Haloarchaea (halophilic archaea, halophilic archaebacteria, halobacteria) are a class of archaea under the 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 of archaea. 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 halophilic microorganisms require high salt concentrations to grow, with most species requiring more than 2M NaCl for growth and survival. Haloarchaea can grow aerobically or anaerobically. Parts of the membranes of haloarchaea are purplish in color, and large blooms of haloarchaea appear reddish from retinal-containing bacteriorhodopsin, a protein related to rhodopsin, which it uses to transform light energy into chemical energy by a process unrelated to chlorophyll-based photosynthesis. Haloarchaea have a potential to solubilize phosphorus. 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 Grant and Larsen 1989 Haladaptataceae Cui et al. 2023 Haloarculaceae Gupta et al. 2016, 10 genera Halobacteriaceae 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 (LPSN) and National Center for Biotechnology Information (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, Halobacteriales, 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 L10e, RecJ-like exonuclease, ribosomal protein 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 NaCl). 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 (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 (aw) close to 0.75, even though aw 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 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 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 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, 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 photosynthesis involving electron transport, however, and haloarchaea are incapable of fixing carbon from carbon dioxide. Early evolution of retinal proteins has been proposed in the purple Earth hypothesis.
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