Other aspects of archaean biochemistry are unique, such as their reliance on ether lipids in their cell membranes. The archaea exploit a much greater variety of sources of energy than eukaryotes: ranging from familiar organic compounds such as sugars, to using ammonia, metal ions or even hydrogen gas as nutrients. Salt-tolerant archaea (the Halobacteria) use sunlight as a source of energy, and other species of archaea fix carbon; however, unlike plants and cyanobacteria, no species of archaea is known to do both. Archaea reproduce asexually and divide by binary fission, fragmentation, or budding; in contrast to bacteria and eukaryotes, no species of archaea are known that form spores.
Initially, archaea were seen as extremophiles that lived in harsh environments, such as hot springs and salt lakes, but they have since been found in a broad range of habitats, such as soils, oceans, and marshlands. Archaea are particularly numerous in the oceans, and the archaea in plankton may be one of the most abundant groups of organisms on the planet. These prokaryotes are now recognized as a major part of life on Earth and may play an important role in both the carbon cycle and nitrogen cycle. No clear examples of archaeal pathogens or parasites are known, but they are often mutualists or commensals. One example are the methanogenic archaea that inhabit the gut of humans and ruminants, where they are present in vast numbers and aid in the digestion of food. Archaea have some importance in technology, with methanogens used to produce biogas and as part of sewage treatment, and enzymes from extremophile archaea that can resist high temperatures and organic solvents are exploited in biotechnology.Contents
By the end of the 20th century, microbiologists realized that the archaea are a large and diverse group of organisms that are widely distributed in nature and are common in much less extreme habitats, such as soils and oceans. This new appreciation of the importance and ubiquity of archaea came from using the polymerase chain reaction to detect prokaryotes in samples of water or soil from their nucleic acids alone. This allows the detection and identification of organisms that cannot be cultured in the laboratory, which is often difficult.
Some early analyses even suggested that the relationship between eukaryotes and the archaeal phylum Euryarchaeota is closer than the relationship between the Euryarchaeota and the phylum Crenarchaeota. However, it is now considered more likely that the ancestor of the eukaryotes diverged early from the Archaea. The discovery of archaean-like genes in certain bacteria, such as Thermotoga maritima, makes these relationships difficult to determine, since horizontal gene transfer has occurred. Some have suggested that eukaryotes arose through fusion of an archaean and eubacterium, which became the nucleus and cytoplasm; this accounts for various genetic similarities but runs into difficulties explaining cell structure.
A particularly elaborate form of multicellular colony is produced by archaea in the genus Pyrodictium. Here, the cells produce arrays of long, thin hollow tubes called cannulae that stick out from the cells' surfaces and connect them together into a dense bush-like colony. The function of these cannulae is not known, but they may allow the cells to communicate or exchange nutrients with their neighbors. Colonies can also be produced by an association between different species. For example, in the "string-of-pearls" community that was discovered in 2001 in a German swamp, round whitish colonies of a novel species of archaea in the phylum Euryarchaeota are spaced along thin filaments that can be up to 15 centimetres (5.9 in) long; these filaments are made of a particular species of bacteria.
Secondly, archaeal lipids are unique because the stereochemistry of the glycerol group is the reverse of that found in other organisms. The glycerol group can occur in two forms that are mirror images of one another, which may be called the right-handed and left-handed forms; in chemical terms these forms are called enantiomers. Just as a right hand does not fit easily into a left-handed glove, a right-handed glycerol molecule generally cannot be used or made by enzymes adapted for the left-handed form. This suggests that archaea use entirely different enzymes for synthesizing their phospholipids than do bacteria and eukaryotes; since such enzymes developed very early in life's history, this in turn suggests that the archaea split off very early from the other two domains.
Thirdly, the lipid tails of the phospholipids of archaea are chemically different from those in other organisms. Archaeal lipids are based upon the isoprenoid sidechain and are long chains with multiple side-branches and sometimes even cyclopropane or cyclohexane rings. This is in contrast to the fatty acids found in other organisms' membranes, which have straight chains with no branches or rings. Although isoprenoids play an important role in the biochemistry of many organisms, only the archaea use them to make phospholipids. These branched chains may help prevent archaean membranes from becoming leaky at high temperatures.
Finally, in some archaea the phospholipid bilayer is replaced by a single monolayer. In effect, the archaea have fused the tails of two independent phospholipid molecules into a single molecule with two polar heads; this fusion may make their membranes more rigid and better able to resist harsh environments. For example, all the lipids in Ferroplasma are of this type, which is thought to aid this organism's survival in the extraordinarily acidic environments in which it thrives.
Cell wall and flagellaMost archaea possess a cell wall - the exceptions being Thermoplasma and Ferroplasma. In most archaea the wall is assembled from surface-layer proteins, which form an S-layer. An S-layer is made of a rigid array of protein molecules that cover the outside of the cell like chain mail. This layer provides both chemical and physical protection, and can act as a barrier preventing macromolecules from coming into contact with the cell membrane. In contrast to bacteria, most archaea lack peptidoglycan in their cell walls. The exception is pseudopeptidoglycan, which is found in Methanobacteriales, but this polymer is different from the peptidoglycan of bacteria since it lacks D-amino acids and N-acetylmuramic acid.
Archaea also have flagella, and these operate in a similar way to bacterial flagella - they are long stalks that are driven by rotatory motors at the base of the flagella. These motors are powered by the proton gradient across the membrane. However, archaeal flagella are notably different in their composition and development. The two types of flagella evolved from different ancestors, the bacterial flagellum evolved from a type III secretion system, while archaeal flagella appear to have evolved from the bacterial type IV pili. In contrast to the bacterial flagellum, which is a hollow stalk and is assembled by subunits moving up the central pore and then adding onto the tip of the flagella, archaeal flagella are synthesized by adding subunits onto their base.
MetabolismArchaea exhibit a great variety of chemical reactions in their metabolism and use many different sources of energy. These forms of metabolism are classified into nutritional groups, depending on the source of energy and the source of carbon. Some archaea obtain their energy from inorganic compounds such as sulfur or ammonia (they are lithotrophs). These archaea include nitrifiers, methanogens and anaerobic methane oxidisers. In these reactions one compound passes electrons to another (in a redox reaction), releasing energy that is then used to fuel the cell's activities. One compound acts as an electron donor and one as an electron 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 happens in the mitochondrion of animal cells. Other groups of archaea use sunlight as a source of energy (they are phototrophs). However, oxygen-generating photosynthesis does not occur in any of these organisms. Many basic metabolic pathways are shared between 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. These similarities with other organisms probably reflect both the early evolution of these parts of metabolism in the history of life and their high level of efficiency.
Nutritional types in archaeal metabolism
Some Euryarchaeota are methanogens and produce methane gas in anaerobic environments such as swamps. This form of metabolism evolved early, and it is even possible that the first free-living organism was a methanogen. A common reaction in these organisms 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. 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.
GeneticsArchaea usually have a single circular chromosome, the size of which may be as great as 5,751,492 base pairs in Methanosarcina acetivorans, the largest archaean genome sequenced to date. At one-tenth of this size is the tiny 490,885 base-pair genome of Nanoarchaeum equitans, which is the smallest archaeal genome known; it is estimated to contain only 537 protein-encoding genes. 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.
Transcription and translation in archaea are more similar to these processes in eukaryotes than in bacteria, with the archaean RNA polymerase and ribosomes being very close to their equivalents in eukaryotes. Although archaea only have 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 assemblies of proteins (the general transcription factors) directing the binding of the RNA polymerase to a gene's promoter. However, other archaean transcription factors are closer to those found in bacteria. Post-transcriptional modification is simpler than in eukaryotes, since most archaean genes lack introns, although there are many introns in their transfer RNA and ribosomal RNA genes, and introns may occur in a few of their protein-encoding genes.
ReproductionArchaea reproduce asexually by binary or multiple fission, fragmentation, or budding; meiosis does not occur, so if a species of archaea exists in more than one form, these will all have the same genetic material. Cell division is controlled in the archaea in a cell cycle; after the cell's chromosome is replicated and the two daughter chromosomes are separated, the cell divides. The details of the archaeal cell cycle have only been investigated in the genus Sulfolobus, but here it has characters that are similar to both bacterial and eukaryotic systems. In this archaean, the chromosomes are replicated from multiple starting-points (origins of replication) using DNA polymerases that resemble the equivalent eukaryotic enzymes. However, the proteins that direct cell division, such as the protein FtsZ, which forms a contracting ring around the cell, and the components of the septum that is constructed across the center of the cell, are similar to their bacterial equivalents.
Spores are made by both bacteria and eukaryotes, but are not formed in any of the known archaea. Some species of Haloarchaea undergo phenotypic switching and grow as several different types of cell, including thick-walled structures that are resistant to osmotic shock and allow the archaea to survive in water at low concentrations of salt, but these are not reproductive structures and may instead help them disperse to new habitats.
Halophiles, including the genus Halobacterium, live in extremely saline environments such as salt lakes and start outnumbering their bacterial counterparts at salinities greater than 20-25%. Thermophiles grow best at temperatures above 45°C, in places such as hot springs; hyperthermophilic archaea are defined as those that grow optimally at temperatures greater than 80°C.
The archaeal Methanopyrus kandleri Strain 116 grows at 122 °C, which is the highest recorded temperature at which any organism will grow. Other archaea exist in very acidic or alkaline conditions. For example, one of the most extreme archaean acidophiles is Picrophilus torridus, which grows at pH 0, which is equivalent to thriving in 1.2 Molar sulfuric acid.
This resistance to extreme environments has made archaea the focus of speculation about the possible properties of extraterrestrial life. This has focused on the possibility that microbial life may exist on Mars, and has even led to the suggestion that viable microbes could be transferred between planets in meteorites.
Recently, several studies have shown that archaea exist not only in mesophilic and thermophilic environments but are also present, sometimes in high numbers, at low temperatures as well. For example, archaea are common in cold oceanic environments such as polar seas. Even more significant are the large numbers of archaea found throughout the world's oceans in the plankton community (as part of the picoplankton). Although these archaea can be present in extremely high numbers (up to 40% of the microbial biomass), almost none of these species have been isolated and studied in pure culture. Consequently, our understanding of the role of archaea in the ecology of the oceans is rudimentary, so their full influence on global biogeochemical cycles remains largely unexplored. Some marine Crenarchaeota are capable of nitrification, suggesting these organisms may be important in the oceanic nitrogen cycle, although these oceanic Crenarchaeota may also use other sources of energy. Vast numbers of archaea are also found in the sediments that cover the sea floor, with these organisms making up the majority of living cells at depths over 1 meter into this sediment.
Archaea carry out many steps in the nitrogen cycle, this includes both dissimilatory reactions that remove nitrogen from ecosystems, such as nitrate-based respiration and denitrification: as well as assimilatory processes that introduce nitrogen, such as nitrate assimilation and nitrogen fixation. The involvement of archaea in ammonia oxidation reactions was recently discovered; these being particularly important in the oceans. The archaea also appear to be crucial for ammonia oxidation in soils, this produces nitrite, which is then oxidized to nitrate by other microbes, and then taken up by plants and other organisms.
In the sulfur cycle, archaea that grow by oxidizing sulfur compounds are important as they release this element from rocks, making it available to other organisms. However, the archaea that do this, such as Sulfolobus, can cause environmental damage since they produce sulfuric acid as a waste product, and the growth of these organisms in abandoned mines can contribute to acid mine drainage.
In the carbon cycle, methanogen archaea are significant as methane producers. The ability of these archaea to remove hydrogen is important in the degradation of organic matter by the populations of microorganisms that act as decomposers in anaerobic ecosystems, such as sediments, marshes and sewage treatment works. 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. Methanogens are the primary source of atmospheric methane, and are responsible for most of the world's yearly methane emissions. As a consequence, these archaea contribute to global greenhouse gas emissions and global warming.
In contrast to the range of applications of archaean enzymes, the use of the organisms themselves in biotechnology is more restricted. However, methanogenic archaea are a vital part of sewage treatment, since they are part of the community of microorganisms that carry out anaerobic digestion and produce biogas. In mineral processing, Acidophilic archaea display promise for the extraction of metals from ores, including gold, cobalt and copper.
A new class of potentially useful antibiotics has been discovered in archaea. A few of these archaeocins have been characterized, but hundreds more are believed to exist, especially within Haloarchaea and Sulfolobus. These compounds are important since they are different in structure to bacterial antibiotics, so they may have novel modes of action. In addition, they may allow the creation of new selectable markers for use in archaeal molecular biology. The discovery of new archaeocins depends on successful recovery and cultivation of new species of archaea from the environment.
» List of sequenced archeal genomes
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