Haloarchaea

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Haloarchaea
Halobacteria.jpg
Halobacterium sp. strain NRC-1, each cell about 5 µm in length.
Scientific classification
Domain:
Archaea
Kingdom:
Euryarchaeota
Phylum:
Euryarchaeota
Class:
Halobacteria

Grant et al. 2002
Order
Synonyms
  • Halomebacteria Cavalier-Smith 2002
  • Haloarchaea DasSarma and DasSarma 2008

Haloarchaea (halophilic archaea, halophilic archaebacteria, halobacteria) [1] are a class of prokaryotic archaea under the phylum Euryarchaeota, [2] 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 or 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. [3] Halophilic archaea are generally referred to as haloarchaea to distinguish them from halophilic bacteria.

Contents

These halophilic microorganisms require high salt concentrations to grow, with most species requiring more than 2M NaCl for growth and survival. [4] 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, [5] 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 making phosphorus available to vegetation growing in hypersaline soils. Haloarchaea may also have applications as inoculants for crops growing in hypersaline regions. [6]

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. [7] [8] divides the class of Halobacteria in three orders.

Phylogeny

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN) [9] and National Center for Biotechnology Information (NCBI). [2]

16S rRNA based LTP_10_2024 [10] [11] [12] 53 marker proteins based GTDB 09-RS220 [13] [14] [15]
Halobacteriales
Halorutilales

Halorutilaceae

Halobacteriales

Salinarchaeum {"Salinarchaeaceae"}

Halostella {Halostellaceae} *

Natronoarchaeum {Natronoarchaeaceae} *

Natrialbaceae

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, 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). [7] 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. [7] 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. [7]

Living environment

Salt ponds with pink colored Haloarchaea on the edge of San Francisco Bay, near Fremont, California San Francisco Bay Salt Ponds.jpg
Salt ponds with pink colored Haloarchaea on the edge of San Francisco Bay, near Fremont, California

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). [16] However, Haloarchaea can grow up to saturation (about 37% salts). [17] 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. [16]

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). [18] The pigmentation will become enhanced when oxygen levels are low due to an increase in a red pigmented ATP. [16] Some of them live in underground rock salt deposits, including one from middle-late Eocene (38-41 million years ago). [19] Some even older ones from more than 250 million years ago have been reported. [20] 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. [16]

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. [21] The high solute concentration causes osmotic stress on microbes, which can cause cell lysis, unfolding of proteins, and inactivation of enzymes. [22] Haloarchaea combat this by retaining compatible solutes such as potassium chloride (KCl) in their intracellular space to allow them to balance osmotic pressure. [23] Retaining these salts is referred to as the “salt-in” method where the cell accumulates a high internal concentration of potassium. [24] Because of the elevated potassium levels, haloarchaea have specialized proteins that have a highly negative surface charge to tolerate high potassium concentrations. [25]

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. [24]

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. [26] Early evolution of retinal proteins has been proposed in the purple Earth hypothesis. [5]

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). 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.

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. [27] 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. [28]

Medical use

Certain types of haloarchaea that produce carotenoids could potentially serve as a source of carotenoids for medical use. [29] Haloarchaea have been proposed to help meet the high demand of carotenoids by pharmaceutical companies due to how easy it can be grown in a lab. [30] Genes in Haloarchaea can also be manipulated in order to produce various strands of carotenoids, further helping meet pharmaceutical companies' needs. [29]

Haloarchaea are 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. [31]

Climate change

Certain types of haloarchaea have been proposed as sources of 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 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. [32]

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 and nitrite. 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. [33] The only type of haloarchaea that has been found to reduce atmospheric nitrogen pollution is Haloferax mediterranei. [34] 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.   

See also

Related Research Articles

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.

<i>Halobacterium</i> Genus of archaea

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.

<span class="mw-page-title-main">Halobacteriales</span> Order of 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.

Haladaptatus is a genus of halophilic archaea in the family of Halobacteriaceae. The members of Haladaptatus thrive in environments with salt concentrations approaching saturation

Halorubrum is a genus in the family Halorubraceae. Halorubrum species are usually halophilic and can be found in waters with high salt concentration such as the Dead Sea or Lake Zabuye.

In taxonomy, Natrialba is a genus of the Natrialbaceae. The genus consists of many diverse species that can survive extreme environmental niches, especially they are capable to live in the waters saturated or nearly saturated with salt (halophiles). They have certain adaptations to live within their salty environments. For example, their cellular machinery is adapted to high salt concentrations by having charged amino acids on their surfaces, allowing the cell to keep its water molecules around these components. The osmotic pressure and these amino acids help to control the amount of salt within the cell.

<i>Haloferax volcanii</i> Species of Halobacteria

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.

<span class="mw-page-title-main">Gas vesicle</span>

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.

<i>Salinibacter ruber</i> Species of bacterium

Salinibacter ruber is an extremely halophilic red bacterium, first found in Spain in 2002.

<span class="mw-page-title-main">Shiladitya DasSarma</span>

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.

Haloterrigena turkmenica is an aerobic chemo organotrophic archeon originally found in Turkmen salt lakes.

<span class="mw-page-title-main">Haloferacaceae</span> Family of bacteria

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 Haloferacales.

Natrialbales is an order of halophilic, chemoorganotrophic archaea within the class Haloarchaea. The type genus of this order is Natrialba.

Haloferacales is an order of halophilic, chemoorganotrophic or heterotrophic archaea within the class Haloarchaea. The type genus of this order is Haloferax.

Halorubraceae is a family of halophilic, chemoorganotrophic or heterotrophic archaea within the order Haloferacales. The type genus of this family is Halorubrum. Its biochemical characteristics are the same as the order Haloferacales.

Haloarculaceae is a family of halophilic and mostly chemoorganotrophic archaea within the order Halobacteriales. The type genus of this family is Haloarcula. Its biochemical characteristics are the same as the order Halobacteriales.

Halococcaceae is a family of halophilic and mostly chemoorganotrophic archaea within the order Halobacteriales. The type genus of this family is Halococcus. Its biochemical characteristics are the same as the order Halobacteriales.

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.

References

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  3. ↑ DasSarma P, DasSarma S (May 2008). "On the origin of prokaryotic "species": the taxonomy of halophilic Archaea". Saline Systems. 4 (1): 5. doi: 10.1186/1746-1448-4-5 . PMC   2397426 . PMID   18485204.
  4. ↑ DasSarma S, DasSarma P (2017). "Halophiles". eLS. John Wiley & Sons, Ltd. pp. 1–13. doi:10.1002/9780470015902.a0000394.pub4. ISBN   9780470015902.
  5. 1 2 DasSarma S, Schwieterman EW (2018). "Early evolution of purple retinal pigments on Earth and implications for exoplanet biosignatures". International Journal of Astrobiology. 20 (3): 241–250. arXiv: 1810.05150 . doi:10.1017/S1473550418000423. ISSN   1473-5504. S2CID   119341330.
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  10. ↑ "The LTP" . Retrieved 10 December 2024.
  11. ↑ "LTP_all tree in newick format" . Retrieved 10 December 2024.
  12. ↑ "LTP_10_2024 Release Notes" (PDF). Retrieved 10 December 2024.
  13. ↑ "GTDB release 09-RS220". Genome Taxonomy Database . Retrieved 10 May 2024.
  14. ↑ "ar53_r220.sp_label". Genome Taxonomy Database . Retrieved 10 May 2024.
  15. ↑ "Taxon History". Genome Taxonomy Database . Retrieved 10 May 2024.
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  17. ↑ Yadav AN, Sharma D, Gulati S, Singh S, Dey R, Pal KK, et al. (July 2015). "Haloarchaea Endowed with Phosphorus Solubilization Attribute Implicated in Phosphorus Cycle". Scientific Reports. 5: 12293. Bibcode:2015NatSR...512293Y. doi:10.1038/srep12293. PMC   4516986 . PMID   26216440.
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  24. 1 2 Williams TJ, Allen M, Tschitschko B, Cavicchioli R (March 2017). "Glycerol metabolism of haloarchaea". Environmental Microbiology. 19 (3): 864–877. doi: 10.1111/1462-2920.13580 . hdl: 1959.4/unsworks_49888 . PMID   27768817.
  25. ↑ Soppa J, Baumann A, Brenneis M, Dambeck M, Hering O, Lange C (September 2008). "Genomics and functional genomics with haloarchaea". Archives of Microbiology. 190 (3): 197–215. doi:10.1007/s00203-008-0376-4. PMID   18493745. S2CID   21222667.
  26. ↑ Bryant DA, Frigaard NU (November 2006). "Prokaryotic photosynthesis and phototrophy illuminated". Trends in Microbiology. 14 (11): 488–496. doi:10.1016/j.tim.2006.09.001. PMID   16997562.
  27. ↑ DasSarma S (2006). "Extreme halophiles are models for astrobiology" (PDF). Microbe-American Society for Microbiology. 1 (3): 120. Archived from the original (PDF) on 2007-02-02.
  28. ↑ DasSarma P, DasSarma S (June 2018). "Survival of microbes in Earth's stratosphere". Current Opinion in Microbiology. Environmental Microbiology * The New Microscopy. 43: 24–30. doi:10.1016/j.mib.2017.11.002. PMID   29156444. S2CID   19041112.
  29. 1 2 Giani M, Miralles-Robledillo JM, Peiró G, Pire C, Martínez-Espinosa RM (March 2020). "Deciphering Pathways for Carotenogenesis in Haloarchaea". Molecules. 25 (5): 1197. doi: 10.3390/molecules25051197 . PMC   7179442 . PMID   32155882.
  30. ↑ Rodrigo-Baños M, Montero Z, Torregrosa-Crespo J, Garbayo I, Vílchez C, Martínez-Espinosa RM (2021). "Haloarchaea: A Promising Biosource for Carotenoid Production". In Misawa N (ed.). Carotenoids: Biosynthetic and Biofunctional Approaches. Advances in Experimental Medicine and Biology. Vol. 1261. Singapore: Springer. pp. 165–174. doi:10.1007/978-981-15-7360-6_13. ISBN   978-981-15-7360-6. PMID   33783738. S2CID   232419066.
  31. ↑ Kim JY, Whon TW, Lim MY, Kim YB, Kim N, Kwon MS, et al. (August 2020). "The human gut archaeome: identification of diverse haloarchaea in Korean subjects". Microbiome. 8 (1): 114. doi: 10.1186/s40168-020-00894-x . PMC   7409454 . PMID   32753050.
  32. ↑ Simó-Cabrera L, García-Chumillas S, Hagagy N, Saddiq A, Tag H, Selim S, et al. (March 2021). "Haloarchaea as Cell Factories to Produce Bioplastics". Marine Drugs. 19 (3): 159. doi: 10.3390/md19030159 . PMC   8003077 . PMID   33803653.
  33. ↑ Torregrosa-Crespo J, Bergaust L, Pire C, Martínez-Espinosa RM (February 2018). "Denitrifying haloarchaea: sources and sinks of nitrogenous gases". FEMS Microbiology Letters. 365 (3). doi: 10.1093/femsle/fnx270 . hdl: 10045/73332 . PMID   29237000.
  34. ↑ Torregrosa-Crespo J, Pire C, Martínez-Espinosa RM, Bergaust L (January 2019). "Denitrifying haloarchaea within the genus Haloferax display divergent respiratory phenotypes, with implications for their release of nitrogenous gases". Environmental Microbiology. 21 (1): 427–436. doi:10.1111/1462-2920.14474. hdl: 10045/83647 . PMID   30421557. S2CID   53292259.

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