Archaea

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.^[10] In 1965, Emile Zuckerkandl and Linus Pauling^[11] 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.^[12]

Archaea were first classified separately from bacteria in 1977 by

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.

A superphylum – TACK – which includes the Thaumarchaeota (now Nitrososphaerota), "Aigarchaeota", Crenarchaeota (now Thermoproteota), and "Korarchaeota" was proposed in 2011 to be related to the origin of eukaryotes.^[28] 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.^[29]

In 2013 the superphylum DPANN was proposed to group "

The classification of archaea into species is also controversial. Ernst Mayr defined a species as a group of interbreeding organisms which are reproductively isolated, but this is of no help since archaea only reproduce asexually.^[37]

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.^[38] On the other hand, studies in Halorubrum found significant genetic transfer to/from less-related populations, limiting the criterion's applicability.^[39] Some researchers question whether such species designations have practical meaning.^[40]

Current knowledge on genetic diversity in archaeans is fragmentary, so the total number of species cannot be estimated with any accuracy.^[22] 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.^[41] The Bacteria also include many uncultured microbes with similar implications for characterization.^[42]

Phyla

Valid phyla

The following phyla have been validly published according to the

• Nitrososphaerota
• Thermoproteota

Provisional phyla

The following phyla have been proposed, but have not been validly published according to the Bacteriological Code (including those that have candidatus status):

Origin and evolution

The

The following table compares some major characteristics of the three domains, to illustrate their similarities and differences.[65]

Archaea were split off as a third domain because of the large differences in their ribosomal RNA structure. The particular molecule

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.[13] These methanogens were much more similar to each other than to other organisms, leading Woese to propose the new domain of Archaea.^[13] His experiments showed that the archaea were genetically more similar to eukaryotes than prokaryotes, even though they were more similar to prokaryotes in structure.^[69] This led to the conclusion that Archaea and Eukarya shared a common ancestor more recent than Eukarya and Bacteria.^[69] The development of the nucleus occurred after the split between Bacteria and this common ancestor.^[69][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.^[70][71][72] 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.^[73]

This difference in the biochemical structure of Bacteria and Archaea has been explained by researchers through evolutionary processes. It is theorized that both domains originated at deep sea alkaline hydrothermal vents. At least twice, microbes evolved lipid biosynthesis and cell wall biochemistry. It has been suggested that the last universal common ancestor was a non-free-living organism.^[74] It may have had a permeable membrane composed of bacterial simple chain amphiphiles (fatty acids), including archaeal simple chain amphiphiles (isoprenoids). These stabilize fatty acid membranes in seawater; this property may have driven the divergence of bacterial and archaeal membranes, "with the later biosynthesis of phospholipids giving rise to the unique G1P and G3P headgroups of archaea and bacteria respectively. If so, the properties conferred by membrane isoprenoids place the lipid divide as early as the origin of life".^[75]

Relationship to bacteria

The relationships among the

It has been proposed that the archaea evolved from gram-positive bacteria in response to antibiotic selection pressure.^[78][80][84] This is suggested by the observation that archaea are resistant to a wide variety of antibiotics that are produced primarily by gram-positive bacteria,^[78][80] 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.^[84] 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;^[84][85] Cavalier-Smith has made a similar suggestion.^[86] This proposal is also supported by other work investigating protein structural relationships^[87] and studies that suggest that gram-positive bacteria may constitute the earliest branching lineages within the prokaryotes.^[88]

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.^[90]

Complicating factors include claims that the relationship between eukaryotes and the archaeal phylum

Some species form aggregates or filaments of cells up to 200 μm long.[103] These organisms can be prominent in biofilms.^[110] Notably, aggregates of Thermococcus coalescens cells fuse together in culture, forming single giant cells.^[111] 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.^[112] The function of these cannulae is not settled, but they may allow communication or nutrient exchange with neighbors.^[113] 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.^[114]

Structure, composition development, and operation

Archaea and bacteria have generally similar

Most archaea (but not

Archaeal flagella are known as

type IV pili.^[123] 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.^[124]

Membranes

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.[125] 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.^[126]

The phospholipids of archaea are unusual in four ways:

• They have membranes composed of glycerol-ether lipids, whereas bacteria and eukaryotes have membranes composed mainly of glycerol-ester lipids.^[127] The difference is the type of bond that joins the lipids to the glycerol moiety; the two types are shown in yellow in the figure at the right. In ester lipids this is an ester bond, whereas in ether lipids this is an ether bond.^[128]
• The stereochemistry of the archaeal glycerol moiety is the mirror image of that found in other organisms. The glycerol moiety can occur in two forms that are mirror images of one another, called enantiomers. Just as a right hand does not fit easily into a left-handed glove, enantiomers of one type generally cannot be used or made by enzymes adapted for the other. The archaeal phospholipids are built on a backbone of sn-glycerol-1-phosphate, which is an enantiomer of sn-glycerol-3-phosphate, the phospholipid backbone found in bacteria and eukaryotes. This suggests that archaea use entirely different enzymes for synthesizing phospholipids as compared to bacteria and eukaryotes. Such enzymes developed very early in life's history, indicating an early split from the other two domains.^[125]
• Archaeal lipid tails differ from those of other organisms in that they are based upon long isoprenoid chains with multiple side-branches, sometimes with cyclopropane or cyclohexane rings.^[129] By contrast, the fatty acids in the membranes of other organisms have straight chains without side branches or rings. Although isoprenoids play an important role in the biochemistry of many organisms, only the archaea use them to make phospholipids. These branched chains may help prevent archaeal membranes from leaking at high temperatures.^[130]
• In some archaea, the lipid bilayer is replaced by a monolayer. In effect, the archaea fuse the tails of two phospholipid molecules into a single molecule with two polar heads (a bolaamphiphile); this fusion may make their membranes more rigid and better able to resist harsh environments.^[131] For example, the lipids in Ferroplasma are of this type, which is thought to aid this organism's survival in its highly acidic habitat.^[132]

Metabolism

Further information: Microbial metabolism

Archaea exhibit a great variety of chemical reactions in their

oxidisers.^[133] 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.^[134]

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.^[134] 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.^[135] These similarities to other organisms probably reflect both early origins in the history of life and their high level of efficiency.^[136]

Nutritional types in archaeal metabolism

Nutritional type	Source of energy	Source of carbon	Examples
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

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.^[139]

Other archaea use CO
₂ in the

reductive acetyl-CoA pathway.^[143] Carbon fixation is powered by inorganic energy sources. No known archaea carry out photosynthesis^[144] (Halobacterium is the only known phototroph archeon but it uses an alternative process to photosynthesis). Archaeal energy sources are extremely diverse, and range from the oxidation of ammonia by the Nitrosopumilales^[145][146] to the oxidation of hydrogen sulfide or elemental sulfur by species of Sulfolobus, using either oxygen or metal ions as electron acceptors.^[134]

plasma membrane. The energy stored in these electrochemical gradients is then converted into ATP by ATP synthase.^[103] 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.^[147]

Genetics

Further information: Plasmid and Genome

Archaea usually have a single circular chromosome,^[148] but many euryarchaea have been shown to bear multiple copies of this chromosome.^[149] The largest known archaeal genome as of 2002 was 5,751,492 base pairs in Methanosarcina acetivorans,^[150]. 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.^[151] 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.^[152][153]

STSV1.^[154] 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.

tRNA genes and their aminoacyl tRNA synthetases.^[156]

Transcription in archaea more closely resembles eukaryotic than bacterial transcription, with the archaeal

promoter,^[158] but other archaeal transcription factors are closer to those found in bacteria.^[159] 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,^[160] and introns may occur in a few protein-encoding genes.^[161][162]

Gene transfer and genetic exchange

Haloferax volcanii, an extreme halophilic archaeon, forms cytoplasmic bridges between cells that appear to be used for transfer of DNA from one cell to another in either direction.^[163]

When the hyperthermophilic archaea

DNA damage. Ajon et al.^[165] 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.^[164][166] and Ajon et al.^[165] 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.^[167]

Archaeal viruses

Archaea are the target of a number of

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).^[169]

These viruses have been studied in most detail in thermophilics, particularly the orders

repetitive DNA sequences that are related to the genes of the viruses.^[176][177]

Reproduction

Further information: Asexual reproduction

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.^[103] Cell division is controlled in a cell cycle; after the cell's chromosome is replicated and the two daughter chromosomes separate, the cell divides.^[178] 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.^[179]

In Euryarchaeota the cell division protein FtsZ, which forms a contracting ring around the cell, and the components of the septum that is constructed across the center of the cell, are similar to their bacterial equivalents.^[178] In cren-^[180][181] and thaumarchaea,^[182] 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.^[183]

Both bacteria and eukaryotes, but not archaea, make spores.^[184] 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.^[185]

Behavior

Communication

Quorum sensing was originally thought to not exist in Archaea, but recent studies have shown evidence of some species being able to perform cross-talk through quorum sensing. Other studies have shown syntrophic interactions between archaea and bacteria during biofilm growth. Although research is limited in archaeal quorum sensing, some studies have uncovered LuxR proteins in archaeal species, displaying similarities with bacteria LuxR, and ultimately allowing for the detection of small molecules that are used in high density communication. Similarly to bacteria, Archaea LuxR solos have shown to bind to AHLs (lactones) and non-AHLs ligans, which is a large part in performing intraspecies, interspecies, and interkingdom communication through quorum sensing.^[186]

Ecology

Habitats

Hot Spring in Yellowstone National Park

produce a bright colour

Archaea exist in a broad range of

PGPR, Archaea are now considered as a source of plant growth promotion as well.^[7]

Extremophile archaea are members of four main

acidophiles.^[188] 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.^[189]

Halophiles, including the genus

Methanopyrus kandleri Strain 116 can even reproduce at 122 °C (252 °F), the highest recorded temperature of any organism.^[191]

Other archaea exist in very acidic or alkaline conditions.[188] 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.^[192]

This resistance to extreme environments has made archaea the focus of speculation about the possible properties of extraterrestrial life.^[193] Some extremophile habitats are not dissimilar to those on Mars,^[194] leading to the suggestion that viable microbes could be transferred between planets in meteorites.^[195]

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.

pure culture.^[198] Consequently, our understanding of the role of archaea in ocean ecology is rudimentary, so their full influence on global biogeochemical cycles remains largely unexplored.^[199] Some marine Thermoproteota are capable of nitrification, suggesting these organisms may affect the oceanic nitrogen cycle,^[145] although these oceanic Thermoproteota may also use other sources of energy.^[200]

Vast numbers of archaea are also found in the

sea floor, with these organisms making up the majority of living cells at depths over 1 meter below the ocean bottom.^[201][202] 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.^[203]

Role in chemical cycling

Further information: Biogeochemical cycle

Archaea recycle elements such as carbon, nitrogen, and sulfur through their various habitats.^[204] 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).^[205][206] Researchers recently discovered archaeal involvement in ammonia oxidation reactions. These reactions are particularly important in the oceans.^[146][207] 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.^[208]

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.^[209]

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.^[210]

Interactions with other organisms

Further information: Biological interaction

The well-characterized interactions between archaea and other organisms are either

parasites,^[211][212] but some species of methanogens have been suggested to be involved in infections in the mouth,^[213][214] 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,^[151] and appears to offer no benefit to its host.^[215]

Mutualism

Mutualism is an interaction between individuals of different species that results in positive (beneficial) effects on per capita reproduction and/or survival of the interacting populations. One well-understood example of mutualism is the interaction between protozoa and methanogenic archaea in the digestive tracts of animals that digest cellulose, such as ruminants and termites.^[216] 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.^[217]

In anaerobic protozoa, such as Plagiopyla frontata, Trimyema, Heterometopus and Metopus contortus, archaea reside inside the protozoa and consume hydrogen produced in their hydrogenosomes.^{[218][219][220][221][222]} Archaea associate with larger organisms, too. For example, the marine archaean Cenarchaeum symbiosum is an endosymbiont of the sponge Axinella mexicana.^[223]

Commensalism

Some archaea are commensals, benefiting from an association without helping or harming the other organism. For example, the methanogen

rhizosphere).^[227][228]

Parasitism

Although Archaea do not have a historical reputation of being pathogens, Archaea are often found with similar genomes to more common pathogen like E. coli,[229] showing metabolic links and evolutionary history with today's pathogens. Archaea have been inconsistently detected in clinical studies because of the lack of categorization of Archaea into more specific species.^[230]

Significance in technology and industry

Further information: Biotechnology

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.^[231][232] 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.^[233] 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.^[232] 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.^[234]

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.^[235] In mineral processing, acidophilic archaea display promise for the extraction of metals from ores, including gold, cobalt and copper.^[236]

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.^[237]

See also

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

References

1. ^
   PMID 2112744
   .
2. ^
   PMID 25527841
   .
3. ^ ^{a b} "NCBI taxonomy page on Archaea".
4. S2CID 4431143
   .
5. PMID 7287626
   .
6. ^ "Archaea Basic Biology". March 2018.
7. ^
   S2CID 252376815
   .
8. PMID 25907112
   .
9. PMID 28826642
   .
10. PMID 17062409
    .
11. PMID 5876245
    .
12. S2CID 52093100
    .
13. ^
    PMID 270744
    .
14. ISBN 978-0-19-973438-2
    .
15. ^ "Archaea". Merriam-Webster Online Dictionary. 2008. Retrieved 1 July 2008.
16. S2CID 1291732
    .
17. PMID 9243007
    .
18. ^
    PMID 9914204
    .
19. S2CID 5829573
    .
20. PMID 17061212. Archived from the original
    (PDF) on 11 September 2008.
21. PMID 17062410
    .
22. ^
    PMID 16236543
    .
23. S2CID 4395094
    .
24. PMID 8799176
    .
25. PMID 18535141
    .
26. S2CID 26033384
    .
27. PMID 20421484
    .
28. PMID 22018741
    .
29. ^
    S2CID 4458094
    .
30. ^ Nina Dombrowski, Jun-Hoe Lee, Tom A Williams, Pierre Offre, Anja Spang (2019). Genomic diversity, lifestyles and evolutionary origins of DPANN archaea. Nature.
31. ^
    PMID 28533395
    .
32. ^
    PMID 29522741
    .
33. ^ ^{a b} "GTDB release 08-RS214". Genome Taxonomy Database. Retrieved 6 December 2021.
34. ^ ^{a b} "ar53_r214.sp_label". Genome Taxonomy Database. Retrieved 10 May 2023.
35. ^ ^{a b} "Taxon History". Genome Taxonomy Database. Retrieved 6 December 2021.
36. PMID 31015394
    .
37. PMID 15851674
    .
38. PMID 17603112
    .
39. PMID 17715057
    .
40. PMID 15965028
    .
41. PMID 11864374
    .
42. S2CID 10781051. Archived from the original
    (PDF) on 2 March 2019.
43. S2CID 239887308
    .
44. ^ "Age of the Earth". U.S. Geological Survey. 1997. Archived from the original on 23 December 2005. Retrieved 10 January 2006.
45. S2CID 130092094
    .
46. doi:10.1016/0012-821X(80)90024-2
    .
47. ^ de Duve C (October 1995). "The Beginnings of Life on Earth". American Scientist. Archived from the original on 6 June 2017. Retrieved 15 January 2014.
48. ^ Timmer J (4 September 2012). "3.5 billion year old organic deposits show signs of life". Ars Technica. Retrieved 15 January 2014.
49. doi:10.1038/ngeo2025
    .
50. ^ Borenstein S (13 November 2013). "Oldest fossil found: Meet your microbial mom". Associated Press. Retrieved 15 November 2013.
51. PMID 24205812
    .
52. ^ 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.
53. PMID 26483481
    .
54. PMID 16754604
    .
55. S2CID 42758483
    .
56. PMID 10446042
    .
57. S2CID 4372071
    .
58. doi:10.1016/S0723-2020(86)80002-9
    .
59. PMID 17908824
    .
60. S2CID 4343245
    .
61. ^
    PMID 9618502
    .
62. ^
    ISBN 978-1-4822-7304-5
    .
63. PMID 16754611
    .
64. ^
    PMID 8177167
    .
65. ^ Information is from Willey JM, Sherwood LM, Woolverton CJ. Microbiology 7th ed. (2008), Ch. 19 pp. 474–475, except where noted.
66. PMID 28659892
    .
67. PMID 21413278
    .
68. ISBN 978-0-19-511183-5
    .
69. ^
    S2CID 21008512
    .
70. S2CID 12874800
    .
71. PMID 17394648
    .
72. PMID 25428416
    .
73. PMID 12102556
    .
74. PMID 12594918
    .
75. PMID 31641436
    .
76. S2CID 1615592
    .
77. S2CID 36270763
    .
78. ^
    PMID 9841678
    .
79. PMID 12706994
    .
80. ^
    S2CID 41206658
    .
81. S2CID 44922755
    .
82. S2CID 21493521
    .
83. PMID 26323756
    .
84. ^
    S2CID 30541897
    .
85. ^ 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.
86. PMID 11837318
    .
87. PMID 21356104
    .
88. PMID 16801395
    .
89. ^
    ISBN 978-0-521-76131-4. Archived
    from the original on 24 March 2019. Retrieved 27 August 2017.
90. S2CID 8666687
    .
91. S2CID 4368082
    .
92. S2CID 4420157
    .
93. S2CID 4315004
    .
94. PMID 18463089
    .
95. S2CID 4461775
    .
96. ^ 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.
97. PMID 25945739
    .
98. PMID 26824177
    .
99. PMID 31384702
    .
100. ^ 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.
101. PMID 31942073
     .
102. PMC 10833476
     .
103. ^
     ISBN 978-0-387-24143-2
     .
104. ^ Barns S, Burggraf S (1997). "Crenarchaeota". The Tree of Life Web Project. Version 01 January 1997.
105. S2CID 4341717
     .
106. PMID 17189356
     .
107. PMID 9144246
     .
108. PMID 8374067
     .
109. ^
     PMID 10843038
     .
110. S2CID 9107205
     .
111. PMID 16280518
     .
112. PMID 12576018
     .
113. PMID 10438790
     .
114. PMID 11319120
     .
115. ^
     PMID 11250034
     .
116. PMID 15803654
     .
117. PMID 10648507
     .
118. PMID 10049812
     .
119. ^
     S2CID 13527169
     .
120. ISBN 978-0-19-511183-5
     .
121. PMID 12909351
     .
122. PMID 10939240
     .
123. S2CID 30386932
     .
124. S2CID 20751743. Archived from the original
     (PDF) on 7 March 2019.
125. ^
     PMID 17347520
     .
126. PMID 29739208
     .
127. PMID 3083222
     .
128. PMID 25229144
     .
129. PMID 12364548
     .
130. S2CID 42237252
     .
131. S2CID 22334666
     .
132. S2CID 15702103
     .
133. ^
     S2CID 12384143
     .
134. ^
     PMID 10477309
     .
135. PMID 1822288
     .
136. PMID 9084754
     .
137. PMID 9889982
     .
138. PMID 2115763
     .
139. PMID 18501543
     .
140. ^ 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.
     S2CID 4395278
     .
141. PMID 17621634
     .
142. S2CID 13218676
     .
143. S2CID 83805878
     .
144. PMID 16997562
     .
145. ^
     S2CID 4340386
     .
146. ^
     PMID 18043610
     .
147. PMID 14977418
     .
148. ^
     S2CID 20229552. Archived from the original
     (PDF) on 20 July 2018. Retrieved 12 September 2019.
149. PMID 21097629
     .
150. PMID 11932238
     .
151. ^
     PMID 14566062
     .
152. PMID 7635827
     .
153. ISBN 978-1-904455-35-6
     .
154. PMID 15994761
     .
155. PMID 10716711
     .
156. ^
     PMID 10508726
     .
157. S2CID 18862794
     .
158. S2CID 28078184
     .
159. PMID 10556324
     .
160. PMID 9301331
     .
161. S2CID 27294545
     .
162. PMID 16781672
     .
163. PMID 2818746
     .
164. ^
     S2CID 12797510
     .
165. ^
     S2CID 42880145
     .
166. PMID 19143598
     .
167. ISBN 978-3-319-65535-2
     .
168. ^
     S2CID 164553336
     .
169. ^
     PMID 29175107
     .
170. PMID 24647075
     .
171. PMID 31139086
     .
172. ISBN 978-0-08-096156-9
     . Retrieved 16 March 2020.
173. S2CID 20018642
     .
174. S2CID 24894269
     .
175. PMID 22826255
     .
176. S2CID 27481111
     .
177. PMID 16545108
     .
178. ^
     S2CID 34816545
     .
179. PMID 15337158
     .
180. ^ 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.
     PMID 18987308
     .
181. PMID 19008417
     .
182. S2CID 1202516
     .
183. PMID 29551994
     .
184. S2CID 34339306
     .
185. S2CID 13316631
     .
186. PMID 28515720
     .
187. PMID 12116647
     .
188. ^
     S2CID 20225471
     .
189. PMID 28777382
     .
190. ISBN 978-0-13-196893-6
     .
191. PMID 18664583
     .
192. PMID 15680761
     .
193. PMID 16376523
     .
194. S2CID 12289639. Archived from the original
     (PDF) on 16 October 2019. Retrieved 24 June 2008.
195. PMID 9243022. {{cite book}}: |journal= ignored (help
     )
196. PMID 11451524
     .
197. S2CID 6789859
     .
198. S2CID 4349881
     .
199. S2CID 4400950
     .
200. S2CID 54566989
     .
201. PMID 18180743
     .
202. S2CID 4316347
     .
203. PMID 27757416
     .
204. S2CID 21697690
     .
205. PMID 15528644
     .
206. ^ Mehta MP, Baross JA (December 2006). "Nitrogen fixation at 92 °C by a hydrothermal vent archaeon". Science. 314 (5806): 1783–86.
     S2CID 84362603
     .
207. PMID 17359272
     .
208. S2CID 4380804
     .
209. PMID 19719632
     .
210. ^ 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.
     PMID 15314221
     .
211. PMID 12540534
     .
212. PMID 14579252
     .
213. PMID 15067114
     .
214. PMID 16597851
     .
215. PMID 18165302
     .
216. PMID 16541146
     .
217. PMID 9184013
     .
218. PMID 29515525
     .
219. ^ Anaerobic ciliates as a model group for studying the biodiversityand symbioses in anoxic environments (PDF) (Thesis). 2020.
220. PMID 23326206
     .
221. S2CID 22582800
     .
222. PMID 10677847
     .
223. PMID 8692799
     .
224. PMID 15831718
     .
225. PMID 16782812
     .
226. doi:10.3354/meps273089
     .
227. S2CID 20069511
     .
228. PMID 11233158
     .
229. PMID 15120140
     .
230. S2CID 88300156
     .
231. PMID 11713183
     .
232. ^
     PMID 16257257
     .
233. S2CID 7208835
     .
234. S2CID 22178563
     .
235. PMID 15803645
     .
236. S2CID 19985179
     .
237. ISBN 978-1-904455-27-1
     .

Further reading

• Howland JL (2000). The Surprising Archaea: Discovering Another Domain of Life. Oxford University.
  ISBN 978-0-19-511183-5
  .
• Martinko JM, Madigan MT (2005). Brock Biology of Microorganisms (11th ed.). Englewood Cliffs, N.J: Prentice Hall.
  ISBN 978-0-13-144329-7
  .
• Garrett RA, Klenk H (2005). Archaea: Evolution, Physiology and Molecular Biology. WileyBlackwell.
  ISBN 978-1-4051-4404-9
  .
• Cavicchioli R (2007). Archaea: Molecular and Cellular Biology. American Society for Microbiology.
  ISBN 978-1-55581-391-8
  .
• Blum P, ed. (2008). Archaea: New Models for Prokaryotic Biology. Caister Academic Press.
  ISBN 978-1-904455-27-1
  .
• Lipps G (2008). "Archaeal Plasmids". Plasmids: Current Research and Future Trends. Caister Academic Press.
  ISBN 978-1-904455-35-6
  .
• Sapp J (2009). The New Foundations of Evolution: On the Tree of Life. New York: Oxford University Press.
  ISBN 978-0-19-538850-3
  .
• Schaechter M (2009). Archaea (Overview) in The Desk Encyclopedia of Microbiology (2nd ed.). San Diego and London: Elsevier Academic Press.
  ISBN 978-0-12-374980-2
  .

External links

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General

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

Classification

• NCBI taxonomy page on Archaea
• Genera of the domain Archaea – list of Prokaryotic names with Standing in Nomenclature
• Shotgun sequencing finds nanoorganisms – discovery of the ARMAN group of archaea

Genomics

• Browse any completed archaeal genome at UCSC
• Comparative Analysis of Archaeal Genomes Archived 16 February 2013 at the Wayback Machine (at DOE's IMG system)