Pseudomonas salinariaHarrison and Kennedy 1922 Serratia salinaria(Harrison and Kennedy 1922) Bergeyet al. 1923 Flavobacterium (subgen.Halobacterium)salinarium(Harrison and Kennedy 1922) Elazari-volcani 1940 Halobacter salinaria(Harrison and Kennedy 1922) Anderson 1954 Halobacterium salinarium(Harrison and Kennedy 1922) Elazari-Volcani 1957 Halobacterium halobium(Petter 1931) Elazari-Volcani 1957 Halobacterium cutirubrum(Lochhead 1934) Elazari-Volcani 1957Halobacterium piscialsi(Yachai et al. 2008)[1]
Halobacterium salinarum, formerly known asHalobacterium cutirubrum orHalobacterium halobium, is an extremelyhalophilicmarineobligate aerobic archaeon.[2] Despite its name, this is not abacterium, but a member of the domainArchaea.[3] It is found in salted fish,hides,hypersaline lakes, andsalterns. 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.[3]H. salinarum has also been found in high-salt food such assalt pork, marine fish, andsausages. The ability ofH. salinarum to live at such high salt concentrations has led to its classification as anextremophile.
Halobacteria are single-celled, rod-shaped microorganisms that are among the most ancient forms of life and appeared on Earth billions of years ago. The membrane consists of a singlelipid bilayer surrounded by anS-layer.[4] The S-layer is made of a cell-surfaceglycoprotein that accounts for approximately 50% of the cell surfaceproteins.[5] These proteins form a lattice in the membrane. Sulfate residues are abundant on theglycan chains of the glycoprotein, giving it a negative charge. The negative charge is believed to stabilize the lattice in high-salt conditions.[6]
Amino acids are the main source of chemical energy forH. salinarum, particularlyarginine andaspartate, though they are able to metabolize other amino acids, as well.[4]H. salinarum have been reported to be unable to grow on sugars, and therefore need to encode enzymes capable of performinggluconeogenesis to create sugars. AlthoughH. salinarum is unable to catabolize glucose, thetranscription factor TrmB has been proven to regulate the gluconeogenic production of sugars found on the S-layer glycoprotein.
To survive in extremely salty environments, this archaeon—as with other halophilic Archaeal species—utilizescompatible solutes (in particular,potassium chloride) to reduce osmotic stress.[7] Potassium levels are not atequilibrium with the environment, soH. salinarum express multipleactive transporters that pump potassium into the cell.[4]At extremely high salt concentrations,protein precipitation will occur. To prevent the salting out of proteins,H. salinarum encodes mainly acidic proteins. The averageisoelectric point ofH. salinarum proteins is 5.03.[8] These highly acidic proteins are overwhelmingly negative in charge and are able to remain in solution even at high salt concentrations.[3]
H. salinarum can grow to such densities in salt ponds that oxygen is quickly depleted. Though it is anobligate aerobe, it is able to survive in low-oxygen conditions by utilizinglight energy.H. salinarum expresses the membrane proteinbacteriorhodopsin,[11] which acts as a light-driven proton pump. It consists of two parts: the 7-transmembrane protein, bacterioopsin, and the light-sensitive cofactor,retinal. Upon absorption of aphoton, retinal changes its conformation, causing a conformational change in the bacterioopsin protein, as well, which drives proton transport.[12] The proton gradient formed thereby can then be used to generate chemical energy viaATP synthase.
To obtain more oxygen,H. salinarum produce gas vesicles, which allow them to float to the surface where oxygen levels are higher and more light is available.[13] These vesicles are complex structures made of proteins encoded by at least 14 genes.[14] Gas vesicles were first discovered in H. salinarum in 1967.[15]
There is little protection from the Sun in salt ponds, soH. salinarum are often exposed to high amounts ofUV radiation. To compensate, they have evolved a sophisticatedDNA repair mechanism. The genome encodes DNA repair enzymes homologous to those in both bacteria and eukaryotes.[3] This allowsH. salinarum to repair damage to DNA faster and more efficiently than other organisms and allows them to be much more UV-tolerant.
Its red color is due primarily to the presence ofbacterioruberin, a 50 carboncarotenoid Alcohol (polyol) pigment present within the membrane ofH. salinarum. The primary role of bacterioruberin in the cell is to protect againstDNA damage incurred by UV light.[16] This protection is not, however, due to the ability of bacterioruberin to absorb UV light. Bacterioruberin protects the DNA by acting as anantioxidant, rather than directly blocking UV light.[17] It is able to protect the cell fromreactive oxygen species produced from exposure to UV by acting as a target. The bacterioruberinradical produced is less reactive than the initial radical, and will likely react with another radical, resulting in termination of the radical chain reaction.[18]
H. salinarum has been found to be responsible for the bright pink or red appearance of some bodies ofhypersaline lakes, includingpink lakes, such as the lake inMelbourne'sWestgate Park; with the exact colour of the lake depending on the balance between the algaDunaliella salina andH. salinarium, with salt concentration having a direct impact.[19][20] However, recent studies atLake Hillier inWestern Australia have shown that other bacteria, notablySalinibacter ruber, along with algal and other factors, cause the pink color of these lakes.[21][22][23][24] The researchers found 10 species of halophilic bacteria and archaea as well as several species ofDunaliella algae, nearly all of which contain some pink, red orsalmon-coloured pigment.[23][22]
Protection against ionizing radiation and desiccation
Whole genome sequences are available for two strains ofH. salinarum, NRC-1[4] and R1.[28] The Halobacterium sp. NRC-1 genome consists of 2,571,010 base pairs on one large chromosome and two mini-chromosomes. The genome encodes 2,360 predicted proteins.[4] The large chromosome is very G-C rich (68%).[29] HighGC-content of the genome increases stability in extreme environments.Wholeproteome comparisons show the definite archaeal nature of this halophile with additional similarities to the Gram-positiveBacillus subtilis and other bacteria.
H. salinarum is as easy to culture asE. coli and serves as an excellent model system. Methods for gene replacement and systematicknockout have been developed,[30] soH. salinarum is an ideal candidate for the study of archaeal genetics andfunctional genomics.
In the 1990s there were claims that DNA samples from Halobacteria from salt formations were millions of years old. Later analysis was unable to replicate the findings.[32]
Then in 2009 it was claimed that a sample of a close genetic relative ofH. salinarum encapsulated in salt allowed for the recovery ofancient DNA fragments estimated at 121 million years old.[33] The curing salt had been derived from a mine inSaskatchewan, the site of the most recent sample described by Jong Soo Park ofDalhousie University inHalifax, Nova Scotia, Canada.[34] Russell Vreeland of Ancient Biomaterials Institute ofWest Chester University inPennsylvania, USA, performed an analysis of all known types of halophilic bacteria, which yielded the finding that Park's bacteria contained six segments ofDNA never seen before in halophiles. Vreeland also tracked down the buffalo skin and determined that the salt came from the same mine as Park's sample. He also claimed to discover ahalophile estimated at 250 million years old inNew Mexico.[35] However, his findings date the crystal surrounding the bacteria, and DNA analysis suggests the bacteria themselves are likely to be less ancient.[36]
In 2022, a study inNature reported that two-million year old preserved genetic material from many species was found in Greenland, and these sequences are currently considered the oldest confirmed DNA discovered, of any species.[37][38]
^Minegishi H, Echigo A, Shimane Y, Kamekura M, Tanasupawat S, Visessanguan W, Usami R (September 2012). "Halobacterium piscisalsi Yachai et al. 2008 is a later heterotypic synonym of Halobacterium salinarum Elazari-Volcani 1957".International Journal of Systematic and Evolutionary Microbiology.62 (Pt 9):2160–2162.doi:10.1099/ijs.0.036905-0.PMID22058320.
^Joshi, J. G.; Guild, W. R.; Handler, P (1963). "The presence of two species of DNA in some halobacteria".Journal of Molecular Biology.6:34–8.doi:10.1016/s0022-2836(63)80079-0.PMID13964964.
^Vreeland, H; Rosenzweig, W D; Lowenstein, T; Satterfield, C; Ventosa, A (December 2006). "Fatty acid and DNA analyses of Permian bacteria isolated from ancient salt crystals reveal differences from their modern relatives".Extremophiles.10 (1):71–8.doi:10.1007/s00792-005-0474-z.PMID16133658.S2CID25102006.
^Kjær KH, Winther Pedersen M, De Sanctis B, De Cahsan B, Korneliussen TS, Michelsen CS, Sand KK, Jelavić S, Ruter AH, Schmidt AM, Kjeldsen KK, Tesakov AS, Snowball I, Gosse JC, Alsos IG, Wang Y, Dockter C, Rasmussen M, Jørgensen ME, Skadhauge B, Prohaska A, Kristensen JÅ, Bjerager M, Allentoft ME, Coissac E, Rouillard A, Simakova A, Fernandez-Guerra A, Bowler C, Macias-Fauria M, Vinner L, Welch JJ, Hidy AJ, Sikora M, Collins MJ, Durbin R, Larsen NK, Willerslev E (December 2022)."A 2-million-year-old ecosystem in Greenland uncovered by environmental DNA".Nature.612 (7939):283–291.Bibcode:2022Natur.612..283K.doi:10.1038/s41586-022-05453-y.PMC9729109.PMID36477129.
Kahaki, Fatemeh Abarghooi; Babaeipour, Valiollah; Memari, Hamid Rajabi; Mofid, Mohammad Reza (2014). "High Overexpression and Purification of Optimized Bacterio-Opsin from Halobacterium Salinarum R1 in E-coli".Applied Biochemistry and Biotechnology.174 (4):1558–1571.doi:10.1007/s12010-014-1137-2.PMID25123363.S2CID7403305.
