Halophile

Halophile

Overview
Halophiles are extremophile
Extremophile
An extremophile is an organism that thrives in physically or geochemically extreme conditions that are detrimental to most life on Earth. In contrast, organisms that live in more moderate environments may be termed mesophiles or neutrophiles...

 organisms that thrive in environment
Environment (biophysical)
The biophysical environment is the combined modeling of the physical environment and the biological life forms within the environment, and includes all variables, parameters as well as conditions and modes inside the Earth's biosphere. The biophysical environment can be divided into two categories:...

s with very high concentrations of salt
Salt
In chemistry, salts are ionic compounds that result from the neutralization reaction of an acid and a base. They are composed of cations and anions so that the product is electrically neutral...

. The name comes from the Greek for "salt-loving". While the term is perhaps most often applied to some halophiles classified into the Archaea
Archaea
The Archaea are a group of single-celled microorganisms. A single individual or species from this domain is called an archaeon...

 domain, there are also bacteria
Bacteria
Bacteria are a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a wide range of shapes, ranging from spheres to rods and spirals...

l halophiles and some eukaryota, such as the alga Dunaliella salina
Dunaliella salina
Dunaliella salina is a type of halophile green micro-algae especially found in sea salt fields. Known for its anti-oxidant activity because of its ability to create large amount of carotenoids, it is used in cosmetics and dietary supplements. Few organisms can survive in such highly saline...

. Some well-known species give off a red color from carotenoid compounds. Such species contain the photosynthetic pigment bacteriorhodopsin
Bacteriorhodopsin
Bacteriorhodopsin is a protein used by Archaea, the most notable one being Halobacteria. 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...

.
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Encyclopedia
Halophiles are extremophile
Extremophile
An extremophile is an organism that thrives in physically or geochemically extreme conditions that are detrimental to most life on Earth. In contrast, organisms that live in more moderate environments may be termed mesophiles or neutrophiles...

 organisms that thrive in environment
Environment (biophysical)
The biophysical environment is the combined modeling of the physical environment and the biological life forms within the environment, and includes all variables, parameters as well as conditions and modes inside the Earth's biosphere. The biophysical environment can be divided into two categories:...

s with very high concentrations of salt
Salt
In chemistry, salts are ionic compounds that result from the neutralization reaction of an acid and a base. They are composed of cations and anions so that the product is electrically neutral...

. The name comes from the Greek for "salt-loving". While the term is perhaps most often applied to some halophiles classified into the Archaea
Archaea
The Archaea are a group of single-celled microorganisms. A single individual or species from this domain is called an archaeon...

 domain, there are also bacteria
Bacteria
Bacteria are a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a wide range of shapes, ranging from spheres to rods and spirals...

l halophiles and some eukaryota, such as the alga Dunaliella salina
Dunaliella salina
Dunaliella salina is a type of halophile green micro-algae especially found in sea salt fields. Known for its anti-oxidant activity because of its ability to create large amount of carotenoids, it is used in cosmetics and dietary supplements. Few organisms can survive in such highly saline...

. Some well-known species give off a red color from carotenoid compounds. Such species contain the photosynthetic pigment bacteriorhodopsin
Bacteriorhodopsin
Bacteriorhodopsin is a protein used by Archaea, the most notable one being Halobacteria. 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...

. Halophiles are categorized slight, moderate or extreme, by the extent of their halotolerance
Halotolerance
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 a group of bacteria that live in highly saline...

. Halophiles can be found anywhere with a concentration of salt five times greater than the salt concentration of the ocean, such as the Great Salt Lake
Great Salt Lake
The Great Salt Lake, located in the northern part of the U.S. state of Utah, is the largest salt water lake in the western hemisphere, the fourth-largest terminal lake in the world. In an average year the lake covers an area of around , but the lake's size fluctuates substantially due to its...

 in Utah, Owens Lake
Owens Lake
Owens Lake is a mostly dry lake in the Owens Valley on the eastern side of the Sierra Nevada in Inyo County, California. It is located about south of Lone Pine, California...

 in California, the Dead Sea
Dead Sea
The Dead Sea , also called the Salt Sea, is a salt lake bordering Jordan to the east and Israel and the West Bank to the west. Its surface and shores are below sea level, the lowest elevation on the Earth's surface. The Dead Sea is deep, the deepest hypersaline lake in the world...

, and in evaporation pond
Evaporation pond
Evaporation ponds are artificial ponds with very large surface areas that are designed to efficiently evaporate water by sunlight and exposure to the ambient temperatures.- Uses :...

s.

Lifestyle


High salinity represents an extreme environment that relatively few organisms have been able to adapt to and occupy. Most halophilic and all halotolerant
Halotolerance
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 a group of bacteria that live in highly saline...

 organisms expend energy
Energy
In physics, energy is an indirectly observed quantity. It is often understood as the ability a physical system has to do work on other physical systems...

 to exclude salt from their cytoplasm
Cytoplasm
The cytoplasm is a small gel-like substance residing between the cell membrane holding all the cell's internal sub-structures , except for the nucleus. All the contents of the cells of prokaryote organisms are contained within the cytoplasm...

 to avoid protein aggregation (‘salting out
Salting out
Salting out is a method of separating proteins based on the principle that proteins are less soluble at high salt concentrations. The salt concentration needed for the protein to precipitate out of the solution differs from protein to protein...

’). In order to survive the high salinities, halophiles employ two differing strategies to prevent desiccation
Desiccation
Desiccation is the state of extreme dryness, or the process of extreme drying. A desiccant is a hygroscopic substance that induces or sustains such a state in its local vicinity in a moderately sealed container.-Science:...

 through osmotic
Osmosis
Osmosis is the movement of solvent molecules through a selectively permeable membrane into a region of higher solute concentration, aiming to equalize the solute concentrations on the two sides...

 movement of water out of their cytoplasm. Both strategies work by increasing the internal osmolarity of the cell. In the first (that is employed by the majority of bacteria, some archaea, yeast
Yeast
Yeasts are eukaryotic micro-organisms classified in the kingdom Fungi, with 1,500 species currently described estimated to be only 1% of all fungal species. Most reproduce asexually by mitosis, and many do so by an asymmetric division process called budding...

s, algae
Algae
Algae are a large and diverse group of simple, typically autotrophic organisms, ranging from unicellular to multicellular forms, such as the giant kelps that grow to 65 meters in length. They are photosynthetic like plants, and "simple" because their tissues are not organized into the many...

 and fungi), organic compounds are accumulated in the cytoplasm – these osmoprotectant
Osmoprotectant
Osmoprotectants or compatible solutes are small molecules that act as osmolytes and help organisms survive extreme osmotic stress. Examples include betaines, amino acids, and the sugar trehalose. These molecules accumulate in cells and balance the osmotic difference between the cell's surroundings...

s are known as compatible solutes. These can be synthesised or accumulated from the environment. The most common compatible solutes are neutral
PH
In chemistry, pH is a measure of the acidity or basicity of an aqueous solution. Pure water is said to be neutral, with a pH close to 7.0 at . Solutions with a pH less than 7 are said to be acidic and solutions with a pH greater than 7 are basic or alkaline...

 or zwitterionic and include amino acid
Amino acid
Amino acids are molecules containing an amine group, a carboxylic acid group and a side-chain that varies between different amino acids. The key elements of an amino acid are carbon, hydrogen, oxygen, and nitrogen...

s, sugar
Sugar
Sugar is a class of edible crystalline carbohydrates, mainly sucrose, lactose, and fructose, characterized by a sweet flavor.Sucrose in its refined form primarily comes from sugar cane and sugar beet...

s, polyol
Polyol
A polyol is an alcohol containing multiple hydroxyl groups. In two technological disciplines the term "polyol" has a special meaning: food science and polymer chemistry.- Polyols in food science :...

s, betaines and ectoine
Ectoine
Ectoine is a natural compound found in several species of bacteria. It is a compatible solute which serves as a protective substance by acting as an osmolyte and thus helps organisms survive extreme osmotic stress...

s, as well as derivatives of some of these compounds.

The second, more radical, adaptation involves the selective influx of potassium
Potassium
Potassium is the chemical element with the symbol K and atomic number 19. Elemental potassium is a soft silvery-white alkali metal that oxidizes rapidly in air and is very reactive with water, generating sufficient heat to ignite the hydrogen emitted in the reaction.Potassium and sodium are...

 (K+) ions into the cytoplasm. This adaptation is restricted to the moderately halophilic bacterial Order Halanerobiales, the extremely halophilic archaeal Family Halobacteriaceae
Halobacteriaceae
In taxonomy, the Halobacteriaceae are a family of the Halobacteriales in the domain Archaea.- Overview :Halobacteriaceae are 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...

 and the extremely halophilic bacterium Salinibacter ruber. The presence of this adaptation in three distinct evolutionary lineages suggests convergent evolution
Convergent evolution
Convergent evolution describes the acquisition of the same biological trait in unrelated lineages.The wing is a classic example of convergent evolution in action. Although their last common ancestor did not have wings, both birds and bats do, and are capable of powered flight. The wings are...

 of this strategy, it being unlikely to be an ancient characteristic retained in only scattered groups or through massive lateral gene transfer. The primary reason for this is that 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.

Of particular note are the extreme halophiles or haloarchaea
Haloarchaea
Haloarchaea are microrganisms and members of the halophile community, in that they require high salt concentrations to grow. They are a distinct evolutionary branch of the Archaea, and are generally considered extremophiles, although not all members of this group can be considered as such.-Living...

 (often known as halobacteria
Halobacteria
In taxonomy, the Halobacteria are a class of the Euryarchaeota, 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...

), 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 deap salterns, where they tint the water column and sediments bright colors. In other words, they will 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 NaCl in their environment limits the availability of oxygen for respiration. Their cellular machinery is adapted to high salt concentrations by having charged amino acid
Amino acid
Amino acids are molecules containing an amine group, a carboxylic acid group and a side-chain that varies between different amino acids. The key elements of an amino acid are carbon, hydrogen, oxygen, and nitrogen...

s on their surfaces, allowing the retention of water molecules around these components. They are heterotroph
Heterotroph
A heterotroph is an organism that cannot fix carbon and uses organic carbon for growth. This contrasts with autotrophs, such as plants and algae, which can use energy from sunlight or inorganic compounds to produce organic compounds such as carbohydrates, fats, and proteins from inorganic carbon...

s that normally respire by aerobic means. Most halophiles are unable to survive outside their high-salt native environment. Indeed, many cells are so fragile that when placed in distilled water they immediately lyse
Cytolysis
Cytolysis, or osmotic lysis, occurs when a cell bursts due to an osmotic imbalance that has caused excess water to move into the cell. It occurs in a hypotonic environment, where water diffuses into the cell and causes its volume to increase. If the volume of water exceeds the cell membrane's...

 from the change in osmotic conditions.

Haloarchaea, and particularly, the family Halobacteriaceae are members of the domain Archaea, and comprise the majority of the prokaryotic population in hypersaline environments
Hypersaline lake
A hypersaline lake is a landlocked body of water that contains significant concentrations of sodium chloride or other mineral salts, with saline levels surpassing that of ocean water . Specific microbial and crustacean species thrive in these high salinity environments that are otherwise...

. There are currently 15 recognised genera in the family. 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. At times, the alga Dunaliella salina
Dunaliella salina
Dunaliella salina is a type of halophile green micro-algae especially found in sea salt fields. Known for its anti-oxidant activity because of its ability to create large amount of carotenoids, it is used in cosmetics and dietary supplements. Few organisms can survive in such highly saline...

can also proliferate in this environment.

A comparatively wide range of taxa have been isolated from saltern crystalliser ponds, including members of the following genera: Haloferax, Halogeometricum, Halococcus, Haloterrigena, Halorubrum, Haloarcula and Halobacterium families (Oren 2002). 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
Svedberg
A svedberg is a non-SI physical unit used for sedimentation coefficients.  It characterizes the behaviour of a particle type in sedimentation processes, notably centrifugation.  The svedberg is technically a measure of time, and is defined as exactly 10-13 seconds A svedberg (symbol S, sometimes...

 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 but commonly appears in isolation studies.

Genomic and proteomic signature of halophiles


The comparative genomic and proteomic analysis showed that there is a distinct molecular signatures for environmental adaptation of halophiles. At the protein level, the halophilic species are characterized by low hydrophobicity, overrepresentation of acidic residues, underrepresentation of Cys, lower propensities for helix formation and higher propensities for coil structure. It is also evident that the core of these proteins is less hydrophobic, such as DHFR, that was found to have narrower β-strands
At the DNA level, the halophiles exhibit distinct dinucleotide and codon usage.

Examples


Halobacterium
Halobacterium
In taxonomy, Halobacterium is a genus of the Halobacteriaceae.The genus Halobacterium consists of several species of archaea with an aerobic metabolism which require an environment with a high concentration of salt; many of their proteins will not function in low-salt environments. They grow on...

 is a group of Archaea
Archaea
The Archaea are a group of single-celled microorganisms. A single individual or species from this domain is called an archaeon...

 that have a high tolerance for elevated levels of salinity
Salinity
Salinity is the saltiness or dissolved salt content of a body of water. It is a general term used to describe the levels of different salts such as sodium chloride, magnesium and calcium sulfates, and bicarbonates...

. Some species of halobacteria have acid
Acid
An acid is a substance which reacts with a base. Commonly, acids can be identified as tasting sour, reacting with metals such as calcium, and bases like sodium carbonate. Aqueous acids have a pH of less than 7, where an acid of lower pH is typically stronger, and turn blue litmus paper red...

ic protein
Protein
Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...

s that resist the denaturing effects of salts. Halococcus
Halococcus
Halococcus is a genus of the Halobacteriaceae.- Description and Significance :Halococcus is a genus of extreme halophilic archaea, meaning that they require high salt levels, sometimes as high as 32% NaCl, for optimal growth...

is a specific genus of the family Halobacterium
Halobacterium
In taxonomy, Halobacterium is a genus of the Halobacteriaceae.The genus Halobacterium consists of several species of archaea with an aerobic metabolism which require an environment with a high concentration of salt; many of their proteins will not function in low-salt environments. They grow on...

.

Some hypersaline lake
Hypersaline lake
A hypersaline lake is a landlocked body of water that contains significant concentrations of sodium chloride or other mineral salts, with saline levels surpassing that of ocean water . Specific microbial and crustacean species thrive in these high salinity environments that are otherwise...

s are a habitat to numerous families of halophiles. For example, the Makgadikgadi Pans in Botswana
Botswana
Botswana, officially the Republic of Botswana , is a landlocked country located in Southern Africa. The citizens are referred to as "Batswana" . Formerly the British protectorate of Bechuanaland, Botswana adopted its new name after becoming independent within the Commonwealth on 30 September 1966...

  is a vast seasonal high salinity water body that manifests halophilic species within the diatom
Diatom
Diatoms are a major group of algae, and are one of the most common types of phytoplankton. Most diatoms are unicellular, although they can exist as colonies in the shape of filaments or ribbons , fans , zigzags , or stellate colonies . Diatoms are producers within the food chain...

 genus Nitzschia
Nitzschia
Nitzschia is a common pennate marine diatom. In the scientific literature this genus is sometimes termed Nitzchia, this taxon has many species described, which all have a similar morphology.-Occurrence:...

in the family Bacillariaceae
Bacillariaceae
Bacillariaceae is a family of diatoms in the phylum Heterokontophyta. Some of the genus members such as Nitzchia are found in halophilic environments; for example, some halophile species of Nitzchia are found in the seasonally flooded Makgadikgadi Pans in Botswana.-References:* C. Michael Hogan *...

 as well as species within the genus Lovenula in the family Diaptomidae
Diaptomidae
Diaptomidae is a family of freshwater pelagic copepods. It includes around 50 genera:*Acanthodiaptomus Kiefer, 1932*Aglaodiaptomus Light, 1938*Allodiaptomus Kiefer, 1936*Arctodiaptomus Kiefer, 1932*Argyrodiaptomus Brehm, 1933...

. Owens lake in California also contains a large population of the halophilic bacteria Halobacterium halobium.

The fermentation of salty foods (such as soy sauce
Soy sauce
Soy sauce is a condiment produced by fermenting soybeans with Aspergillus oryzae or Aspergillus sojae molds, along with water and salt...

, Chinese fermented beans
Douchi
Douchi , also called Chinese fermented black beans , is a flavoring most popular in the cuisine of China, and is used to make black bean sauce....

, salted cod, salted anchovies, sauerkraut
Sauerkraut
Sauerkraut , directly translated from German: "sour cabbage", is finely shredded cabbage that has been fermented by various lactic acid bacteria, including Leuconostoc, Lactobacillus, and Pediococcus. It has a long shelf-life and a distinctive sour flavor, both of which result from the lactic acid...

 etc.) often involves halobacteria, as either essential ingredients or accidental contaminants. One example is Chromohalobacter beijerinckii
Chromohalobacter beijerinckii
Chromohalobacter beijerinckii is a motile, rod-like, salt-loving, Gram-negative soil bacterium, 0.4–0.6 μm by 1.8–2.5 μm.The bacterium was isolated in 1935 by T. Hof from fermented salted beans preserved in brine. Hof named it Pseudomonas beijerinckii and identified it as the organism responsible...

, found in salted bean
Bean
Bean is a common name for large plant seeds of several genera of the family Fabaceae used for human food or animal feed....

s preserved in brine and in salted herring
Herring
Herring is an oily fish of the genus Clupea, found in the shallow, temperate waters of the North Pacific and the North Atlantic oceans, including the Baltic Sea. Three species of Clupea are recognized. The main taxa, the Atlantic herring and the Pacific herring may each be divided into subspecies...

. Tetragenococcus halophilus
Tetragenococcus halophilus
Tetragenococcus halophilus is a halophilic lactic acid bacterium active in the fermentation processes of soy sauce, miso, fish sauce and salted anchovies....

is found in salted anchovies and soy sauce.

General references

  • DasSarma, S. and P. DasSarma 2006. Halophiles, Encyclopedia of Life Sciences, Wiley, London.
  • Madigan, Michael T., and Barry L. Narrs, "Extremophiles" Scientific American, April 1997: 82-88.

External links