Haloarchaea (halophilic archaea, halophilic archaebacteria, halobacteria) are a

class Class, Classes, or The Class may refer to: Common uses not otherwise categorized * Class (biology), a taxonomic rank * Class (knowledge representation), a collection of individuals or objects * Class (philosophy), an analytical concept used d ...

prokaryotic A prokaryote (; less commonly spelled procaryote) is a single-celled organism whose cell lacks a nucleus and other membrane-bound organelles. The word ''prokaryote'' comes from the Ancient Greek (), meaning 'before', and (), meaning 'nut' ...

archaea Archaea ( ) is a Domain (biology), domain of organisms. Traditionally, Archaea only included its Prokaryote, prokaryotic members, but this has since been found to be paraphyletic, as eukaryotes are known to have evolved from archaea. Even thou ...

under the

phylum In biology, a phylum (; : phyla) is a level of classification, or taxonomic rank, that is below Kingdom (biology), kingdom and above Class (biology), class. Traditionally, in botany the term division (taxonomy), division has been used instead ...

Euryarchaeota Methanobacteriota is a phylum in the domain Archaea. Taxonomy The phylum ''Methanobacteriota'' was introduced to prokaryotic nomenclature in 2023. It contains following classes: *Archaeoglobi Garrity & Holt (2002) *Halobacteria Grant ''et al ...

, found in

water Water is an inorganic compound with the chemical formula . It is a transparent, tasteless, odorless, and Color of water, nearly colorless chemical substance. It is the main constituent of Earth's hydrosphere and the fluids of all known liv ...

saturated or nearly saturated with

salt In common usage, salt is a mineral composed primarily of sodium chloride (NaCl). When used in food, especially in granulated form, it is more formally called table salt. In the form of a natural crystalline mineral, salt is also known as r ...

. 'Halobacteria' are now recognized as archaea rather than

bacteria Bacteria (; : bacterium) are ubiquitous, mostly free-living organisms often consisting of one Cell (biology), biological cell. They constitute a large domain (biology), domain of Prokaryote, prokaryotic microorganisms. Typically a few micr ...

and are one of the largest groups of archaea. The name 'halobacteria' was assigned to this group of organisms before the existence of the domain

Archaea Archaea ( ) is a Domain (biology), domain of organisms. Traditionally, Archaea only included its Prokaryote, prokaryotic members, but this has since been found to be paraphyletic, as eukaryotes are known to have evolved from archaea. Even thou ...

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

halophilic A halophile (from the Greek word for 'salt-loving') 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. ...

microorganism A microorganism, or microbe, is an organism of microscopic scale, microscopic size, which may exist in its unicellular organism, single-celled form or as a Colony (biology)#Microbial colonies, colony of cells. The possible existence of unseen ...

s require high salt concentrations to grow, with most species requiring more than 2M

NaCl Sodium chloride , commonly known as edible salt, is an ionic compound with the chemical formula NaCl, representing a 1:1 ratio of sodium and chloride ions. It is transparent or translucent, brittle, hygroscopic, and occurs as the mineral hali ...

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 organic compounds which include fats, waxes, sterols, fat-soluble vitamins (such as vitamins A, D, E and K), monoglycerides, diglycerides, phospholipids, and others. The functions of lipids include storing ...

s and the absence of murein in their

cell wall A cell wall is a structural layer that surrounds some Cell type, cell types, found immediately outside the cell membrane. It can be tough, flexible, and sometimes rigid. Primarily, it provides the cell with structural support, shape, protection, ...

s. 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. Bi ...

s of haloarchaea are purplish in color, and large blooms of haloarchaea appear reddish from the pigment

bacteriorhodopsin Bacteriorhodopsin (Bop) is a protein used by Archaea, most notably by Haloarchaea, a class of the Euryarchaeota. It acts as a proton pump; that is, it captures light energy and uses it to move protons across the membrane out of the cell. The res ...

, 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 ret ...

pigment

rhodopsin Rhodopsin, also known as visual purple, is a protein encoded by the ''RHO'' gene and a G-protein-coupled receptor (GPCR). It is a light-sensitive receptor protein that triggers visual phototransduction in rod cells. Rhodopsin mediates dim ...

, which it uses to transform light energy into chemical energy by a process unrelated to

chlorophyll Chlorophyll is any of several related green pigments found in cyanobacteria and in the chloroplasts of algae and plants. Its name is derived from the Greek words (, "pale green") and (, "leaf"). Chlorophyll allows plants to absorb energy ...

-based

photosynthesis Photosynthesis ( ) is a system of biological processes by which photosynthetic organisms, such as most plants, algae, and cyanobacteria, convert light energy, typically from sunlight, into the chemical energy necessary to fuel their metabo ...

. Haloarchaea have a potential to solubilize

phosphorus Phosphorus is a chemical element; it has Chemical symbol, symbol P and atomic number 15. All elemental forms of phosphorus are highly Reactivity (chemistry), reactive and are therefore never found in nature. They can nevertheless be prepared ar ...

. Phosphorus-solubilizing halophilic archaea may well play a role in making phosphorus available 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 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. Th ...

Grant and Larsen 1989 ** Haladaptataceae Cui et al. 2023 ** Haloarculaceae Gupta et al. 2016, 10 genera **

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 ''Methanocalcul ...

Gibbons 1974, 24 genera ** Halococcaceae Gupta et al. 2016, 1 genus ** Natronoarchaeaceae Sorokin et al. 2023 * Haloferacales Gupta et al. 2015 ** Haloferacaceae Gupta et al. 2015, 10 genera ** Halorubraceae Gupta et al. 2016, 9 genera * Halorutilales Durán-Viseras et al. 2023 ** Halorutilaceae Durán-Viseras et al. 2023 * Natrialbales Gupta et al. 2015 ** Natrialbaceae 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 naming and taxonomy of prokaryotes, following the taxonomy requirements and rulings of the International Code of Nomenclatu ...

(LPSN) and

National Center for Biotechnology Information The National Center for Biotechnology Information (NCBI) is part of the 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 is lo ...

(NCBI). Note: * polyphyletic Natronoarchaeaceae
: ** polyphyletic Haloferacaceae

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, ''

, Haloferacales'' and '' Natrialbales'', which can be reliably distinguished from each other as well as all other archaea/bacteria through molecular signatures known as conserved signature indels (CSIs). These studies have also identified 68 conserved signature proteins (CSPs) whose homologs are only found in the members of these three orders and 13 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 ...

L10e, RecJ-like

exonuclease Exonucleases are enzymes that work by cleaving nucleotides one at a time from the end (exo) of a polynucleotide chain. A hydrolyzing reaction that breaks phosphodiester bonds at either the 3′ or the 5′ end occurs. Its close relative is th ...

S15, adenylosuccinate synthase, phosphopyruvate hydratase, RNA-associated protein, threonine synthase, aspartate aminotransferase, 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 water to grow, and optimal growth usually occurs at much higher concentrations, typically 20–30% (3.4 - 5.2 mol/L of

). However, Haloarchaea can grow up to saturation (about 37% salts). Optimal growth also occurs when pH is neutral or basic and at 45°C temperature. Some haloarchaea 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 ( ) is a geological epoch (geology), epoch that lasted from about 56 to 33.9 million years ago (Ma). It is the second epoch of the Paleogene Period (geology), Period in the modern Cenozoic Era (geology), Era. The name ''Eocene'' comes ...

(38-41 million years ago). Some even older ones from more than 250 million years ago have been reported. Haloarchaea are also used to treat water high in salinity. This is due to its ability to withstand high nutrient levels and the heavy metals that may be present.

Adaptations to environment

Haloarchaea can grow at

water activity In food science, water activity (''aw'') of a food is the ratio of its vapor pressure to the vapor pressure of water at the same temperature, both taken at equilibrium. Pure water has a water activity of one. Put another way, ''aw'' is the equi ...

(a_w) close to 0.75, even though a_w lower than 0.90 is inhibitory to most microbes. The high solute concentration causes osmotic stress on microbes, which can cause cell lysis, unfolding of proteins, and inactivation of enzymes. Haloarchaea combat this by retaining compatible solutes such as potassium chloride (KCl) in their

intracellular space Intracellular space is the interior space of the plasma membrane The cell membrane (also known as the plasma membrane or cytoplasmic membrane, and historically referred to as the plasmalemma) is a biological membrane that separates and prote ...

to allow them to balance

osmotic pressure Osmotic pressure is the minimum pressure which needs to be applied to a Solution (chemistry), solution to prevent the inward flow of its pure solvent across a semipermeable membrane. It is also defined as the measure of the tendency of a soluti ...

. 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 () is a simple triol compound. It is a colorless, odorless, sweet-tasting, viscous liquid. The glycerol backbone is found in lipids known as glycerides. It is also widely used as a sweetener in the food industry and as a humectant in pha ...

as a carbon and energy source in catabolic processes, which is often present in high salt environments due to Dunaliella species that produce glycerol in large quantities.

Phototrophy

Bacteriorhodopsin Bacteriorhodopsin (Bop) is a protein used by Archaea, most notably by Haloarchaea, a class of the Euryarchaeota. It acts as a proton pump; that is, it captures light energy and uses it to move protons across the membrane out of the cell. The res ...

is used to absorb light, which provides energy to transport

proton A proton is a stable subatomic particle, symbol , Hydron (chemistry), H+, or 1H+ with a positive electric charge of +1 ''e'' (elementary charge). Its mass is slightly less than the mass of a neutron and approximately times the mass of an e ...

s (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, which pump 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

involving electron transport, however, and haloarchaea are incapable of fixing carbon from

carbon dioxide Carbon dioxide is a chemical compound with the chemical formula . It is made up of molecules that each have one carbon atom covalent bond, covalently double bonded to two oxygen atoms. It is found in a gas state at room temperature and at norma ...

. Early evolution of retinal proteins has been proposed in 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", classified in 2004 using a very low nutrition solution to allow growth along with a high salt concentration. ''Haloquadratum'' is 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). Then the stamp is affixed 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/ ...

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 Phase (matter), phases (gas, liquid, and solid) of that substance coexist in thermodynamic equilibrium.. It is that temperature and pressure at ...

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 were sent 36 km (about 22 miles) up into Earth's atmosphere, within a balloon. The two types that were sent up were able to survive the freezing temperatures and high radiation levels, supporting the hypothesis that halophiles could survive on Mars.

Medical use

Certain types of haloarchaea that produce

carotenoids Carotenoids () are yellow, orange, and red organic compound, organic pigments that are produced by plants and algae, as well as several bacteria, archaea, and Fungus, fungi. Carotenoids give the characteristic color to pumpkins, carrots, parsnips ...

could potentially serve as a source of carotenoids for medical use. Haloarchaea have been proposed to help meet the high demand of carotenoids by pharmaceutical companies due to how easily 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 are also present within the human gut, mostly predominant in the gut of people who live in

Korea Korea is a peninsular region in East Asia consisting of the Korean Peninsula, Jeju Island, and smaller islands. Since the end of World War II in 1945, it has been politically Division of Korea, divided at or near the 38th parallel north, 3 ...

. Haloarchaea are most abundant in Koreans' guts rather than

methanogens Methanogens are anaerobic archaea that produce methane as a byproduct of their energy metabolism, i.e., catabolism. Methane production, or methanogenesis, is the only biochemical pathway for ATP generation in methanogens. All known methanogens b ...

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

Certain types of haloarchaea have been proposed as sources of 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 Polyhydroxyalkanoates, 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 probabl ...

(PHB), and polyhydroxyvalerate (PHV) when exposed to certain conditions. For large-scale production of these bioplastics, haloarchaea are 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 and the higher recyclability of the process. Certain types of haloarchaea have also been found to have denitrifying characteristics. If haloarchaea are complete denitrifiers, they could aid salt marshes and other salty environments by buffering these areas of

nitrate Nitrate is a polyatomic ion with the chemical formula . salt (chemistry), Salts containing this ion are called nitrates. Nitrates are common components of fertilizers and explosives. Almost all inorganic nitrates are solubility, soluble in wa ...

and

nitrite The nitrite polyatomic ion, ion has the chemical formula . Nitrite (mostly sodium nitrite) is widely used throughout chemical and pharmaceutical industries. The nitrite anion is a pervasive intermediate in the nitrogen cycle in nature. The name ...

. This could help animal diversity and decrease pollution in these waterways. However, when tested in the lab, haloarchaea have been found to be partial denitrifiers. 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 atmospheric nitrogen pollution is Haloferax mediterranei. This shows that haloarchaea may be contributing to nitrogen pollution and are not a suitable solution for reducing nitrate and nitrite within high-salinity areas.

References

External links

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