Halophiles are extremophile organisms that can thrive if the enzyme working in the organism reaches a temperature of over 30 °C (86 °F) while in environments with very high concentrations of salt. The name comes from the Greek for "salt-loving". While the term is perhaps most often applied to some halophiles classified into the Archaea domain, there are also bacterial halophiles and some eukaryota, such as the alga Dunaliella salina. Some well-known species give off a red color from carotenoid compounds. Such species contain the photosynthetic pigment bacteriorhodopsin. Halophiles are categorized slight, moderate or extreme, by the extent of their halotolerance. 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.
High salinity represents an extreme environment that relatively few organisms have been able to adapt to and occupy. Most halophilic and all halotolerant organisms expend energy to exclude salt from their cytoplasm to avoid protein aggregation (‘salting out’). In order 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 (that is employed by the majority of bacteria, some archaea, yeasts, algae and fungi), organic compounds are accumulated in the cytoplasm – these osmoprotectants are known as compatible solutes. These can be 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.
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 Halanerobiales, 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 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 (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 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 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 environment. Indeed, many cells are so fragile that when placed in distilled water they immediately lyse from the change in osmotic conditions.
They are photoheterotrophs, using light for energy and methane as a carbon source. They can be in either aerobic or anaerobic conditions.
Haloarchaea, and particularly, the family Halobacteriaceae are members of the domain Archaea, and comprise the majority of the prokaryotic population in hypersaline environments. 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 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 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.
Halobacterium is a group of Archaea that have 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 Halobacterium.
Some hypersaline lakes are a habitat to numerous families of halophiles. For example, the Makgadikgadi Pans in Botswana is 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 bacteria Halobacterium halobium.
The fermentation of salty foods (such as soy sauce, douchi, salted cod, salted anchovies, sauerkraut, and so on) 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.
See also 
- Santos, H., and da Costa, M.S. (2002) Compatible solutes of organisms that live in hot saline environments. Environmental Microbiology 4: 501-509.
- Oren, A. (2002) Molecular ecology of extremely halophilic Archaea and Bacteria. FEMS Microbiology Ecology: 1-7.
- Gutierrez, M.C., Kamekura, M., Holmes, M.L., Dyall-Smith, M.L., and Ventosa, A. (2002) Taxonomic characterisation of Haloferax sp. ("H. alicantei") strain Aa 2.2: description of Haloferax lucentensis sp. nov. Extremophiles. 2002 December;6(6):479-83
- Anton, J., Rossello-Mora, R., Rodriguez-Valera, F., and Amann, R. (2000) Extremely halophilic bacteria in crystallizer ponds from solar salterns. Applied and Environmental Microbiology 66: 3052-3057.
- Casamayor, E.O., Massana, R., Benlloch, S., Ovreas, L., Diez, B., Goddard, V.J., Gasol, J.M., Joint, I., Rodriguez-Valera, F., and Pedros-Alio, C. (2002) Changes in archaeal, bacterial and eukaryal assemblages along a salinity gradient by comparison of genetic fingerprinting methods in a multipond solar saltern. Environmental Microbiology 4: 338-348.
- Anton, J., Llobet-Brossa, E., Rodriguez-Valera, F., and Amann, R. (1999) Fluorescence in situ hybridization analysis of the prokaryotic community inhabiting crystallizer ponds. Environmental Microbiology 1: 517-523.
- Kastritis, P.L., Papandreou, N.C., Hamodrakas S.J. (2007) Haloadaptation: insights from comparative modeling studies of halophilic archaeal DHFRs. Int J Biol Mac 2007, 41(4):447-453.
- Paul, S., Bag, S.K., Das, S., Harvill, E.T., Dutta, C.(2008) Molecular Signature of Hypersaline Adaptation: Insights from Genome and Proteome Composition of Halophilic Prokaryotes. Genome Biology 2008, 9:R70.
- NCBI taxonomy resources (2007) NCBI webpage on Halobacterium
- Hogan, C. Michael (2008) Makgadikgadi, The Megalithic Portal, ed. A. Burnham
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.
- Important Groups of Prokaryotes - Kenneth Todar
- Astrobiology: extremophiles- life in extreme environments
ALDEN KING- SWAG