Domain Archaea

Domain Archaea is mostly composed of cells that live in extreme environments. While they are able to live elsewhere, they are usually not found there because outside of extreme environments they are competitively excluded by other organisms. Species of the domain Archaea are not inhibited by antibiotics, lack peptidoglycan in their cell wall (unlike bacteria, which have this sugar/polypeptide compound), and can have branched carbon chains in their membrane lipids of the phospholipid bilayer. It is believed that Archaea are very similar to prokaryotes that inhabited the earth billions of years ago. It is also believed that eukaryotes evolved from Archaea, because they share many mRNA sequences, have similar RNA polymerases, and have introns. Therefore, it is believed that the domains Archaea and Bacteria branched from each other very early in history, and membrane infolding produced eukaryotic cells in the archaean branch approximately 1.7 billion years ago.

The Archaea are a group of single-celled microorganisms. A single individual or species from this domain is called an archaeon (sometimes spelled "archeon"). They have no cell nucleus nor any other membrane-bound organelles within their cells. In the past they were viewed as an unusual group of bacteria and named archaebacteria, but the Archaea have an independent evolutionary history and show many differences in their biochemistry from other forms of life, and so they are now classified as a separate domain in the three-domain system. In this system the phylogenetically distinct branches of evolutionary descent are the Archaea, Bacteria and Eukaryota. Archaea are divided into four recognized phyla, but many more phyla may exist. Of these groups the Crenarchaeota and the Euryarchaeota are most intensively studied. Classification 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 from the environment. Although archaea have, in the past, been classed with bacteria as prokaryotes (or Kingdom Monera), this classification is regarded by some as outdated.^[1]

Archaea and bacteria are quite similar in size and shape, although a few archaea have very unusual shapes, such as the flat and square-shaped cells of Haloquadratum walsbyi. Despite this visual similarity to bacteria, archaea possess genes and several metabolic pathways that are more closely related to those of eukaryotes: notably the enzymes involved in transcription and translation. Other aspects of archaean biochemistry are unique, such as their reliance on ether lipids in their cell membranes. Archaea use a much greater variety of sources of energy than eukaryotes: ranging from familiar organic compounds such as sugars, to ammonia, metal ions or even hydrogen gas. Salt-tolerant archaea (the Halobacteria) use sunlight as an energy source 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 known species 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, including 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. Archaea are now recognized as a major part of Earth's life and may play roles in both the carbon cycle and the nitrogen cycle. No clear examples of archaeal pathogens or parasites are known, but they are often mutualists or commensals. One example is the methanogens that inhabit the gut of humans and ruminants, where their vast numbers aid digestion. Methanogens are used in biogas production and sewage treatment, and enzymes from extremophile archaea that can endure high temperatures and organic solvents are exploited in biotechnology.

Archaea recycle elements such as carbon, nitrogen and sulfur through their various habitats. Although these activities are vital for normal ecosystem function, archaea can also contribute to human-made changes, and even cause pollution.

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.^[123][124] Archaean involvement in ammonia oxidation reactions was recently discovered. These reactions are particularly important in the oceans.^[125][126] The archaea also appear to be crucial for ammonia oxidation in soils. They produce nitrite, which other microbes then oxidize to nitrate. Plants and other organisms consume the latter.^[127]

In the sulfur cycle, archaea that grow by oxidizing sulfur compounds release this element from rocks, making it available to other organisms. However, 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.^[128]

In the carbon cycle, methanogen archaea remove hydrogen and are important 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.^[129] However, methane is one of the most abundant greenhouse gases in Earth's atmosphere, constituting 18% of the global total.^[130] It is 25 times more potent as a greenhouse gas than carbon dioxide.^[131] Methanogens are the primary source of atmospheric methane, and are responsible for most of the world's yearly methane emissions.^[132] As a consequence, these archaea contribute to global greenhouse gas emissions and global warming.

Archaea form four major phyla, the

Euryarchaeota, the Crenarchaeota, the

Korarchaeota, and the Nanoarchaeota

Most archaea (but not Thermoplasma and Ferroplasma) possess a cell wall.^[47] In most archaea the wall is assembled from surface-layer proteins, which form an S-layer.^[62] An S-layer is a rigid array of protein molecules that cover the outside of the cell (like chain mail).^[63] This layer provides both chemical and physical protection, and can prevent macromolecules from contacting the cell membrane.^[64] Unlike bacteria, archaea lack peptidoglycan in their cell walls.^[65] Methanobacteriales do have cell walls containing pseudopeptidoglycan, which resembles eubacterial peptidoglycan in morphology, function, and physical structure, but pseudopeptidoglycan is distinct in chemical structure; it lacks D-amino acids and N-acetylmuramic acid.^[64]

Archaea flagella operate like bacterial flagella—their long stalks are driven by rotatory motors at the base. These motors are powered by the proton gradient across the membrane. However, archaeal flagella are notably different in composition and development.^[53] The two types of flagella evolved from different ancestors. The bacterial flagellum shares a common ancestor with the type III secretion system,^[66][67] while archaeal flagella appear to have evolved from bacterial type IV pili.^[68] In contrast to the bacterial flagellum, which is hollow and is assembled by subunits moving up the central pore to the tip of the flagella, archaeal flagella are synthesized by adding subunits at the base

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.^[149][150] 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.^[151] 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.^[150] 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.^[152]

In contrast to 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.^[153] In mineral processing, acidophilic archaea display promise for the extraction of metals from ores, including gold, cobalt and copper.^[154]

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.^[155] 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.^[156]

Thermophiles are microorganisms that live and grow in extremely hot environments that would kill most other microorganisms. Thermophiles are grouped into either prokaryotes or eukaryotes, and these two groups of extremophiles are classified in the group of archaea. They grow best in temperatures that are between 50C/120F- 70C/158F. They will not grow if the temperature reaches 20C/68F. Thermophiles are not easy to study because the extreme conditions that they need to survive are hard to provide in a laboratory.

Thermophiles either live in geothermal habitats, or they live in environments that create heat themselves. A pile of compost and garbage landfills are two examples of environments that produce heat on their own.

Some thermophiles like, Chaetomium thermophile, Humicola insolens, Humicola (Thermomyces) lanuginosus , Thermoascus aurantiacus, a Paecilomyces-like fungus and Aspergillus fumigatus are microorganisms called fungi.

A microorganism that produces methane as a byproduct of its metabolism. All known methanogens are both archaeans and obligate anaerobes, that is, they cannot live in the presence of oxygen. They are commonly found in wetlands, where they generate methane in the form of marsh gas, and in the guts of animals such as ruminants and humans, where they are responsible for flatulence.

Some methanogens, described as hydrotropic, use carbon dioxide as a source of carbon and hydrogen as a source of energy. Some of the carbon dioxide reacts with, and is reduced by, hydrogen to produce methane. The methane is turn gives rise to a proton motive force across a membrane, which is used to generate ATP – a key source of cellular energy. Other methanogens, called acetotrophic, use acetate (CH₃COO-) as a source of both carbon and energy. Still other methanogens exploit methylated compounds such as methylamines, methanol, and methanethiol as well.

More than 50 species of methanogens have been identified, including a number that are extremophiles. Live methanogens were recovered from a core sample taken from 3 kilometers under Greenland by researchers from the University of California, Berkeley. Another study discovered methanogens in soil and vapor samples from the vicinity of the Mars Desert Research Station in Utah. These findings add weigh to speculation by some scientists that methanogens may be responsible for the methane that has been in detected in the atmosphere of Mars.

Halophiles are aerobic microorganisms that live and grow in high saline/salty environments. The saline content in halophilic environments is usually 10 times the saline/salt content of normal ocean water.. Normal ocean water has a saline/salt level of 30 percent. Some environments that halophiles live in are the Great Salt Lake in Utah, Owens Lake in California, the Dead Sea, and saltines (crackers). These microorganisms use osmotic pressure and chemical substances like sugars, alcohols, amino acids to help control the amount of salt inside the cell. Osmotic pressure is relationship of fluids on the inside and outside of a cell. Healthy cells keep the pressure the same on the inside and outside of the cells. Halophiles are like other extremophiles because the proteins inside the microorganisms play the most important role of making it possible for them to survive in extreme saline/salty environments.