ARCHAEBACTERIA

          The Archaea constitute a domain and kingdom of single-celled microorganisms. These microbes are prokaryotes, meaning that they have no true nucleus or any other membrane-bound organelles in their cells. Archaea were initially classified as bacteria, receiving the name Archaebacteria (in the Archaebacteria kingdom), but this classification is outdated. Archaeal cells have unique properties separating them from bacteria and from eukaryotes. The Archaea are further divided into multiple recognized phyla. Classification is difficult because majority of these has not been isolated in the laboratory and have only been detected by analysis of their nucleic acids in samples from their environment.

               HABITATS:

              Archae live on wide range of habitats. Based on the habitat, Archae are divided into the following groups –

         1. Extremophiles:- Extremophile archaea are members of four main physiological groups. These are the halophiles, thermophiles, alkaliphiles, and acidophiles.

            Halophiles, including the genus Halobacterium, live in extremely saline environments such as salt lakes and outnumber their bacterial counterparts at salinities greater than 20–25%. Thermophiles grow best at temperatures above 45 °C (113 °F), in places such as hot springs; hyperthermophilic archaea grow optimally at temperatures greater than 80 °C (176 °F). The archaeal Methanopyrus kandleri Strain 116 can even reproduce at 122 °C (252 °F), the highest recorded temperature of any organism. Alkaliphiles and Acidophiles archaea exist in very alkaline and acidic 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.

            2. Mesophiles:- Archaea include mesophiles that grow in mild conditions, in swamps and marshland, sewage, the oceans, the intestinal tract of animals and soils.

            3. Extra-terrestrial:- Resistance to extreme environments has made archaea the focus of speculation about the possible properties of extraterrestrial life. Some extremophile habitats are not similar to those on Mars, leading to the suggestion that viable microbes could be transferred between planets in meteorites.

             4. Aquatic Archae:- Large numbers of Archaea found throughout the world's oceans in non-extreme habitats among the plankton community (as part of the picoplankton). Some marine Crenarchaeota are capable of nitrification, suggesting these organisms may affect the oceanic nitrogen cycle. Vast numbers of archaea are also found in the sediments that cover the sea floor, with these organisms making up the majority of living cells at depths over 1 meter below the ocean bottom. Some Archaea are common in cold oceanic environments such as polar seas.

             MORPHOLOGY:

            1. Shape and Size:- Individual archaea range from 0.1 – 1.5 μm in diameter, and occur in various shapes, commonly as spheres, rods, spirals or plates. Other morphologies in the Crenarchaeota include irregularly shaped lobed cells in Sulfolobus, needle-like filaments that are less than half a micrometer in diameter in Thermofilum, and almost perfectly rectangular rods in Thermoproteus and Pyrobaculum. Haloquadratum walsbyi are flat, square archaea that live in hypersaline pools.

            Some species form aggregates or filaments of cells up to 200 μm long. These organisms can be prominent in biofilms. Notably, aggregates of Thermococcus coalescens cells fuse together in culture, forming single giant cells.  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. Multi-species colonies exist, such as the "string-of-pearls" community that was discovered in 2001 in a German that can range up to 15 centimetres (5.9 in) long; these filaments are made of a particular bacteria species.

            2. Cell Wall and Flagella:- Archaea and bacteria have generally similar cell structure, but cell composition and organization set the archaea apart. Like bacteria, archaea lack interior membranes and organelles. Like bacteria, archaea cell membranes are usually bounded by a cell wall and they swim using one or more flagella. Structurally, archaea are most similar to gram-positive bacteria.

            Most archaea (but not Thermoplasma and Ferroplasma) possess a cell wall. In most archaea the wall is assembled from surface-layer proteins, which form an S-layer. An S-layer is 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 prevent macromolecules from contacting the cell membrane. Unlike bacteria, archaea lack peptidoglycan in their cell walls.^[101] 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.

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

            3. Membranes:- Archaeal membranes are made of molecules that differ strongly from those in other life forms, showing that archaea are related only distantly to bacteria and eukaryotes. 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.

               METABOLISM:

            Archaea exhibit a great variety of chemical reactions in their metabolism and use many sources of energy. These reactions are classified into nutritional groups, depending on energy and carbon sources. These are as follows –

            1. Lithotrophs:- Some archaea obtain energy from inorganic compounds such as sulfur or ammonia (they are lithotrophs). These include nitrifiers, methanogens and anaerobic methane oxidisers. 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 generates adenosine triphosphate (ATP) through chemiosmosis, in the same basic process that happens in the mitochondrion of eukaryotic cells.

            2. Phototrophs:- 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 to other organisms probably reflect both early origins in the history of life and their high level of efficiency.

            Phototrophic archaea use light to produce chemical energy in the form of ATP. In the Halobacteria, light-activated ion pumps like bacteriorhodopsin and halorhodopsin generate ion gradients by pumping ions out of the cell across the plasma membrane. The energy stored in these electrochemical gradients is then converted into ATP by ATP synthase. 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.

            3. Authotrophs:- Other archaea use CO₂ in the atmosphere as a source of carbon, in a process called carbon fixation (they are autotrophs). This process involves either a highly modified form of the Calvin cycle or a recently discovered metabolic pathway called the 3-hydroxypropionate/4-hydroxybutyrate cycle. The Crenarchaeota also use the reverse Krebs cycle while the Euryarchaeota also use the reductive acetyl-CoA pathway. Carbon–fixation is powered by inorganic energy sources. No known archaea carry out photosynthesis.  Archaeal energy sources are extremely diverse, and range from the oxidation of ammonia by the Nitrosopumilales to the oxidation of hydrogen sulfide or elemental sulfur by species of Sulfolobus, using either oxygen or metal ions as electron acceptors.

            4. Methanogens:- Some Euryarchaeota are methanogens living in anaerobic environments, such as swamps. This form of metabolism evolved early, and it is even possible that the first free-living organism was a methanogen. A common reaction involves the use of carbon dioxide as an electron acceptor to oxidize hydrogen. Methanogenesis involves a range of coenzymes that are unique to these archaea, such as coenzyme M and methanofuran. 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.

                 REPRODUCTION:

            Archaea 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, all have the same genetic material. Cell division is controlled in a cell cycle; after the cell's chromosome is replicated and the two daughter chromosomes separate, the cell divides.

            In 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.

            In euryarchaea the cell division protein FtsZ, which forms a contracting ring around the cell, and the components of the septum that is constructed across the center of the cell, are similar to their bacterial equivalents. In crenarchaea and thaumarchaea, however, 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.

            Both bacteria and eukaryotes, but not archaea, make spores. 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. These are not reproductive structures and may instead help them reach new habitats.

                  CLASSIFICATION:

            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. These classifications rely heavily on the use of the sequence of ribosomal RNA genes to reveal relationships between organisms (molecular phylogenetics). Most of the culturable and well-investigated species of archaea are members of two main phyla, the Euryarchaeota and Crenarchaeota. Other groups have been tentatively created. For example, the peculiar species Nanoarchaeum equitans, which was discovered in 2003, has been given its own phylum, the Nanoarchaeota. A new phylum Korarchaeota has also been proposed. It contains a small group of unusual thermophilic species that shares features of both of the main phyla, but is most closely related to the Crenarchaeota. Other recently detected species of archaea are only distantly related to any of these groups, such as the Archaeal Richmond Mine acidophilic nanoorganisms (ARMAN), which were discovered in 2006 and are some of the smallest organisms known.

            A superphylum – TACK, has been proposed that includes the Thaumarchaeota, Aigarchaeota, Crenarchaeota, and Korarchaeota. This superphylum may be related to the origin of eukaryotes.

            Concept of Species:- The classification of archaea into species is also controversial. Biology defines a species as a group of related organisms. The familiar exclusive breeding criterion (organisms that can breed with each other but not with others) is of no help here because archaea reproduce asexually.

            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. On the other hand, studies in Halorubrum found significant genetic transfer to/from less-related populations, limiting the criterion's applicability. A second concern is to what extent such species designations have practical meaning.

            Current knowledge on genetic diversity is fragmentary and the total number of archaeal species cannot be estimated with any accuracy. Estimates of the number of phyla range from 18 to 23, out 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. The Bacteria also contain many uncultured microbes with similar implications for characterization.

               IMPORTANCE OF ARCHAEA:

            1. Role in chemical cycling:- 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). Researchers recently discovered archaeal involvement in ammonia oxidation reactions. These reactions are particularly important in the oceans. 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. 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.

            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.

            Global methane levels in 2011 had increased by a factor of 2.5 since pre-industrial times: from 722 ppb to 1800 ppb, the highest value in at least 800,000 years. Methane has an anthropogenic global warming potential (AGWP) of 29, which means that it's 29 times stronger in heat-trapping than carbon dioxide is, over a 100-year time scale.

            2. Interactions with other organisms:- The well-characterized interactions between archaea and other organisms are either mutual or commensal. There are no clear examples of known archaeal pathogens or parasites. However, some species of methanogens have been suggested to be involved in infections in the mouth, 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,^[181] and appears to offer no benefit to its host. In contrast, Archaeal Richmond Mine Acidophilic Nanoorganisms (ARMAN) occasionally connect with other archaeal cells in acid mine drainage biofilms. The nature of this relationship is unknown. However, it is distinct from that of Nanarchaeaum–Ignicoccus in that the ultrasmall ARMAN cells are usually seen independent of the Thermoplasmatales cells.

                     Mutualism

            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. 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.

            In anaerobic protozoa, such as Plagiopyla frontata, archaea reside inside the protozoa and consume hydrogen produced in their hydrogenosomes. Archaea also associate with larger organisms. For example, the marine archaean Cenarchaeum symbiosum lives within (is an endosymbiont of) 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 archaean in the human flora, making up about one in ten of all the prokaryotes in the human gut. In termites and in humans, these methanogens may in fact be mutualists, interacting with other microbes in the gut to aid digestion. Archaean communities also associate with a range of other organisms, such as on the surface of corals, and in the region of soil that surrounds plant roots (the rhizosphere).

            3. Significance in technology and industry:- Extremophile archaea, particularly those resistant either to heat or to extremes of acidity and alkalinity, are a source of enzymes that function under these harsh conditions. 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. 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. 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.

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

            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.

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