Halophile

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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.

Contents

While most halophiles are classified into the domain Archaea, there are also bacterial halophiles and some eukaryotic species, such as the alga Dunaliella salina and fungus Wallemia ichthyophaga . Some well-known species give off a red color from carotenoid compounds, notably bacteriorhodopsin.

Halophiles can be found in water bodies with salt concentration more than five times greater than that of the ocean, such as the Great Salt Lake in Utah, Owens Lake in California, the Lake Urmia in Iran, the Dead Sea, and in evaporation ponds. They are theorized to be a possible analogues for modeling extremophiles that might live in the salty subsurface water ocean of Jupiter's Europa and similar moons. [1]

Classification

Halophiles are categorized by the extent of their halotolerance: slight, moderate, or extreme. Slight halophiles prefer 0.3 to 0.8 M (1.7 to 4.8%—seawater is 0.6 M or 3.5%), moderate halophiles 0.8 to 3.4 M (4.7 to 20%), and extreme halophiles 3.4 to 5.1 M (20 to 30%) salt content. [2] Halophiles require sodium chloride (salt) for growth, in contrast to halotolerant organisms, which do not require salt but can grow under saline conditions.

Lifestyle

High salinity represents an extreme environment in which relatively few organisms have been able to adapt and survive. Most halophilic and all halotolerant organisms expend energy to exclude salt from their cytoplasm to avoid protein aggregation ('salting out'). To survive the high salinities, halophiles employ two differing strategies to prevent desiccation through osmotic movement of water out of their cytoplasm. Both strategies work by increasing the internal osmolarity of the cell. The first strategy is employed by some archaea, the majority of halophilic bacteria, yeasts, algae, and fungi; the organism accumulates organic compounds in the cytoplasm—osmoprotectants which are known as compatible solutes. These can be either synthesised or accumulated from the environment. [3] The most common compatible solutes are neutral or zwitterionic, and include amino acids, sugars, polyols, betaines, and ectoines, as well as derivatives of some of these compounds.

The second, more radical adaptation involves selectively absorbing potassium (K+) ions into the cytoplasm. This adaptation is restricted to the extremely halophilic archaeal family Halobacteriaceae , the moderately halophilic bacterial order Halanaerobiales , and the extremely halophilic bacterium Salinibacter ruber . The presence of this adaptation in three distinct evolutionary lineages suggests convergent evolution of this strategy, it being unlikely to be an ancient characteristic retained in only scattered groups or passed on through massive lateral gene transfer. [3] The primary reason for this is the entire intracellular machinery (enzymes, structural proteins, etc.) must be adapted to high salt levels, whereas in the compatible solute adaptation, little or no adjustment is required to intracellular macromolecules; in fact, the compatible solutes often act as more general stress protectants, as well as just osmoprotectants. [3]

Of particular note are the extreme halophiles or haloarchaea (often known as halobacteria), a group of archaea, which require at least a 2 M salt concentration and are usually found in saturated solutions (about 36% w/v salts). These are the primary inhabitants of salt lakes, inland seas, and evaporating ponds of seawater, such as the deep salterns, where they tint the water column and sediments bright colors. These species most likely perish if they are exposed to anything other than a very high-concentration, salt-conditioned environment. These prokaryotes require salt for growth. The high concentration of sodium chloride in their environment limits the availability of oxygen for respiration. Their cellular machinery is adapted to high salt concentrations by having charged amino acids on their surfaces, allowing the retention of water molecules around these components. They are heterotrophs that normally respire by aerobic means. Most halophiles are unable to survive outside their high-salt native environments. Many halophiles are so fragile that when they are placed in distilled water, they immediately lyse from the change in osmotic conditions.

Halophiles use a variety of energy sources and can be aerobic or anaerobic; anaerobic halophiles include phototrophic, fermentative, sulfate-reducing, homoacetogenic, and methanogenic species. [2] [4]

The Haloarchaea, and particularly the family Halobacteriaceae, are members of the domain Archaea , and comprise the majority of the prokaryotic population in hypersaline environments. [5] Currently, 15 recognised genera are in the family. [6] The domain Bacteria (mainly Salinibacter ruber ) can comprise up to 25% of the prokaryotic community, but is more commonly a much lower percentage of the overall population. [7] At times, the alga Dunaliella salina can also proliferate in this environment. [8]

A comparatively wide range of taxa has been isolated from saltern crystalliser ponds, including members of these genera: Haloferax, Halogeometricum, Halococcus, Haloterrigena, Halorubrum, Haloarcula, and Halobacterium. [5] However, the viable counts in these cultivation studies have been small when compared to total counts, and the numerical significance of these isolates has been unclear. Only recently has it become possible to determine the identities and relative abundances of organisms in natural populations, typically using PCR-based strategies that target 16S small subunit ribosomal ribonucleic acid (16S rRNA) genes. While comparatively few studies of this type have been performed, results from these suggest that some of the most readily isolated and studied genera may not in fact be significant in the in situ community. This is seen in cases such as the genus Haloarcula , which is estimated to make up less than 0.1% of the in situ community, [9] but commonly appears in isolation studies.

Genomic and proteomic signature

The comparative genomic and proteomic analysis showed distinct molecular signatures exist for the environmental adaptation of halophiles. At the protein level, the halophilic species are characterized by low hydrophobicity, an overrepresentation of acidic residues, underrepresentation of Cys, lower propensities for helix formation, and higher propensities for coil structure. The core of these proteins is less hydrophobic, such as DHFR, that was found to have narrower β-strands. [10] In one study, the net charges (at pH 7.4) of the ribosomal proteins (r-proteins) that comprise the S10-spc cluster were observed to have an inverse relationship with the halophilicity/halotolerance levels in both bacteria and archaea. [11] At the DNA level, the halophiles exhibit distinct dinucleotide and codon usage. [12]

Examples

Halobacteriaceae is a family that includes a large part of halophilic archaea. [13] The genus Halobacterium under it has a high tolerance for elevated levels of salinity. Some species of halobacteria have acidic proteins that resist the denaturing effects of salts. Halococcus is another genus of the family Halobacteriaceae.

Some hypersaline lakes are habitat to numerous families of halophiles. For example, the Makgadikgadi Pans in Botswana form a vast, seasonal, high-salinity water body that manifests halophilic species within the diatom genus Nitzschia in the family Bacillariaceae, as well as species within the genus Lovenula in the family Diaptomidae. [14] Owens Lake in California also contains a large population of the halophilic bacterium Halobacterium halobium.

Wallemia ichthyophaga is a basidiomycetous fungus, which requires at least 1.5 M sodium chloride for in vitro growth, and it thrives even in media saturated with salt. [15] Obligate requirement for salt is an exception in fungi. Even species that can tolerate salt concentrations close to saturation (for example Hortaea werneckii ) in almost all cases grow well in standard microbiological media without the addition of salt. [16]

The fermentation of salty foods (such as soy sauce, Chinese fermented beans, salted cod, salted anchovies, sauerkraut, etc.) often involves halophiles as either essential ingredients or accidental contaminants. One example is Chromohalobacter beijerinckii , found in salted beans preserved in brine and in salted herring. Tetragenococcus halophilus is found in salted anchovies and soy sauce.

Artemia is a ubiquitous genus of small halophilic crustaceans living in salt lakes (such as Great Salt Lake) and solar salterns that can exist in water approaching the precipitation point of NaCl (340 g/L) [17] [18] and can withstand strong osmotic shocks due to its mitigating strategies for fluctuating salinity levels, such as its unique larval salt gland and osmoregulatory capacity.

North Ronaldsay sheep are a breed of sheep originating from Orkney, Scotland. They have limited access to freshwater sources on the island and their only food source is seaweed. They have adapted to handle salt concentrations that would kill other breeds of sheep. [19]

See also

Related Research Articles

Halotolerance is the adaptation of living organisms to conditions of high salinity. Halotolerant species tend to live in areas such as hypersaline lakes, coastal dunes, saline deserts, salt marshes, and inland salt seas and springs. Halophiles are organisms that live in highly saline environments, and require the salinity to survive, while halotolerant organisms can grow under saline conditions, but do not require elevated concentrations of salt for growth. Halophytes are salt-tolerant higher plants. Halotolerant microorganisms are of considerable biotechnological interest.

<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.

<span class="mw-page-title-main">Haloarchaea</span> Class of salt-tolerant archaea

Haloarchaea are a class of the 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. 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.

<i>Halobacterium salinarum</i> Species of archaeon

Halobacterium salinarum, formerly known as Halobacterium cutirubrum or Halobacterium halobium, is an extremely halophilic marine obligate aerobic archaeon. Despite its name, this is not a bacterium, but a member of the domain Archaea. It is found in salted fish, hides, hypersaline lakes, and salterns. As these salterns reach the minimum salinity limits for extreme halophiles, their waters become purple or reddish color due to the high densities of halophilic Archaea. H. salinarum has also been found in high-salt food such as salt pork, marine fish, and sausages. The ability of H. salinarum to survive at such high salt concentrations has led to its classification as an extremophile.

<i>Haloarcula</i> Genus of archaea

Haloarcula is a genus of extreme halophilic Archaea in the class of Halobactaria.

<i>Haloquadratum</i> Genus of archaea

Haloquadratum is a genus of archaean, belonging to the family Haloferacaceae. The first species to be identified in this group, Haloquadratum walsbyi, is unusual in that its cells are shaped like square, flat boxes.

Halorubrum is a genus in the family Halorubraceae. Halorubrum species areusually 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.

Halocins are bacteriocins produced by halophilic Archaea and a type of archaeocin.

Nanohaloarchaea is a clade of diminutive archaea with small genomes and limited metabolic capabilities, belonging to the DPANN archaea. They are ubiquitous in hypersaline habitats, which they share with the extremely halophilic haloarchaea.

<i>Wallemia ichthyophaga</i> Species of fungus

Wallemia ichthyophaga is one of the three species of fungi in the genus Wallemia, which in turn is the only genus of the class Wallemiomycetes. The phylogenetic origin of the lineage was placed to various parts of Basidiomycota, but according to the analysis of larger datasets it is a (495-million-years-old) sister group of Agaricomycotina. Although initially believed to be asexual, population genomics found evidence of recombination between strains and a mating type locus was identified in all sequenced genomes of the species.

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

Haloferax volcanii is a species of organism in the genus Haloferax in the Archaea.

<i>Haloquadratum walsbyi</i> Species of archaeon

Haloquadratum walsbyi is of the genus Haloquadratum, within the archaea domain known for its square halophilic nature. First discovered in a brine pool in the Sinai peninsula of Egypt, H. walsbyi is noted for its flat, square-shaped cells, and its unusual ability to survive in aqueous environments with high concentrations of sodium chloride and magnesium chloride. The species' genus name Haloquadratum translates from Greek and Latin as "salt square". This archaean is also commonly referred to as "Walsby's Square Bacterium" because of its identifying square shape which makes it unique. In accordance with its name, Haloquadratum walsbyi are most abundantly observed in salty environments.

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.

Halorhodospira halophila is a species of Halorhodospira distinguished by its ability to grow optimally in an environment of 15–20% salinity. It was formerly called Ectothiorhodospira halophila. It is an anaerobic, rod-shaped Gram-negative bacterium. H. halophila has a flagellum.

<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.

<i>Haloferax mediterranei</i> Species of bacterium

Haloferax mediterranei is a species of archaea in the family Haloferacaceae.

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

References

  1. ↑ Marion, Giles M.; Fritsen, Christian H.; Eicken, Hajo; Payne, Meredith C. (2003-12-01). "The search for life on Europa: Limiting environmental factors, potential habitats, and Earth analogues". Astrobiology. 3 (4): 785–811. Bibcode:2003AsBio...3..785M. doi:10.1089/153110703322736105. ISSN   1531-1074. PMID   14987483.
  2. 1 2 Ollivier B, Caumette P, Garcia JL, Mah RA (March 1994). "Anaerobic bacteria from hypersaline environments". Microbiological Reviews. 58 (1): 27–38. doi:10.1128/MMBR.58.1.27-38.1994. PMC   372951 . PMID   8177169.
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  5. 1 2 Oren, Aharon (2002). "Molecular ecology of extremely halophilic Archaea and Bacteria". FEMS Microbiology Ecology. 39 (1): 1–7. doi: 10.1111/j.1574-6941.2002.tb00900.x . ISSN   0168-6496. PMID   19709178.
  6. ↑ Gutierrez MC, Kamekura M, Holmes ML, Dyall-Smith ML, Ventosa A (December 2002). "Taxonomic characterization of Haloferax sp. (" H. alicantei") strain Aa 2.2: description of Haloferax lucentensis sp. nov". Extremophiles. 6 (6): 479–83. doi:10.1007/s00792-002-0282-7. PMID   12486456. S2CID   24337996.
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  9. ↑ Antón J, Llobet-Brossa E, Rodríguez-Valera F, Amann R (December 1999). "Fluorescence in situ hybridization analysis of the prokaryotic community inhabiting crystallizer ponds". Environmental Microbiology. 1 (6): 517–23. doi:10.1046/j.1462-2920.1999.00065.x. PMID   11207773.
  10. ↑ Kastritis PL, Papandreou NC, Hamodrakas SJ (October 2007). "Haloadaptation: Insights from comparative modeling studies of halophilic archaeal DHFRs". International Journal of Biological Macromolecules. 41 (4): 447–453. doi:10.1016/j.ijbiomac.2007.06.005. PMID   17675150.
  11. ↑ Tirumalai MR, Anane-Bediakoh D, Rajesh S, Fox GE (December 2021). "Net Charges of the Ribosomal Proteins of the S10 and spc Clusters of Halophiles Are Inversely Related to the Degree of Halotolerance". Microbiol Spectr. 9 (3): e0178221. doi:10.1128/spectrum.01782-21. PMC   8672879 . PMID   34908470.
  12. ↑ Paul S, Bag SK, Das S, Harvill ET, Dutta C (April 2008). "Molecular signature of hypersaline adaptation: insights from genome and proteome composition of halophilic prokaryotes". Genome Biology. 9 (4): R70. doi: 10.1186/gb-2008-9-4-r70 . PMC   2643941 . PMID   18397532.
  13. ↑ Oren, Aharon (September 2014). "Taxonomy of halophilic Archaea: Current status and future challenges". Extremophiles. 18 (5): 825–834. doi:10.1007/s00792-014-0654-9. PMID   25102811. S2CID   5395569.
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  16. ↑ Gostincar C, Grube M, de Hoog S, Zalar P, Gunde-Cimerman N (January 2010). "Extremotolerance in fungi: evolution on the edge". FEMS Microbiology Ecology. 71 (1): 2–11. doi: 10.1111/j.1574-6941.2009.00794.x . PMID   19878320.
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  18. ↑ de Vos S, Van Stappen G, Vuylsteke M, Rombauts S, Bossier P (2018). "Identification of salt stress response genes using the Artemia transcriptome". Aquaculture. 500: 305–314. doi:10.1016/j.aquaculture.2018.09.067. S2CID   92842322.
  19. ↑ Mirkena T, Duguma G, Haile A, Tibbo M, Okeyo AM, Wurzinger M, Sölkner J (2010). "Genetics of adaptation in domestic farm animals: A review". Livestock Science. 132 (1–3): 3. doi:10.1016/j.livsci.2010.05.003.

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