Halobacteria Grant et al., 2002
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- English Wikipedia - Species Pages
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- Euryarchaeota
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- Euryarchaeota
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- Halobacteria
Abstract
Haloarchaea (halophilic archaea, halophilic archaebacteria, halobacteria) are a class of the Euryarchaeota,See the NCBI webpage on Halobacteria. Data extracted from the 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. These microorganisms are among the halophile organisms, that they require high salt concentrations to grow, with most species requiring more than 2.0M NaCl for growth and survival. They are a distinct evolutionary branch of the Archaea distinguished by the possession of ether-linked lipids and the absence of murein in their cell walls. Haloarchaea can grow aerobically or anaerobically. Parts of the membranes of haloarchaea are purplish in color, and large blooms of haloarchaea appear reddish, from the pigment bacteriorhodopsin, related to the retinal pigment 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 P (phosphorus) nutrition to vegetation growing in hypersaline soils. Haloarchaea may also have applications as inoculants for crops growing in hypersaline regions.
Adaptations to environment
Haloarchaea can grow at an aw close to 0.75, yet a water activity (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 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.
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 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.
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). This shape is probably only permitted by the high osmolarity of the water, permitting cell shapes that would be difficult, if not impossible, under other conditions.
Climate Change
Haloarchaea have been proposed that certain types can be used to make biodegradable plastics, which could help decrease plastic pollution. Haloarchaea are able to produce polyhydroxyalkanote (PHA), polyhydroxybutyrate (PHB) and polyhydroxyvalerate (PHV), when exposed to certain conditions. For large scale production of these bioplastics, 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 and have a higher recyclability of the process. Certain types of haloarchaea have also been found to poses denitrifying 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.
Living environment
Salt ponds with pink colored Haloarchaea on the edge of San Francisco Bay, near Fremont, California
Haloarchaea require salt concentrations in excess of 2 M (or about 10%) 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 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 (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 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.
Haloarchaea require salt concentrations in excess of 2 M (or about 10%) 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 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 (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 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.
Medical Use
Certain types of haloarchaea have been found to produce carotenoids, 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. Haloarchaea are most abundant in Koreans guts rather than methanogens 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.
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. These studies have also identified 68 conserved signature proteins (CSPs) whose homologs are only found in the members of these three order and 13 conserved signature indels (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.
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 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 involving electron transport, however, and haloarchaea are incapable of fixing carbon from carbon dioxide. Early evolution of retinal proteins has been proposed as the purple Earth hypothesis.
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) Haloarculaceae (Gupta et al. 2016), 10 genera Halobacteriaceae (Gibbons 1974), 24 genera Halococcaceae (Gupta et al. 2016), 1 genus Haloferacales (Gupta et al. 2015) Haloferacaceae (Gupta et al. 2015), 10 genera Halorubraceae (Gupta et al. 2016), 9 genera Natrialbales (Gupta et al. 2015) Natrialbaceae (Gupta et al. 2015), 18 genera
Species list Domain: Archaea
Euryarchaeota
Halobacteria Halobacteriales Halobacteriaceae Halolamina [Hlm.] Halolamina pelagica (Type species) Halolamina rubra Halolamina salifodinae Halolamina salina Halolamina sediminis Halomicroarcula [Hma.] Halomicroarcula limicola Halomicroarcula pellucida (Type species) Halomicroarcula salina Halomicrobium [Hmc.] See Halomicrobium Halopelagius [Hpl.] Halopelagius inordinatus (Type species) Halopelagius fulvigenes Halopelagius longus Halopenitus [Hpt.] Halopenitus malekzadehii Halopenitus persicus (Type species) Halopenitus salinus Halopiger [Hpg.] Halopiger aswanensis Halopiger salifodinae Halopiger xanaduensis (Type species) Haloplanus [Hpn.] Haloplanus aerogenes Haloplanus litoreus Haloplanus natans (Type species) Haloplanus ruber Haloplanus salinus Haloplanus vescus
Halorhabdus [Hrd.] Halorhabdus tiamatea Halorhabdus utahensis (Type species) "Halorhabdus rudnickae" (Syst Appl Microbiol., in press) Halorientalis [Hos.] Halorientalis brevis Halorientalis persicus Halorientalis regularis (Type species) Halorubellus [Hrb.] Halorubellus litoreus Halorubellus salinus (Type species) Halorubrum [Hrr.] Halorubrum aquaticum Halorubrum chaoviator Halorubrum cibi Halorubrum gandharaense Halorubrum halodurans Halorubrum halophilum Halorubrum laminariae Halorubrum orientale Halorubrum persicum Halorubrum rubrum "Halorubrum rutilum" (Arch Microbiol.,2015, 197(10):1159-1164) Halorubrum saccharovorum (Type species) Halorubrum salinum Halorubrum yunnanense See also Halorubrum Halorussus [Hrs.] Halorussus amylolyticus Halorussus rarus Halorussus ruber "Halosiccatus" ["Hsc".] "Halosiccatus urmianus" (Type species) (IJSEM, in press) Halosimplex [Hsx.] Halosimplex carlsbadense (Type species) Halosimplex litoreum Halosimplex pelagicum Halosimplex rubrum Halostagnicola [Hst.] Halostagnicola alkaliphila Halostagnicola bangensis Halostagnicola kamekurae Halostagnicola larsenii (Type species) Halovarius [Hvr.] Halovarius luteus (Type species) Halovenus [Hvn.] Halovenus aranensis (Type species) Halovenus rubra Halovenus salina Halovivax [Hvx.] Halovivax asiaticus (Type species) Halovivax cerinus Halovivax limisalsi Halovivax ruber Natrialba [Nab.] Natrialba aegyptia Natrialba asiatica (Type species) Natrialba chahannaoensis Natrialba hulunbeirensis Natrialba magadii Natrialba taiwanensis Natribaculum [Nbl.] Natribaculum breve (Type species) Natribaculum longum Natronoarchaeum [Nac.] Natronoarchaeum mannanilyticum (Type species) Natronoarchaeum philippinense Natronoarchaeum rubrum Natronobacterium [Nbt.] Natronobacterium gregoryi (Type species) Natronobacterium texcoconense Natronococcus [Ncc.] Natronococcus amylolyticus Natronococcus jeotgali Natronococcus occultus (Type species) Natronococcus roseus Natronorubrum [Nrr.] Natronorubrum aibiense Natronorubrum bangense (Type species) Natronorubrum sediminis Natronorubrum sulfidifaciens Natronorubrum texcoconense Natronorubrum tibetense Salarchaeum [Sar.] Salarchaeum japonicum (Type species) Salinarchaeum [Saa.] Salinarchaeum laminariae (Type species) Salinigranum [Sgn.] Salinigranum rubrum (Type species)
non-valid
"Halorubrum sfaxense" "Candidatus Halobonum tyrrellensis "Candidatus Haloectosymbiotes riaformosensis" "Halopiger djelfamassiliensis sp" "Halopiger goleamassiliensis" "Halorubrum tropicale" "Haloarcula rubripromontorii" "Halobacterium hubeiense"
Halobacteriales (Grant and Larsen 1989) Haloarculaceae (Gupta et al. 2016), 10 genera Halobacteriaceae (Gibbons 1974), 24 genera Halococcaceae (Gupta et al. 2016), 1 genus Haloferacales (Gupta et al. 2015) Haloferacaceae (Gupta et al. 2015), 10 genera Halorubraceae (Gupta et al. 2016), 9 genera Natrialbales (Gupta et al. 2015) Natrialbaceae (Gupta et al. 2015), 18 genera
Species list Domain: Archaea
Euryarchaeota
Halobacteria Halobacteriales Halobacteriaceae Halolamina [Hlm.] Halolamina pelagica (Type species) Halolamina rubra Halolamina salifodinae Halolamina salina Halolamina sediminis Halomicroarcula [Hma.] Halomicroarcula limicola Halomicroarcula pellucida (Type species) Halomicroarcula salina Halomicrobium [Hmc.] See Halomicrobium Halopelagius [Hpl.] Halopelagius inordinatus (Type species) Halopelagius fulvigenes Halopelagius longus Halopenitus [Hpt.] Halopenitus malekzadehii Halopenitus persicus (Type species) Halopenitus salinus Halopiger [Hpg.] Halopiger aswanensis Halopiger salifodinae Halopiger xanaduensis (Type species) Haloplanus [Hpn.] Haloplanus aerogenes Haloplanus litoreus Haloplanus natans (Type species) Haloplanus ruber Haloplanus salinus Haloplanus vescus
Halorhabdus [Hrd.] Halorhabdus tiamatea Halorhabdus utahensis (Type species) "Halorhabdus rudnickae" (Syst Appl Microbiol., in press) Halorientalis [Hos.] Halorientalis brevis Halorientalis persicus Halorientalis regularis (Type species) Halorubellus [Hrb.] Halorubellus litoreus Halorubellus salinus (Type species) Halorubrum [Hrr.] Halorubrum aquaticum Halorubrum chaoviator Halorubrum cibi Halorubrum gandharaense Halorubrum halodurans Halorubrum halophilum Halorubrum laminariae Halorubrum orientale Halorubrum persicum Halorubrum rubrum "Halorubrum rutilum" (Arch Microbiol.,2015, 197(10):1159-1164) Halorubrum saccharovorum (Type species) Halorubrum salinum Halorubrum yunnanense See also Halorubrum Halorussus [Hrs.] Halorussus amylolyticus Halorussus rarus Halorussus ruber "Halosiccatus" ["Hsc".] "Halosiccatus urmianus" (Type species) (IJSEM, in press) Halosimplex [Hsx.] Halosimplex carlsbadense (Type species) Halosimplex litoreum Halosimplex pelagicum Halosimplex rubrum Halostagnicola [Hst.] Halostagnicola alkaliphila Halostagnicola bangensis Halostagnicola kamekurae Halostagnicola larsenii (Type species) Halovarius [Hvr.] Halovarius luteus (Type species) Halovenus [Hvn.] Halovenus aranensis (Type species) Halovenus rubra Halovenus salina Halovivax [Hvx.] Halovivax asiaticus (Type species) Halovivax cerinus Halovivax limisalsi Halovivax ruber Natrialba [Nab.] Natrialba aegyptia Natrialba asiatica (Type species) Natrialba chahannaoensis Natrialba hulunbeirensis Natrialba magadii Natrialba taiwanensis Natribaculum [Nbl.] Natribaculum breve (Type species) Natribaculum longum Natronoarchaeum [Nac.] Natronoarchaeum mannanilyticum (Type species) Natronoarchaeum philippinense Natronoarchaeum rubrum Natronobacterium [Nbt.] Natronobacterium gregoryi (Type species) Natronobacterium texcoconense Natronococcus [Ncc.] Natronococcus amylolyticus Natronococcus jeotgali Natronococcus occultus (Type species) Natronococcus roseus Natronorubrum [Nrr.] Natronorubrum aibiense Natronorubrum bangense (Type species) Natronorubrum sediminis Natronorubrum sulfidifaciens Natronorubrum texcoconense Natronorubrum tibetense Salarchaeum [Sar.] Salarchaeum japonicum (Type species) Salinarchaeum [Saa.] Salinarchaeum laminariae (Type species) Salinigranum [Sgn.] Salinigranum rubrum (Type species)
non-valid
"Halorubrum sfaxense" "Candidatus Halobonum tyrrellensis "Candidatus Haloectosymbiotes riaformosensis" "Halopiger djelfamassiliensis sp" "Halopiger goleamassiliensis" "Halorubrum tropicale" "Haloarcula rubripromontorii" "Halobacterium hubeiense"