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Haloarchaea (halophilic archaea, halophilic archaebacteria, halobacteria) are a class of the
Euryarchaeota Euryarchaeota (from Ancient Greek ''εὐρύς'' eurús, "broad, wide") is a phylum of archaea. Euryarchaeota are highly diverse and include methanogens, which produce methane and are often found in intestines, halobacteria, which survive extr ...
, found in
water Water (chemical formula ) is an Inorganic compound, inorganic, transparent, tasteless, odorless, and Color of water, nearly colorless chemical substance, which is the main constituent of Earth's hydrosphere and the fluids of all known living ...
saturated or nearly saturated with
salt Salt is a mineral composed primarily of sodium chloride (NaCl), a chemical compound belonging to the larger class of salts; salt in the form of a natural crystalline mineral is known as rock salt or halite. Salt is present in vast quant ...
. Halobacteria are now recognized as archaea rather than
bacteria Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one Cell (biology), biological cell. They constitute a large domain (biology), domain of prokaryotic microorganisms. Typically a few micrometr ...
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. These
microorganism A microorganism, or microbe,, ''mikros'', "small") and ''organism'' from the el, ὀργανισμός, ''organismós'', "organism"). It is usually written as a single word but is sometimes hyphenated (''micro-organism''), especially in olde ...
s are among the
halophile The halophiles, named after the Greek word for "salt-loving", are extremophiles that thrive in high salt concentrations. While most halophiles are classified into the domain Archaea, there are also bacterial halophiles and some eukaryotic species, ...
organisms, that they require high salt concentrations to grow, with most species requiring more than 2.0M
NaCl Sodium chloride , commonly known as salt (although sea salt also contains other chemical salts), is an ionic compound with the chemical formula NaCl, representing a 1:1 ratio of sodium and chloride ions. With molar masses of 22.99 and 35.45 g/ ...
for growth and survival. They are a distinct evolutionary branch of the Archaea distinguished by the possession of ether-linked
lipid Lipids are a broad group of naturally-occurring molecules which includes fats, waxes, sterols, fat-soluble vitamins (such as vitamins A, D, E and K), monoglycerides, diglycerides, phospholipids, and others. The functions of lipids includ ...
s and the absence of murein in their cell walls. Haloarchaea can grow aerobically or anaerobically. Parts of the
membrane A membrane is a selective barrier; it allows some things to pass through but stops others. Such things may be molecules, ions, or other small particles. Membranes can be generally classified into synthetic membranes and biological membranes. ...
s of haloarchaea are purplish in color, and large blooms of haloarchaea appear reddish, from the pigment bacteriorhodopsin, related to the
retinal Retinal (also known as retinaldehyde) is a polyene chromophore. Retinal, bound to proteins called opsins, is the chemical basis of visual phototransduction, the light-detection stage of visual perception (vision). Some microorganisms use reti ...
pigment rhodopsin, which it uses to transform light energy into chemical energy by a process unrelated to chlorophyll-based
photosynthesis Photosynthesis is a process used by plants and other organisms to convert light energy into chemical energy that, through cellular respiration, can later be released to fuel the organism's activities. Some of this chemical energy is stored i ...
. Haloarchaea have a potential to solubilize phosphorus. Phosphorus-solubilizing halophilic archaea may well play a role in P (phosphorus) nutrition to vegetation growing in hypersaline soils. Haloarchaea may also have applications as inoculants for crops growing in hypersaline regions.


Taxonomy

The extremely halophilic, aerobic members of Archaea are classified within the family Halobacteriaceae, order Halobacteriales in Class III. Halobacteria of the phylum Euryarchaeota (International Committee on Systematics of Prokaryotes, Subcommittee on the taxonomy of Halobacteriaceae). As of May 2016, the family Halobacteriaceae comprises 213 species in 50 genera. Gupta et al. divides the class of Halobacteria in three orders. *
Halobacteriales In taxonomy, the 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 ...
Grant and Larsen 1989 ** Haloarculaceae Gupta et al. 2016, 10 genera ** Halobacteriaceae Gibbons 1974, 24 genera ** Halococcaceae Gupta et al. 2016, 1 genus *
Haloferacales ''Haloferacales'' is an order of halophilic, chemoorganotrophic or heterotrophic archaea within the class Haloarchaea. The type genus of this order is ''Haloferax.'' The name ''Haloferacales'' is derived from the Latin term ''Haloferax,'' referri ...
Gupta et al. 2015 **
Haloferacaceae ''Haloferacaceae'' is a family of halophilic, chemoorganotrophic or heterotrophic archaea within the order '' Haloferacales.'' The type genus of this family is ''Haloferax.'' Its biochemical characteristics are the same as the order '' Haloferaca ...
Gupta et al. 2015, 10 genera ** Halorubraceae Gupta et al. 2016, 9 genera *
Natrialbales ''Natrialbales'' is an order of halophilic, chemoorganotrophic archaea within the class Haloarchaea. The type genus of this order is ''Natrialba.'' The name ''Natrialbales'' is derived from the Latin term ''Natriabla,'' referring to the type gen ...
Gupta et al. 2015 **
Natrialbaceae ''Natrialbales'' is an order of halophilic, chemoorganotrophic archaea within the class Haloarchaea. The type genus of this order is ''Natrialba.'' The name ''Natrialbales'' is derived from the Latin term ''Natriabla,'' referring to the type gen ...
Gupta et al. 2015, 18 genera


Phylogeny

The currently accepted taxonomy is based on the
List of Prokaryotic names with Standing in Nomenclature List of Prokaryotic names with Standing in Nomenclature (LPSN) is an online database that maintains information on the nomenclature, naming and Taxonomy (biology), taxonomy of prokaryotes, following the taxonomy requirements and rulings of the In ...
(LPSN) and
National Center for Biotechnology Information The National Center for Biotechnology Information (NCBI) is part of the United States National Library of Medicine (NLM), a branch of the National Institutes of Health (NIH). It is approved and funded by the government of the United States. The ...
(NCBI). Note: * paraphyletic Halobacteriaceae


Molecular Signatures

Detailed phylogenetic and comparative analyses of genome sequences from members of the class Haloarchaea has led to division of this class into three orders, ''
Halobacteriales In taxonomy, the 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 ...
,
Haloferacales ''Haloferacales'' is an order of halophilic, chemoorganotrophic or heterotrophic archaea within the class Haloarchaea. The type genus of this order is ''Haloferax.'' The name ''Haloferacales'' is derived from the Latin term ''Haloferax,'' referri ...
'' and ''
Natrialbales ''Natrialbales'' is an order of halophilic, chemoorganotrophic archaea within the class Haloarchaea. The type genus of this order is ''Natrialba.'' The name ''Natrialbales'' is derived from the Latin term ''Natriabla,'' referring to the type gen ...
'', which can be reliably distinguished from each other as well as all other archaea/bacteria through molecular signatures known as conserved signature indels. These studies have also identified 68 conserved signature proteins (CSPs) whose homologs are only found in the members of these three orders and 13
conserved signature indels Conserved signature inserts and deletions (CSIs) in protein sequences provide an important category of molecular markers for understanding phylogenetic relationships. CSIs, brought about by rare genetic changes, provide useful phylogenetic markers ...
(CSIs) in different proteins that are uniquely present in the members of the class Haloarchaea. These CSIs are present in the following proteins: DNA topoisomerase VI, nucleotide sugar dehydrogenase,
ribosomal protein A ribosomal protein (r-protein or rProtein) is any of the proteins that, in conjunction with rRNA, make up the ribosomal subunits involved in the cellular process of translation. ''E. coli'', other bacteria and Archaea have a 30S small subunit an ...
L10e, RecJ-like exonuclease,
ribosomal protein A ribosomal protein (r-protein or rProtein) is any of the proteins that, in conjunction with rRNA, make up the ribosomal subunits involved in the cellular process of translation. ''E. coli'', other bacteria and Archaea have a 30S small subunit an ...
S15, adenylosuccinate synthase,
phosphopyruvate hydratase Phosphopyruvate hydratase, usually known as enolase, is a metalloenzyme () that catalyses the conversion of 2-phosphoglycerate (2-PG) to phosphoenolpyruvate (PEP), the ninth and penultimate step of glycolysis. The chemical reaction is: :2-p ...
, RNA-associated protein,
threonine synthase The enzyme threonine synthase (EC 4.2.3.1) catalyzes the chemical reaction :''O''-phospho-L-homoserine + H2O \rightleftharpoons L-threonine + phosphate This enzyme belongs to the family of lyases, specifically those carbon-oxygen lyases acting ...
,
aspartate aminotransferase Aspartate transaminase (AST) or aspartate aminotransferase, also known as AspAT/ASAT/AAT or (serum) glutamic oxaloacetic transaminase (GOT, SGOT), is a pyridoxal phosphate (PLP)-dependent transaminase enzyme () that was first described by Arthur ...
, precorrin-8x methylmutase, protoporphyrin IX magnesium chelatase and geranylgeranylglyceryl phosphate synthase-like protein.


Living environment

Haloarchaea require salt concentrations in excess of 2 mol/L (or about 10%, three times the ocean salinity which is around 35g/L salt – 3.5%) in the to grow, and optimal growth usually occurs at much higher concentrations, typically 20–30% (3.4 - 5.2 mol/L of
NaCl Sodium chloride , commonly known as salt (although sea salt also contains other chemical salts), is an ionic compound with the chemical formula NaCl, representing a 1:1 ratio of sodium and chloride ions. With molar masses of 22.99 and 35.45 g/ ...
). However, Haloarchaea can grow up to saturation (about 37% salts). Optimal growth also occurs when pH is neutral or basic and temperatures at 45°C. Some haloarchaea though can grow even when temperatures exceed 50°C. Haloarchaea are found mainly in hypersaline lakes and solar salterns. Their high densities in the water often lead to pink or red colourations of the water (the cells possessing high levels of carotenoid pigments, presumably for UV protection). The pigmentation will become enhanced when oxygen levels are low due to an increase in a red pigmented ATP. Some of them live in underground rock salt deposits, including one from middle-late
Eocene The Eocene ( ) Epoch is a geological epoch that lasted from about 56 to 33.9 million years ago (mya). It is the second epoch of the Paleogene Period in the modern Cenozoic Era. The name ''Eocene'' comes from the Ancient Greek (''ēṓs'', " ...
(38-41 million years ago). Some even older ones from more than 250 million years ago have been reported. Haloarchaea is also used to treat water that is high in salinity. This is due to its ability to its ability to withstand high nutrient levels and the heavy metals that may be present.


Adaptations to environment

Haloarchaea can grow at an aw close to 0.75, yet a
water activity Water activity (''aw'') is the partial vapor pressure of water in a solution divided by the standard state partial vapor pressure of water. In the field of food science, the standard state is most often defined as pure water at the same tempe ...
(aw) lower than 0.90 is inhibitory to most microbes. The number of solutes causes osmotic stress on microbes, which can cause cell lysis, unfolding of proteins and inactivation of enzymes when there is a large enough imbalance. Haloarchaea combat this by retaining
compatible solutes Osmoprotectants or compatible solutes are small organic molecules with neutral charge and low toxicity at high concentrations that act as osmolytes and help organisms survive extreme osmotic stress. Osmoprotectants can be placed in three chemical ...
such as potassium chloride (KCl) in their
intracellular space Intracellular space is the interior space of the plasma membrane. It contains about two-thirds of TBW. Cellular rupture may occur if the intracellular space becomes dehydrated, or if the opposite happens, where it becomes too bloated. Thus it i ...
to allow them to balance osmotic pressure. Retaining these salts is referred to as the “salt-in” method where the cell accumulates a high internal concentration of potassium. Because of the elevated potassium levels, haloarchaea have specialized proteins that have a highly negative surface charge to tolerate high potassium concentrations. Haloarchaea have adapted to use
glycerol Glycerol (), also called glycerine in British English and glycerin in American English, is a simple triol compound. It is a colorless, odorless, viscous liquid that is sweet-tasting and non-toxic. The glycerol backbone is found in lipids known ...
as a carbon and energy source in catabolic processes, which is often present in high salt environments due to
Dunaliella ''Dunaliella'' is a single-celled, photosynthetic green alga, that is characteristic for its ability to outcompete other organisms and thrive in hypersaline environments. It is mostly a marine organism, though there are a few freshwater species ...
species that produce glycerol in large quantities.


Phototrophy

Bacteriorhodopsin is used to absorb light, which provides energy to transport protons (H+) across the cellular membrane. The concentration gradient generated from this process can then be used to synthesize ATP. Many haloarchaea also possess related pigments, including
halorhodopsin Halorhodopsin is a light-gated ion pump, specific for chloride ions, found in archaea, known as halobacteria. It is a seven-transmembrane retinylidene protein from microbial rhodopsin family. It is similar in tertiary structure (but not primary se ...
, which pumps chloride ions in the cell 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 Photosynthesis is a process used by plants and other organisms to convert light energy into chemical energy that, through cellular respiration, can later be released to fuel the organism's activities. Some of this chemical energy is stored i ...
involving electron transport, however, and haloarchaea are incapable of fixing carbon from
carbon dioxide Carbon dioxide ( chemical formula ) is a chemical compound made up of molecules that each have one carbon atom covalently double bonded to two oxygen atoms. It is found in the gas state at room temperature. In the air, carbon dioxide is trans ...
. Early evolution of retinal proteins has been proposed as the purple Earth hypothesis.


Cellular shapes

Haloarchaea are often considered pleomorphic, or able to take on a range of shapes—even within a single species. This makes identification by microscopic means difficult, and it is now more common to use gene sequencing techniques for identification instead. One of the more unusually shaped Haloarchaea is the " Square Haloarchaeon of Walsby". It was classified in 2004 using a very low nutrition solution to allow growth along with a high salt concentration, square in shape and extremely thin (like a
postage stamp A postage stamp is a small piece of paper issued by a post office, postal administration, or other authorized vendors to customers who pay postage (the cost involved in moving, insuring, or registering mail), who then affix the stamp to the f ...
). This shape is probably only permitted by the high
osmolarity Osmotic concentration, formerly known as osmolarity, is the measure of solute concentration, defined as the number of osmoles (Osm) of solute per litre (L) of solution (osmol/L or Osm/L). The osmolarity of a solution is usually expressed as Osm/L ...
of the water, permitting cell shapes that would be difficult, if not impossible, under other conditions.


As exophiles

Haloarchaea have been proposed as a kind of life that could live on Mars; since the Martian atmosphere has a pressure below the
triple point In thermodynamics, the triple point of a substance is the temperature and pressure at which the three phases (gas, liquid, and solid) of that substance coexist in thermodynamic equilibrium.. It is that temperature and pressure at which the sub ...
of water, freshwater species would have no habitat on the Martian surface. The presence of high salt concentrations in water lowers its freezing point, in theory allowing for halophiles to exist in saltwater on Mars. Recently, haloarchaea was sent 36 km (about 22 miles) up into Earths atmosphere, within a balloon. The two types that were sent up were able to survive the freezing temperatures and high radiation levels. This only further extends the theory that halophiles could exist on Mars.


Medical Use

Certain types of haloarchaea have been found to produce
carotenoids Carotenoids (), also called tetraterpenoids, are yellow, orange, and red organic pigments that are produced by plants and algae, as well as several bacteria, and fungi. Carotenoids give the characteristic color to pumpkins, carrots, parsnips, co ...
, which normally has to be synthesized using chemicals. With haloarchaea naturally producing it, there is now a natural way to synthesize carotenoids for medical use. Haloarchaea has also been proposed to help meet the high demand of carotenoids by pharmaceutical companies due to how easy it can be grown in a lab. Genes in Haloarchaea can also be manipulated in order to produce various strands of carotenoids, further helping meet pharmaceutical companies needs. Haloarchaea is also present within the human gut, mostly predominant in the gut of people who live in
Korea Korea ( ko, 한국, or , ) is a peninsular region in East Asia. Since 1945, it has been divided at or near the 38th parallel, with North Korea (Democratic People's Republic of Korea) comprising its northern half and South Korea (Republic o ...
. Haloarchaea are most abundant in Koreans guts rather than
methanogens Methanogens are microorganisms that produce methane as a metabolic byproduct in hypoxic conditions. They are prokaryotic and belong to the domain Archaea. All known methanogens are members of the archaeal phylum Euryarchaeota. Methanogens are co ...
due to their saltier diets. This also shows that the archaeome in the human gut can vary drastically depending on region and what is eaten.


Climate Change

Haloarchaea have been proposed that certain types can be used to make biodegradable plastics, which could help decrease
plastic pollution Plastic pollution is the accumulation of plastic objects and particles (e.g. plastic bottles, bags and microbeads) in the Earth's environment that adversely affects humans, wildlife and their habitat. Plastics that act as pollutants are catego ...
. Haloarchaea are able to produce polyhydroxyalkanote (PHA),
polyhydroxybutyrate Polyhydroxybutyrate (PHB) is a polyhydroxyalkanoate (PHA), a polymer belonging to the polyesters class that are of interest as bio-derived and biodegradable plastics. The poly-3-hydroxybutyrate (P3HB) form of PHB is probably the most common typ ...
(PHB) and polyhydroxyvalerate (PHV), when exposed to certain conditions. For large scale production of these
bioplastics Bioplastics are plastic materials produced from renewable biomass sources, such as vegetable fats and oils, corn starch, straw, woodchips, sawdust, recycled food waste, etc. Some bioplastics are obtained by processing directly from natural ...
, haloarchaea is favored due to the low cost, fast growth, and lack of need to sterilize area due to the salty environment they prefer. They are also a cleaner option for bioplastics due to them not needing chemicals for
cell lysis Lysis ( ) is the breaking down of the membrane of a cell, often by viral, enzymic, or osmotic (that is, "lytic" ) mechanisms that compromise its integrity. A fluid containing the contents of lysed cells is called a ''lysate''. In molecular bio ...
and have a higher recyclability of the process. Certain types of haloarchaea have also been found to poses
denitrifying Denitrification is a microbially facilitated process where nitrate (NO3−) is reduced and ultimately produces molecular nitrogen (N2) through a series of intermediate gaseous nitrogen oxide products. Facultative anaerobic bacteria perform denitr ...
characteristics. If haloarchaea are complete denitrifies, they could aid salt marsh and other salty environments by buffering these areas of nitrate and nitrite. This could help animal diversity and decrease pollution with in these waterways. However, when tested in the lab, haloarchaea have been found to be partial denitrifies. This means that if haloarchaea are used to treat areas that are high in nitrite and nitrate, they could contribute to nitrogen contaminates and cause an increase in ozone depletion, furthering climate change. The only type of haloarchaea that has been found to reduce nitrogen pollution to atmospheric nitrogen has been Haloferax mediterranei. This shows that haloarchaea may be contributing to nitrogen pollution and isn't a suitable solution to reducing nitrate and nitrite within high salinity areas.   


See also

*
Life on Mars The possibility of life on Mars is a subject of interest in astrobiology due to the planet's proximity and similarities to Earth. To date, no proof of past or present life has been found on Mars. Cumulative evidence suggests that during the ...
* Purple Earth hypothesis * List of Archaea genera


References


Further reading


Journals

* * * *


Books

* *


Databases


External links


An educational website on haloarchaeaHaloArchaea.com
{{Taxonbar, from=Q1054206 Halophiles Euryarchaeota Archaea classes