Halophiles are organisms that thrive in high salt concentrations. They are a type of extremophile organism. The name comes from the Greek word for "salt-loving". While most halophiles are classified into the Archaea domain, there are also bacterial halophiles and some eukaryota, such as the alga Dunaliella salina or fungus Wallemia ichthyophaga . Some well-known species give off a red color from carotenoid compounds, notably bacteriorhodopsin. 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 in Utah, Owens Lake in California, the Dead Sea, and in evaporation ponds.
Salt is a mineral composed primarily of sodium chloride (NaCl), a chemical compound belonging to the larger class of salts; salt in its natural form as a crystalline mineral is known as rock salt or halite. Salt is present in vast quantities in seawater, where it is the main mineral constituent. The open ocean has about 35 grams (1.2 oz) of solids per liter of sea water, a salinity of 3.5%.
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.
Archaea constitute a domain of single-celled microorganisms. These microbes are prokaryotes, meaning they have no cell nucleus. Archaea were initially classified as bacteria, receiving the name archaebacteria, but this classification is outdated.
Halophiles are categorized as slight, moderate, or extreme, by the extent of their halotolerance. 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.Halophiles require sodium chloride (salt) for growth, in contrast to halotolerant organisms, which do not require salt but can grow under saline conditions.
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.
High salinity represents an extreme environment to which relatively few organisms have been able to adapt and occupy. 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. In the first (which is employed by the majority of halophilic bacteria, some archaea, yeasts, algae and fungi), organic compounds are accumulated in the cytoplasm—osmoprotectants which are known as compatible solutes. These can be either synthesised or accumulated from the environment.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.
In cell biology, the cytoplasm is all of the material within a cell, enclosed by the cell membrane, except for the cell nucleus. The material inside the nucleus and contained within the nuclear membrane is termed the nucleoplasm. The main components of the cytoplasm are cytosol – a gel-like substance, the organelles – the cell's internal sub-structures, and various cytoplasmic inclusions. The cytoplasm is about 80% water and usually colorless.
Salting out is an effect based on the electrolyte–non-electrolyte interaction, in which the non-electrolyte could be less soluble at high salt concentrations. It is used as a method of purification for proteins, as well as preventing protein denaturation due to excessively diluted samples during experiments. The salt concentration needed for the protein to precipitate out of the solution differs from protein to protein. This process is also used to concentrate dilute solutions of proteins. Dialysis can be used to remove the salt if needed.
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.
The second, more radical adaptation involves the selective influx of potassium (K+) ions into the cytoplasm. This adaptation is restricted to the moderately halophilic bacterial order Halanaerobiales, the extremely halophilic archaeal family Halobacteriaceae, 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.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.
Potassium is a chemical element with symbol K and atomic number 19. Potassium metal is silvery- white in appearance, and soft enough to be cut with a knife, with little to no force.. Potassium metal reacts with atmospheric Oxygen to form flaky white Potassium Oxide in only seconds of exposure. It was first isolated from potash, the ashes of plants, from which its name derives. In the periodic table, potassium is one of the alkali metals. All of the alkali metals have a single valence electron in the outer electron shell, which is easily removed to create an ion with a positive charge – a cation, which combines with anions to form salts. Potassium in nature occurs only in ionic salts. Elemental potassium is a soft silvery-white alkali metal that oxidizes rapidly in air and reacts vigorously with water, generating sufficient heat to ignite hydrogen emitted in the reaction, and burning with a lilac-colored flame. It is found dissolved in sea water, and is part of many minerals.
The Halanaerobiales are an order of bacteria placed within the class Clostridia, and encompassing two families, the Halanaerobiaceae and the Halobacteroidaceae. Originally placed within the highly polyphyletic class Clostridia, according to the NCBI and LPSN, it is now thought to lie outside the Firmicutes. Halanaerobiales are halophilic obligate anaerobes with a fermentative or homoacetogenic metabolism.
In taxonomy, the Halobacteriaceae are a family of the Halobacteriales in 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(due to bacterioruberin carotenoids), 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.
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. Indeed, many cells are so fragile that when placed in distilled water, they immediately lyse from the change in osmotic conditions.
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 remains valid according to taxonomic rules. In a non-taxonomic context, halophilic archaea are referred to as haloarchaea to distinguish them from halophilic bacteria.
A saltern is an area or installation for making salt. Salterns include modern salt-making works, as well as hypersaline waters that usually contain high concentrations of halophilic microorganisms, primarily haloarchaea but also other halophiles including algae and bacteria.
Amino acids are organic compounds containing amine (-NH2) and carboxyl (-COOH) functional groups, along with a side chain (R group) specific to each amino acid. The key elements of an amino acid are carbon (C), hydrogen (H), oxygen (O), and nitrogen (N), although other elements are found in the side chains of certain amino acids. About 500 naturally occurring amino acids are known (though only 20 appear in the genetic code) and can be classified in many ways. They can be classified according to the core structural functional groups' locations as alpha- (α-), beta- (β-), gamma- (γ-) or delta- (δ-) amino acids; other categories relate to polarity, pH level, and side chain group type (aliphatic, acyclic, aromatic, containing hydroxyl or sulfur, etc.). In the form of proteins, amino acid residues form the second-largest component (water is the largest) of human muscles and other tissues. Beyond their role as residues in proteins, amino acids participate in a number of processes such as neurotransmitter transport and biosynthesis.
Halophiles may use a variety of energy sources. They can be aerobic or anaerobic. Anaerobic halophiles include phototrophic, fermentative, sulfate-reducing, homoacetogenic, and methanogenic species.
The Haloarchaea, and particularly the family Halobacteriaceae, are members of the domain Archaea, and comprise the majority of the prokaryotic population in hypersaline environments.Currently, 15 recognised genera are 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 can also proliferate in this environment.
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.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, but commonly appears in isolation studies.
The comparative genomic and proteomic analysis showed distinct molecular signatures exist 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. 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.
Halobacteriumis a genus of the Archaea that 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 a specific genus of the family Halobacteriaceae.
Some hypersaline lakes are a 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.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.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.
The fermentation of salty foods (such as soy sauce, Chinese fermented beans, salted cod, salted anchovies, sauerkraut, etc.) often involves halobacteria, 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−1and can withstand strong osmotic shocks thanks 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 fresh water sources on the island and to their only food source is seaweed. They have adapted to handle salt concentrations that would kill other breeds of sheep.
In taxonomy, Halobacterium is a genus of the Halobacteriaceae.
Halobacterium salinarum is an extremely halophilic marine Gram-negative obligate aerobic archaeon. Despite its name, this is not a bacterium, but rather 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.
In taxonomy, Haloarcula is a genus of the Halobacteriaceae.
Halococcus is a genus of the Halobacteriaceae.
Haloquadratum is a halophilic genus of the family Halobacteriaceae. The first species to be identified in this group, Haloquadratum walsbyi, is unusual in that its cells are shaped like flat, square boxes.
In taxonomy, Natrialba is a genus of the Halobacteriaceae. 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.
Dunaliella is a single-celled, photosynthetic green alga, that is characteristic for its’ ability to outcompete other organisms and thrive in hypersaline environments. It is mostly a marine organism, though there are a few freshwater species that tend to be more rare. It is a genus where certain species can accumulate relatively large amounts of β-carotenoids and glycerol in very harsh growth conditions consisting of high light intensities, high salt concentrations, and limited oxygen and nitrogen levels, yet is still very abundant in lakes and lagoons all around the world. It becomes very complicated to distinguish and interpret species of this genus on simply a morphological and physiological level due to the organism’s lack of cell wall that allows it to have malleability and change shape and its’ different pigments that allows it to change colours depending on the environmental conditions. Molecular phylogeny analysis has become a critical protocol in discovering the taxonomy of Dunaliella. The genus has been studied for over a hundred years, becoming a critical model organism for studying algal salt adaptation processes. It has remained relevant due to its’ numerous biotechnological applications, including β-carotenoid cosmetic and food products, medicine, and biofuel research.
Halocins are bacteriocins produced by halophilic Archaea and a type of archaeocin.
Archaeocin is the name given to a new type of potentially useful antibiotic that is derived from the Archaea group of organisms. Eight archaeocins have been partially or fully characterized, but hundreds of archaeocins are believed to exist, especially within the haloarchaea. Production of these archaeal proteinaceous antimicrobials is a nearly universal feature of the rod-shaped haloarchaea.
"Halorubrum salsolis" is an undescribed species of halobacteria which is known to live in the Great Salt Lake in the United States.
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. The genome of the fungus contains no mating type locus and the species appears to be asexual.
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.
Gas vesicles are nanocompartments in certain prokaryotic organisms, that help in buoyancy. Gas vesicles are composed entirely of protein; no lipids or carbohydrates have been detected.
Salinibacter ruber is an extremely halophilic red bacterium that was found in saltern crystallizer ponds in Alicante and Mallorca, Spain in 2002 by Antón et al.. This environment has very high salt concentrations, and Salinibacter ruber itself cannot grow at below 15% salt concentration, with an ideal concentration between 20–30%.
Shiladitya DasSarma is a molecular biologist well known for his contributions to the biology of halophilic microorganisms. He obtained a BS degree in Chemistry from Indiana University and a PhD degree in Biochemistry from the Massachusetts Institute of Technology. He conducted postdoctoral research at Massachusetts General Hospital, Harvard Medical School, and Pasteur Institute, Paris.
Haloterrigena turkmenica is an aerobic chemo organotrophic archeon originally found in Turkish salt lakes.