Archaea

The archaea (Archaea; et: from the Greek αρχαία [arjaía], «the ancient ones»), sometimes called archaea, are a large group of unicellular prokaryotic microorganisms that, like bacteria, do not have a nucleus or internal membranous organelles, but are fundamentally different from them, in such a way that they make up their own domain or realm.

In the past they were grouped in the ancient kingdom Monera, and when they were identified as a group in 1977, they were called archaebacteria (kingdom Archaebacteria), but this classification is no longer used. Actually, the archaea have an independent evolutionary history and show many biochemical and genetic differences from other life forms, which is why they were classified in a separate domain within the three-domain system: Archaea, Bacteria, and Eukarya.

The Archaea are a domain (and also a kingdom) that is divided into multiple phyla. The Crenarchaeota (Thermoproteia) and Euryarchaeota groups are the most studied. The classification of archaea is still difficult, because the vast majority have never been studied in the laboratory and have only been detected by analysis of their nucleic acids in samples taken from various environments.

Archaea and bacteria are quite similar in size and shape, although some archaea have very unusual shapes, such as the flattened, square cells of Haloquadratum walsbyi. Despite this visual resemblance to bacteria, archaea possess genes and several metabolic pathways that are closer to those of eukaryotes, especially in the enzymes involved in transcription and translation. Other aspects of archaeal biochemistry are unique, such as the lipid ethers of their cell membranes. Archaea exploit a much larger variety of resources than eukaryotes, from common organic compounds like sugars, to using ammonia, metal ions, or even hydrogen as nutrients. Salt-tolerant archaea (haloarchaea) use sunlight as a source of energy, and other archaeal species fix carbon; however, unlike plants and cyanobacteria, no archaeal species is known to be capable of salt-tolerant archaea. of both things. Archaea reproduce asexually and divide by binary fission, fragmentation, or budding; unlike bacteria and eukaryotes, no spore-forming species of archaea is known.

Initially, the archaea were considered all methanogens or extremophiles that lived in hostile environments such as hot springs and salt lakes, but now it is known that they are present in the most diverse habitats, such as soil, oceans, swamps and in the human colon. Archaea are especially numerous in the oceans, and those that are part of the plankton could be one of the most abundant groups of organisms on the planet. They are currently considered an important part of life on Earth and could play an important role in both the carbon cycle and the nitrogen cycle. No clear examples of pathogenic or parasitic archaea are known, but they are usually mutualists or commensals. Examples are the methanogenic archaea that live in the intestine of humans and ruminants, where they are present in large numbers and help digest feed. Archaea are important in technology, there are methanogens that are used to produce biogas and as part of the water purification process, and enzymes from extremophile archaea are capable of resisting high temperatures and organic solvents, which is why they are used in biotechnology.

Haloarqueas, each cell measures approximately 5 μm in length.

History

The group of archaea that has always been studied since the oldest is that of the methanogens. Methanogenesis was discovered in Italy's Lake Maggiore in 1776, by observing the bubbling of "combustible air" in it. In 1882 it was observed that the production of methane in the intestine of animals was due to the presence of microorganisms (Popoff, Tappeiner, and Hoppe-Seyler).

In 1936, the year that marked the beginning of the modern era in the study of methanogenesis, H.A Barker provided the scientific basis for the study of its physiology and managed to develop an appropriate culture medium for the growth of methanogens. In that same year, the genera Methanococcus and Methanosarcina were identified.

The first extremophile archaea were found in hot environments. In 1970, Thomas D. Brock of the University of Wisconsin discovered Thermoplasma, a thermoacidophilic archaea, and in 1972 Sulfolobus, a hyperthermophile. field of hyperthermophile biology with the discovery of the Thermus bacterium.

In 1977, the archaea were identified as the most distant prokaryotic group after discovering that the methanogens present a profound divergence with all the bacteria studied. That same year he proposed the category of superkingdom for this group with the name Archaebacteria . In 1978, Bergey's manual gave it the category of phylum with the name Mendosicutes and in 1984 divided the kingdom Procaryotae or Monera into 4 divisions, grouping them into the division Mendosicutes.

Hyperthermophilic archaea were grouped in 1984 under the name Eocyta, identifying them as an independent group from what were then called archaebacteria (referring to methanogens) and eubacteria, also discovering that Eocyta was the group closest to eukaryotes. The phylogenetic relationship between methanogens and hyperthermophiles led to the renaming of the Eocyta as Crenarchaeota in 1990 and the methanogens as Euryarchaeota, forming the new group Archaea as part of the three-domain system.

Classification

New domain

In the early 20th century, prokaryotes were considered a single group of organisms and were classified based on their biochemistry, morphology, and metabolism. For example, microbiologists tried to classify microorganisms according to the structure of their cell wall, their shape, and the substances they consumed. However, in 1965 a new system was proposed, using the genetic sequences of these organisms to find out which prokaryotes are really related to each other. This method, known as molecular phylogeny, is the main method used since then.

Execule arches were initially detected in extreme environments, such as hydrothermal sources. (In photography: aerial view of the Great Prismatic Fountain, a lake in the Yellowstone National Park (USA). The lagoon is approximately 75 × 91 m.

The Archaea were first classified in 1977 as a separate superkingdom from Bacteria, by Carl Woese and George E. Fox in phylogenetic trees based on ribosomal RNA (rRNA) gene sequences. These two groups were originally named Eubacteria and Archaebacteria, what Woese and Fox called the "original kingdoms". Woese argued that this group of prokaryotes is a fundamentally different kind of life. To emphasize this difference, they used the term domain in 1990 and renamed them Bacteria and Archaea. The scientific name Archaea comes from the Ancient Greek ἀρχαῖα, meaning "the ancient". The term "archaebacteria" It comes from the combination of this root and the Greek term baktērion, which means "little staff".

Originally, only methanogens were classified in this new domain, then those considered extremophiles that only lived in habitats like hot springs and salt lakes. In the late 20th century, microbiologists realized that Archaea are a large and diverse group of organisms widely distributed in nature, and that they are common in much less extreme habitats, such as soils and oceans. This new awareness of the importance and omnipresence of these organisms came from the use of the polymerase chain reaction to detect prokaryotes in water or soil samples based solely on their nucleic acids. This makes it possible to detect and identify organisms that are complex to grow in the laboratory.

Current Ranking

The classification of archaea, and of prokaryotes in general, is a constantly fluctuating subject. Current classification systems attempt to organize archaea into groups that share common structural traits and ancestors. These classifications are based primarily on the use of ribosomal RNA gene sequences to reveal relationships between organisms (molecular DNA analyses). In (2016) five phyla were listed in LPSN (List of Prokaryotic names with Standing in Nomenclature). These were: Euryarchaeota, Crenarchaeota, Korarchaeota, Nanoarchaeota, and Thaumarchaeota. Most well-investigated cultivar species of archaea are members of two main groups, Euryarchaeota and Crenarchaeota (Thermoproteia). The peculiar species Nanoarchaeum equitans, which was discovered in 2003, has been given its own phylum, Nanoarchaeota. The recent candidate Korarchaeia contains a small number of unusual thermophilic species that share traits from the two groups. main, but which are closer to Thermoproteia (Crenarchaeota).

Genomic analyzes of samples taken from the environment have revealed a large number of new species of archaea that are distantly related to any of the known groups. For example, the Archaeobacterial Acidophilic Nanoorganisms from the Richmond Mine (ARMAN), which were discovered in 2006 and are among the smallest known organisms. Thus, the number of candidate phyla in 2018 is fourteen. The 19 candidate taxa Known archaea are grouped into four supergroups, usually with phylum or superphylum rank: DPANN, Euryarchaeota, Thermoproteota or TACK, and Asgardarchaeota or Asgard.

ARMAN organisms (Micrarchaeota and Parvarchaeales) are a group of archaees discovered in 2006 in the acid drains of mines. Found for example in the mines of Río Tinto, Huelva, Spain.

The characteristics of the edges are:

• Euryarchaeota: It is the most varied group, four classes are methogens, three are thermoaccidophils and two hyperhalophilates. They also abound in marine environments.
• Thermoproteota or TACK:
  • Nitrososphaeria: They are nitriphic chemotherapists of marine and terrestrial environments.
  • Korarchaeia: They are scarce and are found in thermal sources.
  • Thermoproteia, Crenarchaeota or Eocyta: They have several common features and are usually hypertherophiles, acidophylls, reducers and/or oxidizers of sulfur and chemolythotrophos.
  • Candidates: Caldarchaeales (proposed in 2011, of intermediate features between mesophiles and hyperthermophiles), Bathyarchaeia and Gearchaeales.
• Asgardarchaeota or Asgard: It contains the arches closest to the eukaryotes.
  • Candidates: Lokiarchaeia, Odinarchaeia, Thorarchaeia and Heimdallarchaeia.
• DPANN Group:
  • Nanoarchaeota: Hyperthermals or very small acidophiles. It is considered that nanoarcheas with 300 nm of diameter are the smallest procarotes.
  • Candidates: Diapherotrites, Micrarchaeota (the previous two, containing very small arches, were previously known as ARMAN), Aenigmarchaeota, Nanohaloarchaeota, Altiarchaeota, Huberarchaeota and Undinarchaeota.

Phylogeny

A somewhat agreed phylogeny in the GTDB database and the Annotree is the following:

Other phylogenetic analyzes have suggested that DPANN as a clade may not be monophyletic and would be caused by attraction of long branches. Phylogenetic analyzes suggested that DPANN belongs to the Euryarchaeota, with the Nanohaloarchaeota phylum being entirely separate from the rest. The DPANN clade without Nanohaloarchaeota has been named "Micrarchaea". For this reason an alternative phylogeny for DPANN is as follows:

Species

The classification of archaea into species is also controversial. In biology, a species is a group of related organisms. A widely held definition of a species among animals is a set of organisms that can reproduce with each other and that are reproductively isolated from other groups of organisms (i.e., they cannot reproduce with other species). However, efforts to classify prokaryotes, like archaea, in species are complicated by the fact that they are asexual and that they exhibit a high level of horizontal gene transfer between lineages. This topic is controversial; for example, some data suggest that in archaea such as Ferroplasma, individual cells can clump together in populations of very similar genomes and rarely transfer genes to more divergent groups of cells. Some argue that these groups of cells They are analogous to species. On the other hand, studies of Halorubrum discovered significant genetic exchange between these populations. These results have led to the belief that classifying these groups of organisms as species would make little practical sense.

Current knowledge about the diversity of archaea is fragmentary, and the total number of extant species cannot be estimated with any precision. Even the total number of archaeabacterial phyla is unknown, of which there are currently 16 proposed and only eight have representatives that have been directly cultivated and studied. Many of these hypothetical groups are known only from a single rRNA sequence, indicating that the diversity of these organisms remains completely unknown. The problem of how to study and classify non-cultured microbes also occurs in bacteria. Recently, and although the project poses the difficulties mentioned above, the public consortium GEBA (acronym in English for Genomic Encyclopedy of Bacteria and Archaea, Genomic Encyclopedia of Bacteria and Archaea) is carrying out the task of completing and annotate the largest number of genomes from these two domains in order, among others, to carry out a genome-based classification.

Origin and evolution

Situation of arches in Carl Woese's phylogenetic tree et al. based on data from genetic sequences of RNA 16S. Click on each edge to go to the page.

Phylogenetic tree showing the divergence of the modern species of its common ancestor in the center. The three domains are coloured as follows; the bacteria in blue, archaea in green, and the eukaryotes in red.

Cladogram showing the temporal divergence between the main archaee, bacteria and eukaryotes.

Although likely fossils of prokaryotes dating to about 3.77–4.28 billion years old have been found, the morphology of most prokaryotes and their fossils does not allow one to distinguish between bacteria and archaea. In contrast, "chemical fossils" Characteristic lipids of archaea are more informative, because such compounds do not occur in other organisms. Some publications suggest that lipids characteristic of archaea or eukaryotes are found in sediments from 2.7 billion years ago; but these data have been disputed. These lipids have been detected in rocks dating from the Precambrian. The oldest known remains of isoprene lipids date from the Isua belt of western Greenland, which includes sediments formed 3.8 billion years ago, these being the oldest found to date. The archaean lineage may be the oldest. ancient of the Earth.

Woese considered bacteria, archaea, and eukaryotes to represent separate lines of descent that diverged early in the evolution of ancestral colonies of organisms. One possibility is that this occurred before the evolution of cells, when the lack of of a typical cell membrane allowed for unrestricted lateral gene transfer, and that the common ancestor of the three domains arose by fixation of a specific subset of genes. It is possible that the last common ancestor of bacteria and archaea was a thermophile, which presents the possibility that low temperatures are "extreme environments" for archaea, and that organisms living in cooler environments appeared later in the history of life on Earth. Since Archaea and Bacteria are no longer related to each other than they are to eukaryotes, the term prokaryota only has the meaning of "non-eukaryote", which limits its usefulness.

Gupta, for his part, proposes that archaea evolved from gram-positive bacteria in response to selective pressure exerted by antibiotics released by other bacteria. This idea is supported because archaea are resistant to a wide variety of antibiotics produced mainly by gram-positives, and these antibiotics act mainly on genes that distinguish archaea. Their proposal is that the selective pressure toward antibiotic resistance generated by the Gram-positive antibiotics was ultimately sufficient to cause large changes in many of the genes that were targeted, and that these strains of microorganisms represented common ancestor. of extant archaea. The evolution of archaea in response to selection by antibiotics, or any other competitive selection pressure, could also explain their adaptation to extreme environments (such as high temperature or acidity) as a result of a search for ecological niches. vacated to escape antibiotic-producing organisms; Gupta's proposal is also supported by other research on the relationship between structural proteins and by studies suggesting that gram-positive bacteria may constitute one of the lineages that first branched into prokaryotes. Cavalier-Smith made a similar suggestion, au nwho considers that gram-negative bacteria are the oldest and that gram-positives and archaea originated from them by the loss of the outer membrane. However, until now there is no molecular analysis that can support these theories because both the Bacteria like Archaea form monophyletic groups indicating that both are equally ancient and evolved from the last universal common ancestor.

It has been suggested that the last universal common ancestor of bacteria and archaea is a thermophile that lived 4.35 billion years ago during the Hadic eon. The bifurcation between archaea and bacteria occurred in the middle of the Hadic, while eukaryotes are more recent and emerged at the end of the Paleoproterozoic. The ultrasmall archaea (DPANN) and the phylum Euryarchaeota diverged from the rest of the archaea in the late Hadic and early Archaic. Proteoarchaeota which includes the Thermoproteota and Asgard supergroups originated in the mid-Archaic. The separation of Asgard and eukaryotes was calculated in the late Archean (Neoarchaic period).

Relationships with other prokaryotes

The relationship between the three domains is of great importance in understanding the origin of life. Most metabolic pathways, involving most genes in an organism, are common between archaea and bacteria, and most genes involved in genome expression are common between Archaea and Eukarya. In prokaryotes the structure Archaeal cell structure is very similar to Gram-positive bacteria, mainly because both have a lipid bilayer and generally contain a thick saccule of varied chemical composition. In phylogenetic trees based on the sequences of different genes/proteins of prokaryotic homologues, archaeal homologues are closer to those of Gram-positive bacteria. Archaea and Gram-positive bacteria also share indels on several important proteins, such as Hsp70 and glutamine synthetase I.

Relationships with Eukaryotes

The evolutionary relationship between archaea and eukaryotes is generally accepted, although details are still unknown. In addition to the similarities in cell structure and function that will be discussed later, many gene trees group the two lineages together. The main hypothesis is that the archaean ancestor of eukaryotes diverged very early and that eukaryotes are the result of the fusion of this archaea with a proteobacterium. This would explain several genetic similarities, but the cell structure is difficult to explain. An important step in understanding the archaean origin of the first eukaryotic cell was the discovery of the TACK clade or Thermoproteota phylum. of archaea that combines all the archaean characteristics shared with eukaryotes that were previously distributed among different groups of archaea. A new supergroup or phylum of archaea related to Lokiarchaeia was eventually identified and named Asgardarchaeota or Asgard.

Crossing these data, a phylogenetic tree is obtained that groups several groups of archaea with Eukarya (eocyte hypothesis) combined with pre-eukaryotic symbiogenesis, which can be summarized as follows:

Questioning the three-domain system

In earlier hypotheses such as Woese's, they argued that bacteria, archaea, and eukaryotes represented three distinct evolutionary lineages that diverged many millions of years ago from an ancestral group of organisms. Others argued that archaea and eukaryotes eukaryotes arose from a group of bacteria. Cavalier-Smith proposed the Neomura clade to represent this theory; Neomura means "new walls" and refers to the theory that archaea and eukaryotes have derived from bacteria that (among other adaptations) would replace the peptidoglycan walls with other glycoproteins. According to Woese, since archaea and bacteria would not be more closely related to each other than to eukaryotes, he proposed that the term & # 34;prokaryota & # 34; would not make genuine evolutionary sense and should be discarded altogether. However, many evolutionary biologists believe that the three-domain system exaggerates the difference between archaea and bacteria, and argue that the most dramatic transition was between Prokaryota and Prokaryota. Eukaryote (system of two empires), the latter of more recent origin by eukaryogenesis and as a result of the endosymbiotic fusion of at least two prokaryotes: an archaea and a bacterium.

Morphology

Range of sizes that present prokaryota cells in relation to other organisms and biomolecules.

Archaea range in size from 0.1 μm to more than 15 μm and occur in various shapes, with spheres, rods, spirals, and plates being common. The Crenarchaeota group includes other morphologies, such as irregularly lobed cells in Sulfolobus, fine filaments less than 0.5 μm in diameter in Thermofilum and almost perfectly rectangular bars in Thermoproteus and Pyrobaculum. Recently, a species with a square and flat shape (like a postage stamp) called Haloquadra walsbyi has been discovered in hypersaline pools. These unusual shapes are probably maintained by both the cell wall and a prokaryotic cytoskeleton, but these cell structures, unlike in the case of bacteria, are poorly understood. Proteins related to the components of the cytoskeleton have been identified in archaeal cells, as well as filaments.

Some species form cell aggregates or filaments up to 200 μm in length and can be important members of microbial communities that make up biofilms. A particularly elaborate example of multicellular colonies is the archaea of the genus Pyrodictium. In this case, the cells arrange themselves into long, thin, hollow tubes, called cannulas, which connect and give rise to dense, branching colonies. The function of these cannulas is unknown, but they may allow cells to communicate or exchange nutrients. with their neighbors. Colonies can also be formed by association between different species. For example, in a community discovered in 2001 in a German wetland, round white colonies of a new species of archaea of the phylum Euryarchaeota were scattered along thin filaments that can be up to 15 cm long; these filaments are made up of a particular species of bacteria.

Structure and composition

Archaea are similar to bacteria in their general cell structure, but the composition and organization of some of these structures are very different. Like bacteria, archaea lack internal membranes, so their cells do not contain organelles. They also resemble bacteria in that their cell membrane is usually bounded by a cell wall and that they swim by means of one or more flagella. In their general structure, archaea are especially similar to gram-positive bacteria, as most have a single plasma membrane and cell wall, and lack a periplasmic space; The exception to this general rule is the archaea Ignicoccus, which have a particularly large periplasmic space containing membrane-bounded vesicles, and which is closed by an outer membrane.

The following table describes some of the main features that archaea share with other domains or are unique to. Many of these features will be discussed below.

Membranes

Membrane structure. Up, archaic phospholipid: 1isoprene chains; 2ether links; 3the rest of L-glicerol; 4, phosphate group. In the middle, bacterial phospholipid or eucarithic: 5, fatty acid chains; 6, links ester; 7the rest of D-glicerol; 8, phosphate group. Down: 9, lipid bicapa of bacteria or eukaryotes; 10, lipidic monolayer of some arches.

Archeal membranes are composed of molecules that differ greatly from those found in other forms of life, which is evidence that archaea are only distantly related to bacteria and eukaryotes. In all organisms, archaea are only distantly related to bacteria and eukaryotes. Cell membranes are made up of molecules known as phospholipids. These molecules have a polar part that dissolves in water (the polar "head"), and a "fatty" part that dissolves in water. nonpolar that does not dissolve in water (the nonpolar "tail"). These different parts are connected by glycerol. In water, phospholipids clump together, with the polar heads toward the water and the nonpolar lipid tails away from it. This causes them to be structured in layers. The main structure of the cell membrane is a double layer of these phospholipids, which is called the lipid bilayer.

The phospholipids of archal membranes are unusual in four ways. Firstly, bacteria have membranes composed mainly of lipids linked to glycerol through ester bonds, whereas in archaea lipids are linked to glycerol through ether bonds. The difference between these two types of phospholipids is the type of bond that joins them to the glycerol. Ether bonds have superior chemical resistance to ester bonds, which could contribute to the ability of some archaea to survive at extreme temperatures or in highly acidic or alkaline environments. Bacteria and eukaryotes also contain some ether-bonded lipids., but unlike archaebacteria, these lipids do not form a major part of their membranes.

Second, archaeal lipids are unique in that the stereochemistry of the glycerol group is the reverse of that seen in other organisms. The glycerol group can exist in two forms that are mirror images of each other, and can be referred to as "right-handed" forms; and "sinister"; In chemical language they are called enantiomers. Just as a right hand does not easily fit into a left-handed glove, a right-handed glycerol molecule generally cannot be used or created by sinister-shaped adapted enzymes. This suggests that archaea use completely different enzymes to synthesize their phospholipids from those used by bacteria and eukaryotes; as these enzymes developed very early in the history of life, this in turn suggests that the archaea diverged from the other two domains very early.

Third, the lipid tails of archaean phospholipids have a different chemical composition than those of other organisms. Archaeal lipids are based on an isoprenoid chain and are long chains with multiple side branches and sometimes even cyclopropane or cyclohexane rings. This is in contrast to the fatty acids found in the membranes of other organisms, which have straight chains without branches or rings. Although isoprenoids play an important role in the biochemistry of many organisms, only archaea use them to produce phospholipids. These branched chains could help prevent archaea membranes from leaking at high temperatures.

Finally, in some archaea the lipid bilayer is replaced by a single monolayer. In fact, archaea fuse the tails of two independent phospholipid molecules into a single molecule with two polar heads, this fusion could make their membrane more rigid and better able to withstand harsh environments. For example, all the lipids of Ferroplasma are of this type, which is believed to help this organism survive in the extremely acidic environments in which it inhabits.

Cell wall and flagella

Most archaea have a cell wall, the exceptions being Thermoplasma and Ferroplasma. In most archaea, the wall is made up of surface proteins, which form an S layer. An S layer is a rigid grouping of protein molecules that covers the outside of the cell like chain mail. This layer offers chemical and physical protection, and can serve as a barrier, preventing them from entering into contact with each other. macromolecules contact the cell membrane. Unlike bacteria, most archaea lack peptidoglycan in the cell wall. The exception is pseudopeptidoglycan, which is found in methanogenous archaea, but this polymer is different from bacterial peptidoglycan, since it lacks amino acids and N-acetylmuramic acid.

Archaea also have flagella, which function in a similar way to bacterial flagella—they are long tails that are moved by rotating motors at the base of the flagella. These motors are driven by the proton gradient of the membrane. However, the archaeal bacterial flagella are remarkably different in their composition and development. Each type of flagellum evolved from a different ancestor, the bacterial flagellum evolved from a type III secretion system, while the archean flagella appear to have evolved from the type IV bacterial pili. archaeans are synthesized by adding subunits at their base.

Metabolism

The haloarqueas that grow in Lake Magadi (Kenia) are of reddish colors due to carotenoid pigments such as bacterioruberin.

Archaea present a great variety of chemical reactions in their metabolism; being identical to those of the other domains, and using many different power sources. These forms of metabolism are classified into nutritional groups, depending on the source of energy and carbon. Some archaea obtain energy from inorganic compounds such as sulfur or ammonia (they are lithotrophs). These archaea include nitrifiers, methanogens, and anaerobic methane oxidizers. In these reactions, one compound passes electrons to the other (in a redox reaction), releasing energy that is used to fuel the activities of cells. One compound acts as an electron donor and the other as an acceptor. A common feature of all these reactions is that the energy released is used to generate adenosine triphosphate (ATP) through chemiosmosis, which is the same basic process that takes place in the mitochondria of animal cells.

Other groups of archaea use sunlight as a source of energy (they are phototrophs), such as algae, protists, and bacteria. However, none of these organisms engage in oxygen-generating photosynthesis (oxygenic photosynthesis) like cyanobacteria. Many of the basic metabolic pathways are shared by all life, for example, archaea use a modified form of glycolysis. (the Entner-Doudoroff pathway), and a full or partial Krebs cycle. These similarities to other organisms probably reflect both the early evolution of these parts of metabolism in the history of life, and their high level of efficiency..

Some Euryarchaeota are methanogens, producing methane gas in anaerobic environments such as swamps. This type of metabolism evolved early, and it is even possible that the first free-living organism was a methanogen. A typical reaction of these organisms involves the use of carbon dioxide as an electron acceptor to oxidize hydrogen. Methanogenesis involves a variety of coenzymes that are unique to these archaea, such as coenzyme M or methanefuran. Other organic compounds such as alcohols, acetic acid, or formic acid are used as electron acceptors for methanogens. These reactions are common in intestinal archaea. Acetic acid is also broken down into methane and carbon dioxide directly, by acetotrophic archaea. These acetotrophs belong to the order Metanosarcinales, and are an important part of communities of biogas-producing microorganisms.

Bacteriorodopsin Halobacterium salinarum. The model shows the retinol cofactor and waste involved in the transfer of protons.

Other archaea use CO₂ from the atmosphere as a carbon source, in a process called carbon fixation (they are autotrophs). In archaea, this process involves either a highly modified form of the Calvin cycle, or a recently discovered metabolic pathway known as the 3-hydroxypropionate/4-hydroxybutyrate cycle. The Crenarchaeota also use the reverse Krebs cycle, and the Euryarchaeota they also use the reductive pathway of acetyl-CoA. In these organisms, carbon fixation is powered by inorganic sources of energy, rather than sunlight as is the case in plants and cyanobacteria. No archaea are known to be able to carry out photosynthesis, which is when light is used by photoautotrophs as an energy source, as well as a food source for carbon dioxide fixation. The energy sources used by archaea to fixing carbon are extremely diverse, ranging from the oxidation of ammonia by Nitrosopumilales to the oxidation of hydrogen sulfide or elemental sulfur by Sulfolobus, using oxygen or metal ions as electron acceptors.

Phototrophic archaea use light to produce chemical energy in the form of ATP. In haloarchaea, there are light-activated ion pumps, such as bacteriorhodopsin and halorhodopsin, which generate ion gradients by pumping ions out of the cell across the plasma membrane. The energy stored in these electrochemical gradients is later converted to ATP by ATP synthase. This process is a form of photophosphorylation. The structure and function of these light-activated pumps have been studied in great detail, revealing that their ability to move ions across membranes depends on light-induced changes in the structure of a retinol cofactor. in the center of the protein.

Genetics

Archaea generally have a single circular chromosome like bacteria, which ranges in size from 5,751,492 base pairs in Methanosarcina acetivorans, the largest sequenced genome to to date, up to 490,885 base pairs in Nanoarchaeum equitans, the smallest known genome that may contain only 537 protein-coding genes. Archaea may also present plasmids that can be spread by physical contact between cells, in a process that may be similar to bacterial conjugation. Plasmids are increasingly important as genetic tools, allowing genetic studies to be carried out in Archaea.

Sulfolobus infected by STSV1 virus. The bar measures 1 μm.

Like bacteriophages that infect bacteria, there are viruses that replicate in archaea. This includes viruses with shapes already known in bacteria and eukaryotes and others with a variety of unusual shapes, such as bottles, bars with a hook, or even tears that do not appear to be evolutionarily related to other viruses, the latter of which have been described in more detail in thermophiles, particularly the orders Sulfolobales and Thermoproteales. Defense against these viruses may involve RNA interference by repetitive DNA sequences in the archaeal genome.

Archaea are genetically distinct from other organisms, with up to 15% unique proteins encoded by the genome of any one archaea. Genes that are shared among Archaea, Bacteria, and Eukarya form a core of cell functions, related primarily with transcription, translation, and nucleotide metabolism. Most archaeal-unique genes have no known function, but of those that do have an identified function, most are involved in methanogenesis. Other characteristic elements of archaeal genomes are the organization of genes with related function, such as enzymes that catalyze steps in the same metabolic pathway, novel operons, and large differences in tRNA genes and their aminoacyl tRNA synthetases.

Transcription and translation in Archaea are more similar to Eukarya than to Bacteria; for example, in RNA polymerase II subunits and sequences, and in ribosomes. The functions and interactions of RNA polymerase in transcription in Archaea also appear to be related to that of the Eukarya, with a similar assembly of proteins (reduction factors). generic transcription) by directing the binding of RNA polymerase to a gene promoter. However, many other transcription factors in archaea are similar to those in bacteria.

Ecology

Habitats

Archaea exist in a wide variety of habitats, are an important part of global ecosystems, and could account for up to 20% of the total biomass on Earth. Many archaea are extremophiles, and archaea are extremophiles. habitat was historically seen as their ecological niche. Indeed, some archaea survive at high temperatures, such as Geogemma barossii strain 121, often above 100 °C, such as those found in geysers, mineralized chimneys, and oil wells. Others live in very cold habitats, and still others in highly saline, acidic, or alkaline waters. However, other archaea are mesophiles, living in much softer and more humid conditions such as sewers, oceans, and soil.

Plankton in the ocean (light see); arches constitute the majority of ocean life.

Extremophile archaea are members of four main physiological groups. They are halophiles, thermophiles, alkaliphiles, and acidophiles. These groups are not inclusive or related to the phylum to which a given archaea belongs, nor are they mutually exclusive, since some archaea belong to several of these groups. However, they are useful as a starting point for the classification of these organisms.

Halophiles, including the genus Halobacterium, live in extremely saline environments, such as salt lakes, and begin to outcompete their bacterial counterparts at salinities greater than 20-25%. Thermophiles thrive at temperatures above 45°C, in places like hot springs; hyperthermophilic archaea are those that thrive in temperatures above 80 °C. Methanopyrus kandleri strain 116 grows at 122 °C, which is the highest recorded temperature in which an organism can live. Other archaea exist in highly acidic or alkaline conditions. For example, one of the most extreme archaea acidophiles is Picrophilus torridus, which grows at pH 0, which is equivalent to thriving in sulfuric acid with a molar concentration of 1.2.

This resistance to extreme environments has made archaea the center of speculation about the possible properties of extraterrestrial life. This hypothesis raises the odds that microbial life exists on Mars, and it has even been suggested that viable microbes could travel between planets on meteorites. Several studies have recently shown that archaea not only exist in mesophilic and thermophilic environments, but are also present, sometimes in high numbers, at low temperatures. For example, archaea are common in cold ocean environments such as polar seas. Even more significant are the large numbers of archaea that live worldwide in the planktonic community (as part of the picoplankton). Although these archaea may be present in extremely large numbers (up to 40% of microbial biomass), almost none of these species have been isolated and studied in pure culture. Therefore, current understanding of the role of archaea in ocean ecology is rudimentary., so their full influence on global biogeochemical cycles remains unknown. Also, a recent study has shown that a group of marine Crenarchaeota are capable of carrying out nitrification, suggesting that these organisms could be important in the cycle of the ocean. oceanic nitrogen. Large numbers of archaea are also found in the sediments that cover the seafloor, and these organisms smos form the majority of living cells at depths of more than a meter within this sediment.

Role in chemical cycles

Archaea recycle elements such as carbon, nitrogen, and sulfur from the various habitats of each ecosystem. These activities are vital for the normal functioning of ecosystems, but archaea can contribute to increasing human-caused changes, and can even cause pollution.

Archaea can carry out many of the steps of the nitrogen cycle. This includes both dissimilatory reactions that remove nitrogen from ecosystems (such as nitrate-based respiration and denitrification), and assimilatory processes that introduce nitrogen, such as nitrate assimilation and nitrogen fixation. The role of archaea in nitrogen reactions ammonia oxidation was discovered in 2007. These reactions are particularly important in the oceans. Archaea are also important in ammonia oxidation in soil. They produce nitrites, which are subsequently oxidized by other microbes into nitrates. Plants and other organisms consume the latter.

In the sulfur cycle, archaea that grow by oxidizing sulfur compounds release this element from rocks, making it available to other organisms. However, 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 the formation of acid mine drainage fluids. and others. environmental damage.

In the carbon cycle, methanogenic archaea release hydrogen and are important in the decomposition of organic matter carried out by populations of microorganisms that act as decomposers in anaerobic systems, such as sediment deposits, swamps, and in the treatment of sewage. However, methane is one of the most abundant greenhouse gases in Earth's atmosphere, constituting 18% of the global total. It is 25 times more potent as a greenhouse gas than carbon dioxide. Methanogenic microorganisms are the primary source of atmospheric methane, and are responsible for the majority of the world's annual methane emissions. As a consequence, these archaea contribute to global greenhouse gas emissions and global warming.

Interactions with other organisms

Methanogenic arches form a symbiosis with the termites.

Well-defined interactions between archaea and other organisms are either mutualistic or commensalistic. As of 2007, no clear example of an archaeal pathogen or parasite was yet known. However, a relationship has been suggested between the presence of some methanogen species and infections in the mouth, and Nanoarchaeum equitans could be a parasite, as it only survives and reproduces inside the cells of the Crenarchaeota Ignicoccus hospitalis, and appears to offer no benefit to its host.

Mutualism

A well-understood example of mutualism is the interaction between protozoa and methanogenous archaea in the digestive systems of cellulose-digesting animals, such as ruminants and termites. In these anaerobic environments, protozoa break down cellulose in plant material to obtain Energy. This process releases hydrogen as a waste product, but high hydrogen levels reduce the energy generated by this reaction. When methanogens convert hydrogen to methane, the protozoa benefit, as they will be able to get more energy from breaking down cellulose.

These associations between methanogens and protozoa go a step further in several anaerobic protozoan species, such as Plagiopyla frontata, in which case, the archaea live in the protozoan and consume the hydrogen produced in their hydrogenosomes.. Similar associations with larger organisms are being discovered, with the discovery of the marine archaea Cenarchaeum symbiosum living inside the sponge Axinella mexicana.

Commensalism

Archaea can also be commensals, benefiting from an association without helping or harming the other organism. For example, the methanogen Methanobrevibacter smithii is by far the most common archaea of the human flora, accounting for approximately 10% of all prokaryotes in the human intestine. As in the case of termites, it is possible that these methanogens are actually mutualistic in humans, interacting with other microbes in the gut to facilitate the digestion of food. There are also archaeal communities associated with a variety of other organisms, such as on the surface of corals, and on the bottom of the soil that surrounds the roots of plants (the rhizosphere).

Playback

Archaea reproduce asexually by binary or multiple fission, fragmentation, or budding. Meiosis does not occur, so if an archaeal species exists in more than one form, they all have the same number of chromosomes (they have the same karyotype). Cell division is controlled as part of a complex cell cycle, where the chromosome replicates, the copies separate, and then the cell divides. Details of the cell cycle have only been investigated in the genus Sulfolobus, being similar to those of bacteria and eukaryotes: chromosomes replicate from multiple starting points (origin of replication) using DNA polymerases that are similar to equivalent eukaryotic enzymes. However, proteins that direct cell division, such as the FtsZ protein that forms a contractile ring around the cell, appear to be more closely related to their bacterial counterparts.

Endospores do not form in any species of archaea, although some haloarchaeal species can alternate between phenotypes and grow as different cell types, including thick-walled structures that are resistant to osmotic shock and allow them to survive at low concentrations of salt. These are not reproductive structures, but may help these species disperse into new habitats.

Use of archaea in technology and industry

Extremophile archaea, particularly those resistant to high temperatures or extremes of acidity and alkalinity, are an important source of enzymes that can function under these harsh conditions. These enzymes have a wide range of uses. For example, thermostable DNA polymerases, such as the Pfu DNA polymerase from Pyrococcus furiosus, have revolutionized molecular biology, allowing the use of the polymerase chain reaction as a simple and rapid method for cloning. of the DNA. In industry, amylases, galactosidases and pullulanases from other Pyrococcus species perform their function at temperatures above 100 °C, which allows the preparation of foods at high temperatures, such as low-lactose milk and whey. Enzymes from these thermophilic archaea also tend to be highly stable in organic solvents, so they can be used in a wide range of environmentally friendly processes for the synthesis of organic compounds.

In contrast to the wide range of applications for enzymes, the use in biotechnology of the organisms themselves is more limited. However, methanogenous archaea are a vital part of wastewater treatment, performing anaerobic digestion of waste and producing biogas. Acidophilic archaea are also promising in mining for the extraction of metals such as gold, cobalt, and copper.

A new class of potentially useful antibiotics are derived from this group of organisms. Eight of those substances have already been characterized, but there could be many more, especially in haloarchaea. These compounds are important because they have a different structure than bacterial antibiotics, so they may have a different mode of action. In addition, they could allow the creation of new selectable markers for use in archaeal molecular biology. The discovery of new substances depends on the recovery of these organisms from the environment and their cultivation.