Halobacterium salinarum | |
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Halobacterium salinarum NRC-1 Size bar = 270 nm | |
Scientific classification | |
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Species: | H. salinarum |
Binomial name | |
Halobacterium salinarum corrig. (Harrison and Kennedy 1922) Elazari-Volcani 1957 | |
Synonyms | |
Pseudomonas salinariaHarrison and Kennedy 1922 Contents |
Halobacterium salinarum, formerly known as Halobacterium cutirubrum or Halobacterium halobium, is an extremely halophilic marine obligate aerobic archaeon. Despite its name, this is not a bacterium, but a member of the domain Archaea. [2] It is found in salted fish, hides, hypersaline lakes, and salterns. As these salterns reach the minimum salinity limits for extreme halophiles, their waters become purple or reddish color due to the high densities of halophilic Archaea. [2] H. salinarum has also been found in high-salt food such as salt pork, marine fish, and sausages. The ability of H. salinarum to survive at such high salt concentrations has led to its classification as an extremophile.
Halobacteria are single-celled, rod-shaped microorganisms that are among the most ancient forms of life and appeared on Earth billions of years ago. The membrane consists of a single lipid bilayer surrounded by an S-layer. [3] The S-layer is made of a cell-surface glycoprotein that accounts for approximately 50% of the cell surface proteins. [4] These proteins form a lattice in the membrane. Sulfate residues are abundant on the glycan chains of the glycoprotein, giving it a negative charge. The negative charge is believed to stabilize the lattice in high-salt conditions. [5]
Amino acids are the main source of chemical energy for H. salinarum, particularly arginine and aspartate, though they are able to metabolize other amino acids, as well. [3] H. salinarum have been reported to be unable to grow on sugars, and therefore need to encode enzymes capable of performing gluconeogenesis to create sugars. Although H. salinarum is unable to catabolize glucose, the transcription factor TrmB has been proven to regulate the gluconeogenic production of sugars found on the S-layer glycoprotein.
To survive in extremely salty environments, this archaeon—as with other halophilic Archaeal species—utilizes compatible solutes (in particular, potassium chloride) to reduce osmotic stress. [6] Potassium levels are not at equilibrium with the environment, so H. salinarum express multiple active transporters that pump potassium into the cell. [3] At extremely high salt concentrations, protein precipitation will occur. To prevent the salting out of proteins, H. salinarum encodes mainly acidic proteins. The average isoelectric point of H. salinarum proteins is 5.03. [7] These highly acidic proteins are overwhelmingly negative in charge and are able to remain in solution even at high salt concentrations. [2]
H. salinarum can grow to such densities in salt ponds that oxygen is quickly depleted. Though it is an obligate aerobe, it is able to survive in low-oxygen conditions by utilizing light energy. H. salinarum expresses the membrane protein bacteriorhodopsin, [10] which acts as a light-driven proton pump. It consists of two parts: the 7-transmembrane protein, bacterioopsin, and the light-sensitive cofactor, retinal. Upon absorption of a photon, retinal changes its conformation, causing a conformational change in the bacterioopsin protein, as well, which drives proton transport. [11] The proton gradient formed thereby can then be used to generate chemical energy via ATP synthase.
To obtain more oxygen, H. salinarum produce gas vesicles, which allow them to float to the surface where oxygen levels are higher and more light is available. [12] These vesicles are complex structures made of proteins encoded by at least 14 genes. [13] Gas vesicles were first discovered in H. salinarum in 1967. [14]
There is little protection from the Sun in salt ponds, so H. salinarum are often exposed to high amounts of UV radiation. To compensate, they have evolved a sophisticated DNA repair mechanism. The genome encodes DNA repair enzymes homologous to those in both bacteria and eukaryotes. [2] This allows H. salinarum to repair damage to DNA faster and more efficiently than other organisms and allows them to be much more UV-tolerant.
Its red color is due primarily to the presence of bacterioruberin, a 50 carbon carotenoid Alcohol (polyol) pigment present within the membrane of H. salinarum. The primary role of bacterioruberin in the cell is to protect against DNA damage incurred by UV light. [15] This protection is not, however, due to the ability of bacterioruberin to absorb UV light. Bacterioruberin protects the DNA by acting as an antioxidant, rather than directly blocking UV light. [16] It is able to protect the cell from reactive oxygen species produced from exposure to UV by acting as a target. The bacterioruberin radical produced is less reactive than the initial radical, and will likely react with another radical, resulting in termination of the radical chain reaction. [17]
H. salinarum has been found to be responsible for the bright pink or red appearance of some bodies of hypersaline lakes, including pink lakes, such as the lake in Melbourne's Westgate Park; with the exact colour of the lake depending on the balance between the alga Dunaliella salina and H. salinarium, with salt concentration having a direct impact. [18] [19] However, recent studies at Lake Hillier in Western Australia have shown that other bacteria, notably Salinibacter ruber , along with algal and other factors, cause the pink color of these lakes. [20] [21] [22] [23] The researchers found 10 species of halophilic bacteria and archaea as well as several species of Dunaliella algae, nearly all of which contain some pink, red or salmon-coloured pigment. [22] [21]
H. salinarum is polyploid [24] and highly resistant to ionizing radiation and desiccation, conditions that induce DNA double-strand breaks. [25] Although chromosomes are initially shattered into many fragments, complete chromosomes are regenerated by making use of over-lapping fragments. Regeneration occurs by a process involving DNA single-stranded binding protein and is likely a form of homologous recombinational repair. [26]
Whole genome sequences are available for two strains of H. salinarum, NRC-1 [3] and R1. [27] The Halobacterium sp. NRC-1 genome consists of 2,571,010 base pairs on one large chromosome and two mini-chromosomes. The genome encodes 2,360 predicted proteins. [3] The large chromosome is very G-C rich (68%). [28] High GC-content of the genome increases stability in extreme environments. Whole proteome comparisons show the definite archaeal nature of this halophile with additional similarities to the Gram-positive Bacillus subtilis and other bacteria.
H. salinarum is as easy to culture as E. coli and serves as an excellent model system. Methods for gene replacement and systematic knockout have been developed, [29] so H. salinarum is an ideal candidate for the study of archaeal genetics and functional genomics.
Hydrogen production using H. salinarum coupled to a hydrogenase donor like E. coli are reported in literature. [30]
A sample of encapsulated inments from a close genetic relative of H. salinarum is estimated to be 121 million years old[ citation needed ]. Oddly, the material had also been recovered previously, but it was so similar to that of the modern descendants that the scientists who examined those earlier samples had mistakenly identified them as such, albeit contaminated.[ citation needed ]
Scientists have previously recovered similar genetic material from the Michigan Basin,[ clarification needed ] the same region where the latest discovery was made. But that DNA, discovered in a salt-cured buffalo hide in the 1930s, was so similar to that of modern microbes that many scientists believed the samples had been contaminated. [31] The curing salt had been derived from a mine in Saskatchewan, the site of the most recent sample described by Jong Soo Park of Dalhousie University in Halifax, Nova Scotia, Canada. [32]
Russell Vreeland of Ancient Biomaterials Institute of West Chester University in Pennsylvania, USA, performed an analysis of all known types of halophilic bacteria, which yielded the finding that Park's bacteria contained six segments of DNA never seen before in halophiles. Vreeland also tracked down the buffalo skin and determined that the salt came from the same mine as Park's sample. He has also discovered an even older halophile estimated at 250 million years old in New Mexico. [33] However, his findings date the crystal surrounding the bacteria, and DNA analysis suggests the bacteria themselves are likely to be less ancient. [34]
A halophile is an extremophile that thrives in high salt concentrations. In chemical terms, halophile refers to a Lewis acidic species that has some ability to extract halides from other chemical species.
Halobacterium is a genus in the family Halobacteriaceae.
Halobacteriaceae is a family in the order Halobacteriales and the domain Archaea. Halobacteriaceae represent a large part of halophilic Archaea, along with members in two other methanogenic families, Methanosarcinaceae and Methanocalculaceae. The family consists of many diverse genera that can survive extreme environmental niches. Most commonly, Halobacteriaceae are found in hypersaline lakes and can even tolerate sites polluted by heavy metals. They include neutrophiles, acidophiles, alkaliphiles, and there have even been psychrotolerant species discovered. Some members have been known to live aerobically, as well as anaerobically, and they come in many different morphologies. These diverse morphologies include rods in genus Halobacterium, cocci in Halococcus, flattened discs or cups in Haloferax, and other shapes ranging from flattened triangles in Haloarcula to squares in Haloquadratum, and Natronorubrum. Most species of Halobacteriaceae are best known for their high salt tolerance and red-pink pigmented members, but there are also non-pigmented species and those that require moderate salt conditions. Some species of Halobacteriaceae have been shown to exhibit phosphorus solubilizing activities that contribute to phosphorus cycling in hypersaline environments. Techniques such as 16S rRNA analysis and DNA-DNA hybridization have been major contributors to taxonomic classification in Halobacteriaceae, partly due to the difficulty in culturing halophilic Archaea.
Halobacteriales are an order of the Halobacteria, found in water saturated or nearly saturated with salt. They are also called halophiles, though this name is also used for other organisms which live in somewhat less concentrated salt water. They are common in most environments where large amounts of salt, moisture, and organic material are available. Large blooms appear reddish, from the pigment bacteriorhodopsin. This pigment is used to absorb light, which provides energy to create ATP. Halobacteria also possess a second pigment, halorhodopsin, which pumps in chloride ions in response to photons, creating a voltage gradient and assisting in the production of energy from light. The process is unrelated to other forms of photosynthesis involving electron transport; however, and halobacteria are incapable of fixing carbon from carbon dioxide.
Haloarchaea are a class of prokaryotic organisms under the archaeal phylum Euryarchaeota, found in water saturated or nearly saturated with salt. Halobacteria are now recognized as archaea rather than bacteria and are one of the largest groups. The name 'halobacteria' was assigned to this group of organisms before the existence of the domain Archaea was realized, and while valid according to taxonomic rules, should be updated. Halophilic archaea are generally referred to as haloarchaea to distinguish them from halophilic bacteria.
Microbial genetics is a subject area within microbiology and genetic engineering. Microbial genetics studies microorganisms for different purposes. The microorganisms that are observed are bacteria and archaea. Some fungi and protozoa are also subjects used to study in this field. The studies of microorganisms involve studies of genotype and expression system. Genotypes are the inherited compositions of an organism. Genetic Engineering is a field of work and study within microbial genetics. The usage of recombinant DNA technology is a process of this work. The process involves creating recombinant DNA molecules through manipulating a DNA sequence. That DNA created is then in contact with a host organism. Cloning is also an example of genetic engineering.
Sulfolobales is an order of archaeans in the class Thermoprotei.
Haloarcula is a genus of extreme halophilic Archaea in the class of Halobactaria.
Halocins are bacteriocins produced by halophilic Archaea and a type of archaeocin.
Archaea is a domain of single-celled organisms. These microorganisms lack cell nuclei and are therefore prokaryotic. Archaea were initially classified as bacteria, receiving the name archaebacteria, but this term has fallen out of use.
A pink lake is a lake that has a red or pink colour. This is often caused by the presence of salt-tolerant algae that produces carotenoids, such as Dunaliella salina, usually in conjunction with specific bacteria and archaea, which may vary from lake to lake. The most common archaeon is Halobacterium salinarum.
Haloferax volcanii is a species of organism in the genus Haloferax in the Archaea.
Halobacterium noricense is a halophilic, rod-shaped microorganism that thrives in environments with salt levels near saturation. Despite the implication of the name, Halobacterium is actually a genus of archaea, not bacteria. H. noricense can be isolated from environments with high salinity such as the Dead Sea and the Great Salt Lake in Utah. Members of the Halobacterium genus are excellent model organisms for DNA replication and transcription due to the stability of their proteins and polymerases when exposed to high temperatures. To be classified in the genus Halobacterium, a microorganism must exhibit a membrane composition consisting of ether-linked phosphoglycerides and glycolipids.
Gas vesicles, also known as gas vacuoles, are nanocompartments in certain prokaryotic organisms, which help in buoyancy. Gas vesicles are composed entirely of protein; no lipids or carbohydrates have been detected.
Salinibacter ruber is an extremely halophilic red bacterium, first found in Spain in 2002.
Shiladitya DasSarma is a molecular biologist well-known for contributions to the biology of halophilic and extremophilic microorganisms. He is a Professor in the University of Maryland Baltimore. He earned a PhD degree in biochemistry from the Massachusetts Institute of Technology and a BS degree in chemistry from Indiana University Bloomington. Prior to taking a faculty position, he conducted research at the Massachusetts General Hospital, Harvard Medical School, and Pasteur Institute, Paris.
Haloferax mediterranei is a species of archaea in the family Haloferacaceae.
Archaerhodopsin proteins are a family of retinal-containing photoreceptors found in the archaea genera Halobacterium and Halorubrum. Like the homologous bacteriorhodopsin (bR) protein, archaerhodopsins harvest energy from sunlight to pump H+ ions out of the cell, establishing a proton motive force that is used for ATP synthesis. They have some structural similarities to the mammalian G protein-coupled receptor protein rhodopsin, but are not true homologs.
Natrialbales is an order of halophilic, chemoorganotrophic archaea within the class Haloarchaea. The type genus of this order is Natrialba.
Halorubrum kocurii is a halophilic archaean belonging to the genus Halorubrum. This genus contains a total of thirty-seven different species, all of which thrive in high-salinity environments. Archaea belonging to this genus are typically found in hypersaline environments due to their halophilic nature, specifically in solar salterns. Halorubrum kocurii is a rod-shaped, Gram-negative archaeon. Different from its closest relatives, Halorubrum kocurii is non-motile and contains no flagella or cilia. This archaeon thrives at high pH levels, high salt concentrations, and moderate temperatures. It has a number of close relatives, including Halorubrum aidingense, Halorubrum lacusprofundi, and more.
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