the third way" (PDF). Nature Reviews Genetics. 6 (1): 58–73. doi:10.1038/nrg1504. PMID   15630422.
  140. Galagan JE, Nusbaum C, Roy A, Endrizzi MG, Macdonald P, FitzHugh W, et al. (April 2002). "The genome of M. acetivorans reveals extensive metabolic and physiological diversity". Genome Research. 12 (4): 532–42. doi:10.1101/gr.223902. PMC   187521 . PMID   11932238.
  141. 1 2 Waters E, Hohn MJ, Ahel I, Graham DE, Adams MD, Barnstead M, et al. (October 2003). "The genome of Nanoarchaeum equitans: insights into early archaeal evolution and derived parasitism". Proceedings of the National Academy of Sciences of the United States of America. 100 (22): 12984–88. Bibcode:2003PNAS..10012984W. doi:10.1073/pnas.1735403100. PMC   240731 . PMID   14566062.
  142. Schleper C, Holz I, Janekovic D, Murphy J, Zillig W (August 1995). "A multicopy plasmid of the extremely thermophilic archaeon Sulfolobus effects its transfer to recipients by mating". Journal of Bacteriology. 177 (15): 4417–26. doi:10.1128/jb.177.15.4417-4426.1995. PMC   177192 . PMID   7635827.
  143. Sota M, Top EM (2008). "Horizontal Gene Transfer Mediated by Plasmids". Plasmids: Current Research and Future Trends. Caister Academic Press. ISBN   978-1-904455-35-6.
  144. Xiang X, Chen L, Huang X, Luo Y, She Q, Huang L (July 2005). "Sulfolobus tengchongensis spindle-shaped virus STSV1: virus-host interactions and genomic features". Journal of Virology. 79 (14): 8677–86. doi:10.1128/JVI.79.14.8677-8686.2005. PMC   1168784 . PMID   15994761.
  145. Graham DE, Overbeek R, Olsen GJ, Woese CR (March 2000). "An archaeal genomic signature". Proceedings of the National Academy of Sciences of the United States of America. 97 (7): 3304–08. Bibcode:2000PNAS...97.3304G. doi:10.1073/pnas.050564797. PMC   16234 . PMID   10716711.
  146. 1 2 Gaasterland T (October 1999). "Archaeal genomics". Current Opinion in Microbiology. 2 (5): 542–47. doi:10.1016/S1369-5274(99)00014-4. PMID   10508726.
  147. Dennis PP (June 1997). "Ancient ciphers: translation in Archaea". Cell. 89 (7): 1007–10. doi:10.1016/S0092-8674(00)80288-3. PMID   9215623.
  148. Werner F (September 2007). "Structure and function of archaeal RNA polymerases". Molecular Microbiology. 65 (6): 1395–404. doi:10.1111/j.1365-2958.2007.05876.x. PMID   17697097.
  149. Aravind L, Koonin EV (December 1999). "DNA-binding proteins and evolution of transcription regulation in the archaea". Nucleic Acids Research. 27 (23): 4658–70. doi:10.1093/nar/27.23.4658. PMC   148756 . PMID   10556324.
  150. Lykke-Andersen J, Aagaard C, Semionenkov M, Garrett RA (September 1997). "Archaeal introns: splicing, intercellular mobility and evolution". Trends in Biochemical Sciences. 22 (9): 326–31. doi:10.1016/S0968-0004(97)01113-4. PMID   9301331.
  151. Watanabe Y, Yokobori S, Inaba T, Yamagishi A, Oshima T, Kawarabayasi Y, et al. (January 2002). "Introns in protein-coding genes in Archaea". FEBS Letters. 510 (1–2): 27–30. doi:10.1016/S0014-5793(01)03219-7. PMID   11755525.
  152. Yoshinari S, Itoh T, Hallam SJ, DeLong EF, Yokobori S, Yamagishi A, et al. (August 2006). "Archaeal pre-mRNA splicing: a connection to hetero-oligomeric splicing endonuclease". Biochemical and Biophysical Research Communications. 346 (3): 1024–32. doi:10.1016/j.bbrc.2006.06.011. PMID   16781672.
  153. Rosenshine I, Tchelet R, Mevarech M (September 1989). "The mechanism of DNA transfer in the mating system of an archaebacterium". Science. 245 (4924): 1387–89. Bibcode:1989Sci...245.1387R. doi:10.1126/science.2818746. PMID   2818746.
  154. 1 2 3 Fröls S, Ajon M, Wagner M, Teichmann D, Zolghadr B, Folea M, et al. (November 2008). "UV-inducible cellular aggregation of the hyperthermophilic archaeon Sulfolobus solfataricus is mediated by pili formation". Molecular Microbiology. 70 (4): 938–52. doi:10.1111/j.1365-2958.2008.06459.x. PMID   18990182.
  155. 1 2 3 Ajon M, Fröls S, van Wolferen M, Stoecker K, Teichmann D, Driessen AJ, et al. (November 2011). "UV-inducible DNA exchange in hyperthermophilic archaea mediated by type IV pili" (PDF). Molecular Microbiology. 82 (4): 807–17. doi:10.1111/j.1365-2958.2011.07861.x. PMID   21999488.
  156. Fröls S, White MF, Schleper C (February 2009). "Reactions to UV damage in the model archaeon Sulfolobus solfataricus". Biochemical Society Transactions. 37 (Pt 1): 36–41. doi:10.1042/BST0370036. PMID   19143598.
  157. Bernstein H, Bernstein C (2017). "Sexual Communication in Archaea, the Precursor to Eukaryotic Meiosis". In Witzany G (ed.). Biocommunication of Archaea. Springer Nature. pp. 301–117. doi:10.1007/978-3-319-65536-9_7. ISBN   978-3-319-65535-2.
  158. 1 2 Blohs M, Moissl-Eichinger C, Mahnert A, Spang A, Dombrowski N, Krupovic M, Klingl A (1 January 2019). Schmidt TM (ed.). Archaea – An Introduction. Encyclopedia of Microbiology (Fourth ed.). Academic Press. pp. 243–252. doi:10.1016/B978-0-12-809633-8.20884-4. ISBN   978-0-12-811737-8 . Retrieved 16 March 2020.
  159. 1 2 3 Krupovic M, Cvirkaite-Krupovic V, Iranzo J, Prangishvili D, Koonin EV (January 2018). "Viruses of archaea: Structural, functional, environmental and evolutionary genomics". Virus Research. 244: 181–193. doi:10.1016/j.virusres.2017.11.025. PMC   5801132 . PMID   29175107.
  160. Pietilä MK, Demina TA, Atanasova NS, Oksanen HM, Bamford DH (June 2014). "Archaeal viruses and bacteriophages: comparisons and contrasts". Trends in Microbiology. 22 (6): 334–44. doi:10.1016/j.tim.2014.02.007. PMID   24647075.
  161. Principi N, Silvestri E, Esposito S (2019). "Advantages and Limitations of Bacteriophages for the Treatment of Bacterial Infections". Frontiers in Pharmacology. 10: 513. doi: 10.3389/fphar.2019.00513 . PMID   31139086.
  162. Prangishvili D (1 January 2013). Maloy S, Hughes K (eds.). Viruses of the Archaea. Brenner's Encyclopedia of Genetics (Second Edition). Academic Press. pp. 295–298. doi:10.1016/B978-0-12-374984-0.01627-2. ISBN   978-0-08-096156-9 . Retrieved 16 March 2020.
  163. Prangishvili D, Garrett RA (April 2004). "Exceptionally diverse morphotypes and genomes of crenarchaeal hyperthermophilic viruses" (PDF). Biochemical Society Transactions. 32 (Pt 2): 204–08. doi:10.1042/BST0320204. PMID   15046572.
  164. Pietilä MK, Roine E, Paulin L, Kalkkinen N, Bamford DH (April 2009). "An ssDNA virus infecting archaea: a new lineage of viruses with a membrane envelope". Molecular Microbiology. 72 (2): 307–19. doi:10.1111/j.1365-2958.2009.06642.x. PMID   19298373.
  165. Mochizuki T, Krupovic M, Pehau-Arnaudet G, Sako Y, Forterre P, Prangishvili D (August 2012). "Archaeal virus with exceptional virion architecture and the largest single-stranded DNA genome". Proceedings of the National Academy of Sciences of the United States of America. 109 (33): 13386–91. Bibcode:2012PNAS..10913386M. doi:10.1073/pnas.1203668109. PMC   3421227 . PMID   22826255.
  166. Mojica FJ, Díez-Villaseñor C, García-Martínez J, Soria E (February 2005). "Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements". Journal of Molecular Evolution. 60 (2): 174–82. Bibcode:2005JMolE..60..174M. doi:10.1007/s00239-004-0046-3. PMID   15791728.
  167. Makarova KS, Grishin NV, Shabalina SA, Wolf YI, Koonin EV (March 2006). "A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action". Biology Direct. 1: 7. doi:10.1186/1745-6150-1-7. PMC   1462988 . PMID   16545108.
  168. 1 2 Bernander R (August 1998). "Archaea and the cell cycle". Molecular Microbiology. 29 (4): 955–61. doi:10.1046/j.1365-2958.1998.00956.x. PMID   9767564.
  169. Kelman LM, Kelman Z (September 2004). "Multiple origins of replication in archaea". Trends in Microbiology. 12 (9): 399–401. doi:10.1016/j.tim.2004.07.001. PMID   15337158.
  170. Lindås AC, Karlsson EA, Lindgren MT, Ettema TJ, Bernander R (December 2008). "A unique cell division machinery in the Archaea". Proceedings of the National Academy of Sciences of the United States of America. 105 (48): 18942–46. Bibcode:2008PNAS..10518942L. doi:10.1073/pnas.0809467105. PMC   2596248 . PMID   18987308.
  171. Samson RY, Obita T, Freund SM, Williams RL, Bell SD (December 2008). "A role for the ESCRT system in cell division in archaea". Science. 322 (5908): 1710–13. Bibcode:2008Sci...322.1710S. doi:10.1126/science.1165322. PMC   4121953 . PMID   19008417.
  172. Pelve EA, Lindås AC, Martens-Habbena W, de la Torre JR, Stahl DA, Bernander R (November 2011). "Cdv-based cell division and cell cycle organization in the thaumarchaeon Nitrosopumilus maritimus". Molecular Microbiology. 82 (3): 555–66. doi:10.1111/j.1365-2958.2011.07834.x. PMID   21923770.
  173. Caspi Y, Dekker C (2018). "Dividing the Archaeal Way: The Ancient Cdv Cell-Division Machinery". Frontiers in Microbiology. 9: 174. doi:10.3389/fmicb.2018.00174. PMC   5840170 . PMID   29551994.
  174. Onyenwoke RU, Brill JA, Farahi K, Wiegel J (October 2004). "Sporulation genes in members of the low G+C Gram-type-positive phylogenetic branch ( Firmicutes)". Archives of Microbiology. 182 (2–3): 182–92. doi:10.1007/s00203-004-0696-y. PMID   15340788.
  175. Kostrikina NA, Zvyagintseva IS, Duda VI (1991). "Cytological peculiarities of some extremely halophilic soil archaeobacteria". Arch. Microbiol. 156 (5): 344–49. doi:10.1007/BF00248708.
  176. DeLong EF, Pace NR (August 2001). "Environmental diversity of bacteria and archaea". Systematic Biology. 50 (4): 470–78. doi:10.1080/106351501750435040. PMID   12116647.
  177. 1 2 Pikuta EV, Hoover RB, Tang J (2007). "Microbial extremophiles at the limits of life". Critical Reviews in Microbiology. 33 (3): 183–209. doi:10.1080/10408410701451948. PMID   17653987.
  178. Adam PS, Borrel G, Brochier-Armanet C, Gribaldo S (November 2017). "The growing tree of Archaea: new perspectives on their diversity, evolution and ecology". The ISME Journal. 11 (11): 2407–2425. doi:10.1038/ismej.2017.122. PMC   5649171 . PMID   28777382.
  179. Madigan MT, Martino JM (2006). Brock Biology of Microorganisms (11th ed.). Pearson. p. 136. ISBN   978-0-13-196893-6.
  180. Takai K, Nakamura K, Toki T, Tsunogai U, Miyazaki M, Miyazaki J, Hirayama H, Nakagawa S, Nunoura T, Horikoshi K (August 2008). "Cell proliferation at 122 degrees C and isotopically heavy CH4 production by a hyperthermophilic methanogen under high-pressure cultivation". Proceedings of the National Academy of Sciences of the United States of America. 105 (31): 10949–54. Bibcode:2008PNAS..10510949T. doi:10.1073/pnas.0712334105. PMC   2490668 . PMID   18664583.
  181. Ciaramella M, Napoli A, Rossi M (February 2005). "Another extreme genome: how to live at pH 0". Trends in Microbiology. 13 (2): 49–51. doi:10.1016/j.tim.2004.12.001. PMID   15680761.
  182. Javaux EJ (2006). "Extreme life on Earth--past, present and possibly beyond". Research in Microbiology. 157 (1): 37–48. doi:10.1016/j.resmic.2005.07.008. PMID   16376523.
  183. Nealson KH (January 1999). "Post-Viking microbiology: new approaches, new data, new insights" (PDF). Origins of Life and Evolution of the Biosphere. 29 (1): 73–93. Bibcode:1999OLEB...29...73N. doi:10.1023/A:1006515817767. PMID   11536899.
  184. Davies PC (1996). "The transfer of viable microorganisms between planets". Ciba Foundation Symposium. Novartis Foundation Symposia. 202: 304–14, discussion 314–17. doi:10.1002/9780470514986.ch16. ISBN   9780470514986. PMID   9243022.
  185. López-García P, López-López A, Moreira D, Rodríguez-Valera F (July 2001). "Diversity of free-living prokaryotes from a deep-sea site at the Antarctic Polar Front". FEMS Microbiology Ecology. 36 (2–3): 193–202. doi:10.1016/s0168-6496(01)00133-7. PMID   11451524.
  186. Karner MB, DeLong EF, Karl DM (January 2001). "Archaeal dominance in the mesopelagic zone of the Pacific Ocean". Nature. 409 (6819): 507–10. Bibcode:2001Natur.409..507K. doi:10.1038/35054051. PMID   11206545.
  187. Giovannoni SJ, Stingl U (September 2005). "Molecular diversity and ecology of microbial plankton". Nature. 437 (7057): 343–48. Bibcode:2005Natur.437..343G. doi:10.1038/nature04158. PMID   16163344.
  188. DeLong EF, Karl DM (September 2005). "Genomic perspectives in microbial oceanography". Nature. 437 (7057): 336–42. Bibcode:2005Natur.437..336D. doi:10.1038/nature04157. PMID   16163343.
  189. Agogué H, Brink M, Dinasquet J, Herndl GJ (December 2008). "Major gradients in putatively nitrifying and non-nitrifying Archaea in the deep North Atlantic" (PDF). Nature. 456 (7223): 788–91. Bibcode:2008Natur.456..788A. doi:10.1038/nature07535. PMID   19037244.
  190. Teske A, Sørensen KB (January 2008). "Uncultured archaea in deep marine subsurface sediments: have we caught them all?". The ISME Journal. 2 (1): 3–18. doi: 10.1038/ismej.2007.90 . hdl:10379/14139. PMID   18180743.
  191. Lipp JS, Morono Y, Inagaki F, Hinrichs KU (August 2008). "Significant contribution of Archaea to extant biomass in marine subsurface sediments". Nature. 454 (7207): 991–94. Bibcode:2008Natur.454..991L. doi:10.1038/nature07174. PMID   18641632.
  192. Danovaro R, Dell'Anno A, Corinaldesi C, Rastelli E, Cavicchioli R, Krupovic M, Noble RT, Nunoura T, Prangishvili D (October 2016). "Virus-mediated archaeal hecatomb in the deep seafloor". Science Advances. 2 (10): e1600492. Bibcode:2016SciA....2E0492D. doi:10.1126/sciadv.1600492. PMC   5061471 . PMID   27757416.
  193. Liu X, Pan J, Liu Y, Li M, Gu JD (October 2018). "Diversity and distribution of Archaea in global estuarine ecosystems". The Science of the Total Environment. 637–638: 349–358. doi:10.1016/j.scitotenv.2018.05.016. PMID   29753224.
  194. Cabello P, Roldán MD, Moreno-Vivián C (November 2004). "Nitrate reduction and the nitrogen cycle in archaea". Microbiology. 150 (Pt 11): 3527–46. doi:10.1099/mic.0.27303-0. PMID   15528644.
  195. Mehta MP, Baross JA (December 2006). "Nitrogen fixation at 92 degrees C by a hydrothermal vent archaeon". Science. 314 (5806): 1783–86. Bibcode:2006Sci...314.1783M. doi:10.1126/science.1134772. PMID   17170307.
  196. Coolen MJ, Abbas B, van Bleijswijk J, Hopmans EC, Kuypers MM, Wakeham SG, et al. (April 2007). "Putative ammonia-oxidizing Crenarchaeota in suboxic waters of the Black Sea: a basin-wide ecological study using 16S ribosomal and functional genes and membrane lipids". Environmental Microbiology. 9 (4): 1001–16. doi:10.1111/j.1462-2920.2006.01227.x. hdl: 1912/2034 . PMID   17359272.
  197. Leininger S, Urich T, Schloter M, Schwark L, Qi J, Nicol GW, Prosser JI, Schuster SC, Schleper C (August 2006). "Archaea predominate among ammonia-oxidizing prokaryotes in soils". Nature. 442 (7104): 806–09. Bibcode:2006Natur.442..806L. doi:10.1038/nature04983. PMID   16915287.
  198. Baker BJ, Banfield JF (May 2003). "Microbial communities in acid mine drainage". FEMS Microbiology Ecology. 44 (2): 139–52. doi: 10.1016/S0168-6496(03)00028-X . PMID   19719632.
  199. Schimel J (August 2004). "Playing scales in the methane cycle: from microbial ecology to the globe". Proceedings of the National Academy of Sciences of the United States of America. 101 (34): 12400–01. Bibcode:2004PNAS..10112400S. doi:10.1073/pnas.0405075101. PMC   515073 . PMID   15314221.
  200. Eckburg PB, Lepp PW, Relman DA (February 2003). "Archaea and their potential role in human disease". Infection and Immunity. 71 (2): 591–96. doi:10.1128/IAI.71.2.591-596.2003. PMC   145348 . PMID   12540534.
  201. Cavicchioli R, Curmi PM, Saunders N, Thomas T (November 2003). "Pathogenic archaea: do they exist?". BioEssays. 25 (11): 1119–28. doi:10.1002/bies.10354. PMID   14579252.
  202. Lepp PW, Brinig MM, Ouverney CC, Palm K, Armitage GC, Relman DA (April 2004). "Methanogenic Archaea and human periodontal disease". Proceedings of the National Academy of Sciences of the United States of America. 101 (16): 6176–81. Bibcode:2004PNAS..101.6176L. doi:10.1073/pnas.0308766101. PMC   395942 . PMID   15067114.
  203. Vianna ME, Conrads G, Gomes BP, Horz HP (April 2006). "Identification and quantification of archaea involved in primary endodontic infections". Journal of Clinical Microbiology. 44 (4): 1274–82. doi:10.1128/JCM.44.4.1274-1282.2006. PMC   1448633 . PMID   16597851.
  204. Jahn U, Gallenberger M, Paper W, Junglas B, Eisenreich W, Stetter KO, et al. (March 2008). "Nanoarchaeum equitans and Ignicoccus hospitalis: new insights into a unique, intimate association of two archaea". Journal of Bacteriology. 190 (5): 1743–50. doi:10.1128/JB.01731-07. PMC   2258681 . PMID   18165302.
  205. Chaban B, Ng SY, Jarrell KF (February 2006). "Archaeal habitats--from the extreme to the ordinary". Canadian Journal of Microbiology. 52 (2): 73–116. doi:10.1139/w05-147. PMID   16541146.
  206. Schink B (June 1997). "Energetics of syntrophic cooperation in methanogenic degradation". Microbiology and Molecular Biology Reviews. 61 (2): 262–80. doi:10.1128/.61.2.262-280.1997. PMC   232610 . PMID   9184013.
  207. Lange M, Westermann P, Ahring BK (February 2005). "Archaea in protozoa and metazoa". Applied Microbiology and Biotechnology. 66 (5): 465–74. doi:10.1007/s00253-004-1790-4. PMID   15630514.
  208. van Hoek AH, van Alen TA, Sprakel VS, Leunissen JA, Brigge T, Vogels GD, et al. (February 2000). "Multiple acquisition of methanogenic archaeal symbionts by anaerobic ciliates". Molecular Biology and Evolution. 17 (2): 251–58. doi:10.1093/oxfordjournals.molbev.a026304. PMID   10677847.
  209. Preston CM, Wu KY, Molinski TF, DeLong EF (June 1996). "A psychrophilic crenarchaeon inhabits a marine sponge: Cenarchaeum symbiosum gen. nov., sp. nov". Proceedings of the National Academy of Sciences of the United States of America. 93 (13): 6241–46. Bibcode:1996PNAS...93.6241P. doi:10.1073/pnas.93.13.6241. PMC   39006 . PMID   8692799.
  210. Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, Sargent M, et al. (June 2005). "Diversity of the human intestinal microbial flora". Science. 308 (5728): 1635–38. Bibcode:2005Sci...308.1635E. doi:10.1126/science.1110591. PMC   1395357 . PMID   15831718.
  211. Samuel BS, Gordon JI (June 2006). "A humanized gnotobiotic mouse model of host-archaeal-bacterial mutualism". Proceedings of the National Academy of Sciences of the United States of America. 103 (26): 10011–16. Bibcode:2006PNAS..10310011S. doi:10.1073/pnas.0602187103. PMC   1479766 . PMID   16782812.
  212. Wegley L, Yu Y, Breitbart M, Casas V, Kline DI, Rohwer F (2004). "Coral-associated Archaea" (PDF). Marine Ecology Progress Series. 273: 89–96. Bibcode:2004MEPS..273...89W. doi:10.3354/meps273089. Archived from the original (PDF) on 11 September 2008.
  213. Chelius MK, Triplett EW (April 2001). "The Diversity of Archaea and Bacteria in Association with the Roots of Zea mays L". Microbial Ecology. 41 (3): 252–263. doi:10.1007/s002480000087. JSTOR   4251818. PMID   11391463.
  214. Simon HM, Dodsworth JA, Goodman RM (October 2000). "Crenarchaeota colonize terrestrial plant roots". Environmental Microbiology. 2 (5): 495–505. doi:10.1046/j.1462-2920.2000.00131.x. PMID   11233158.
  215. Breithaupt H (November 2001). "The hunt for living gold. The search for organisms in extreme environments yields useful enzymes for industry". EMBO Reports. 2 (11): 968–71. doi:10.1093/embo-reports/kve238. PMC   1084137 . PMID   11713183.
  216. 1 2 Egorova K, Antranikian G (December 2005). "Industrial relevance of thermophilic Archaea". Current Opinion in Microbiology. 8 (6): 649–55. doi:10.1016/j.mib.2005.10.015. PMID   16257257.
  217. Synowiecki J, Grzybowska B, Zdziebło A (2006). "Sources, properties and suitability of new thermostable enzymes in food processing". Critical Reviews in Food Science and Nutrition. 46 (3): 197–205. doi:10.1080/10408690590957296. PMID   16527752.
  218. Jenney FE, Adams MW (January 2008). "The impact of extremophiles on structural genomics (and vice versa)". Extremophiles. 12 (1): 39–50. doi:10.1007/s00792-007-0087-9. PMID   17563834.
  219. Schiraldi C, Giuliano M, De Rosa M (September 2002). "Perspectives on biotechnological applications of archaea". Archaea. 1 (2): 75–86. doi:10.1155/2002/436561. PMC   2685559 . PMID   15803645.
  220. Norris PR, Burton NP, Foulis NA (April 2000). "Acidophiles in bioreactor mineral processing". Extremophiles. 4 (2): 71–76. doi:10.1007/s007920050139. PMID   10805560.
  221. Shand RF, Leyva KJ (2008). "Archaeal Antimicrobials: An Undiscovered Country". In Blum P (ed.). Archaea: New Models for Prokaryotic Biology. Caister Academic Press. ISBN   978-1-904455-27-1.

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