Halobacterium

Last updated

Halobacterium
Halobacteria.jpg
Halobacterium sp. strain NRC-1, each cell about 5 μm in length
Scientific classification
Domain:
Archaea
Phylum:
Euryarchaeota
Class:
Halobacteria
Order:
Halobacteriales
Family:
Halobacteriaceae
Genus:
Halobacterium

(Elazari-Volcani 1940) Elazari-Volcani 1957 non Schoop 1935
Type species
Halobacterium salinarum
(Harrison & Kennedy 1922) Elazari-Volcani 1957
Species
Synonyms
  • Flavobacterium ("Halobacterium") Elazari-Volcani 1940
  • "Halobacter" Anderson 1954

Halobacterium (common abbreviation Hbt.) is a genus in the family Halobacteriaceae. [1]

Contents

The genus Halobacterium ("salt" or "ocean bacterium") consists of several species of Archaea with an aerobic metabolism which requires an environment with a high concentration of salt; many of their proteins will not function in low-salt environments. They grow on amino acids in their aerobic conditions. Their cell walls are also quite different from those of bacteria, as ordinary lipoprotein membranes fail in high salt concentrations. In shape, they may be either rods or cocci, and in color, either red or purple. They reproduce using binary fission (by constriction), and are motile. Halobacterium grows best in a 42 °C environment. The genome of an unspecified Halobacterium species, sequenced by Shiladitya DasSarma, comprises 2,571,010 bp (base pairs) of DNA compiled into three circular strands: one large chromosome with 2,014,239 bp, and two smaller ones with 191,346 and 365,425 bp. This species, called Halobacterium sp. NRC-1, has been extensively used for postgenomic analysis. Halobacterium species can be found in the Great Salt Lake, the Dead Sea, Lake Magadi, and any other waters with high salt concentration. Purple Halobacterium species owe their color to bacteriorhodopsin, a light-sensitive protein which provides chemical energy for the cell by using sunlight to pump protons out of the cell. The resulting proton gradient across the cell membrane is used to drive the synthesis of the energy carrier ATP. Thus, when these protons flow back in, they are used in the synthesis of ATP (this proton flow can be emulated with a decrease in pH outside the cell, causing a flow of H+ ions). The bacteriorhodopsin protein is chemically very similar to the light-detecting pigment rhodopsin, found in the vertebrate retina.

Species of Halobacterium

Phylogeny

The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN) [2] and National Center for Biotechnology Information (NCBI). [3]

16S rRNA based LTP_08_2023 [4] [5] [6] 53 marker proteins based GTDB 08-RS214 [7] [8] [9]

H. zhouiiWang et al. 2023

H. litoreumLu et al. 2017

H. bonnevilleiMyers & King 2020

H. noricense Gruber et al. 2005

H. wangiaeWang et al. 2023

H. jilantaiense Yang et al. 2006

H. rubrumHan & Cui 2015

H. salinarum

H. bonnevillei

"H. hubeiense" Jaakkola et al. 2016

H. noricense

H. litoreum

H. jilantaiense

H. salinarum

Synonyms

Halobacterium salinarum NRC-1 Size bar = 270 nm Halobacterium salinarum NRC-1.png
Halobacterium salinarum NRC-1
Size bar = 270 nm

Genome structure

The Halobacterium NRC-1 genome is 2,571,010 bp compiled into three circular replicons. More specifically, it is divided into one large chromosome with 2,014,239 bp and two small replicons pNRC100 (191,346 bp) and pNRC200 (365,425 bp). While much smaller than the large chromosome, the two plasmids account for most of the 91 insertion sequences and include genes for a DNA polymerase, seven transcription factors, genes in potassium and phosphate uptake, and cell division. The genome was discovered to contain a high G+C content at 67.9% on the large chromosome and 57.9% and 59.2% on the two plasmids. The genome also contained 91 insertion sequence elements constituting 12 families, including 29 on pNRC100, 40 on pNRC200, and 22 on the large chromosome. This helps explain the genetic plasticity that has been observed in Halobacterium. Of the archaea, halobacteria are viewed as being involved in the most lateral genetics (gene transfer between domains) and a proof that this transfer does take place.

Cell structure and metabolism

Halobacterium species are rod-shaped and enveloped by a single lipid bilayer membrane surrounded by an S-layer made from the cell-surface glycoprotein. They grow on amino acids in aerobic conditions. Although Halobacterium NRC-1 contains genes for glucose degradation, as well as genes for enzymes of a fatty acid oxidation pathway, it does not seem able to use these as energy sources. Though the cytoplasm retains an osmotic equilibrium with the hypersaline environment, the cell maintains a high potassium concentration using many active transporters.

Many Halobacterium species possess proteinaceous organelles called gas vesicles.

Ecology

Halobacteria can be found in highly saline lakes such as the Great Salt Lake, the Dead Sea, and Lake Magadi. Halobacterium can be identified in bodies of water by the light-detecting pigment bacteriorhodopsin, which not only provides the archaeon with chemical energy, but adds to its reddish hue as well. An optimal temperature for growth has been observed at 37 °C.

Halobacterium may be a candidate for a life form present on Mars. One of the problems associated with the survival on Mars is the destructive ultraviolet light. These microorganisms develop a thin crust of salt that can moderate some of the ultraviolet light. Sodium chloride is the most common salt and chloride salts are opaque to short-wave ultraviolet. Their photosynthetic pigment, bacteriorhodopsin, is actually opaque to the longer-wavelength ultraviolet (its red color). In addition, Halobacterium makes pigments called bacterioruberins that are thought to protect cells from damage by ultraviolet light. The obstacle they need to overcome is being able to grow at a low temperature during a presumably short time when a pool of water could be liquid.

Applications

Food Industry

There is potential for Halobacterium species to be used in the food industry. [10] Some examples of uses can include the production of Beta-Carotene, a pigment in halophilic bacteria that contributes to their red coloration, is used in the food industry as a natural food dye. Halophiles also produce degradative enzymes such as lipases, amylases, proteases, and xylanases that are used in various food processing methods. Notable applications of these enzymes include enhancing the fermentation process of salty foods, improving dough quality for the baking of breads, and contributing to the production of coffee. [10] [11]

Bioremediation

Many species of halophilic bacteria produce exopolysaccharides (EPS) which are used industrially as bioremediation agents. Biosurfactants are also released by many halophilic bacteria and these amphiphilic compounds have been used for soil remediation. Many halophiles are highly tolerant of heavy metals making them potentially useful in the bioremediation of xenobiotic compounds and heavy metals that are released into the environment from mining and metal plating. Halophiles contribute to the bioremediation of contaminants by converting xenobiotics into less toxic compounds. [11] Some Halobacterium species have been shown to be effective in the bioremediation of pollutants including aliphatic hydrocarbons, such as those found in crude oil; and aromatic hydrocarbons such as 4-hydroxybenzoic acid, a contaminant in some high salinity industrial runoffs.[ citation needed ]

Pharmaceuticals

Some strains of Halobacterium, including Halobacterium salinarum , are being explored for medical applications of their radiation-resistance mechanisms. Bacterioruberin is a carotenoid pigment found in Halobacterium which decreases the bacteria’s sensitivity to γ-radiation and UV radiation. [12]

It has been shown in knockout studies, that the absence of bacterioruberin increases the sensitivity of the bacterium to oxidative DNA-damaging agents. Hydrogen peroxide, for example, reacts with bacteroruberin which prevents the production of reactive oxygen species, and thus protects the bacterium by reducing the oxidative capacity of the DNA-damaging agent. [13]

H. salinarum also exhibits high intracellular concentrations of potassium chloride which has also been shown to confer radiation resistance. Halobacterium are also being explored for the pharmaceutical applications of bioactive compounds they produce, including anticancer agents, antimicrobial biosurfactancts, and antimicrobial metabolites. [12]

Significance and applications

Halobacteria are halophilic microorganisms that are currently being studied for their uses in scientific research and biotechnology. For instance, genomic sequencing of the Halobacterium species NRC-1 revealed their use of eukaryotic-like RNA polymerase II and translational machinery that are related to Escherichia coli and other Gram-negative bacteria. In addition, they possess genes for DNA replication, repair, and recombination that are similar to those present in bacteriophages, yeasts, and bacteria. The ability of this Halobacterium species to be easily cultured and genetically modified allows it to be used as a model organism in biological studies. [14] Furthermore, Halobacterium NRC-1 have also been employed as a potential vector for delivering vaccines. In particular, they produce gas vesicles that can be genetically engineered to display specific epitopes. Additionally, the gas vesicles demonstrate the ability to function as natural adjuvants to help evoke stronger immune responses. Because of the requirement of Halobacteria for a high-salt environment, the preparation of these gas vesicles is inexpensive and efficient, needing only tap water for their isolation. [15]

Halobacteria also contain a protein called Bacteriorhodopsins which are light-driven proton pumps found on the cell membrane. Although most proteins in halophiles need high salt concentrations for proper structure and functioning, this protein has shown potential to be used for biotechnological purposes because of its stability even outside of these extreme environments. Bacteriorhodopsins isolated from Halobacterium salinarum have been especially studied for their applications in electronics and optics. Particularly, bacteriorhodopsins have been used in holographic storage, optical switching, motion detection, and nanotechnology. Although numerous uses of this protein have been presented, there are yet to be any high-scale commercial applications established at this time. [16]

Recombination and mating

UV irradiation of Halobacterium sp. strain NRC-1 induces several gene products employed in homologous recombination. [17] For instance, a homolog of the rad51 / recA gene, which plays a key role in recombination, is induced 7-fold by UV. Homologous recombination may rescue stalled replication forks, and/or facilitate recombinational repair of DNA damage. [17] In its natural habitat, homologous recombination is likely induced by the UV irradiation in sunlight.

Halobacterium volcanii has a distinctive mating system in which cytoplasmic bridges between cells appear to be used for transfer of DNA from one cell to another. [18] In wild populations of Halorubrum, genetic exchange and recombination occur frequently. [19] This exchange may be a primitive form of sexual interaction, similar to the more well studied bacterial transformation that is also a process for transferring DNA between cells leading to homologous recombinational repair of DNA damage.[ citation needed ]

See also

Further reading

Scientific journals

Scientific books

Related Research Articles

A halophile 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.

Gene knockouts are a widely used genetic engineering technique that involves the targeted removal or inactivation of a specific gene within an organism's genome. This can be done through a variety of methods, including homologous recombination, CRISPR-Cas9, and TALENs.

<span class="mw-page-title-main">Bacteroidota</span> Phylum of Gram-negative bacteria

The phylum Bacteroidota is composed of three large classes of Gram-negative, nonsporeforming, anaerobic or aerobic, and rod-shaped bacteria that are widely distributed in the environment, including in soil, sediments, and sea water, as well as in the guts and on the skin of animals.

<i>Sulfolobus</i> Genus of archaea

Sulfolobus is a genus of microorganism in the family Sulfolobaceae. It belongs to the archaea domain.

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.

<span class="mw-page-title-main">Halorhodopsin</span> Family of transmembrane proteins


Halorhodopsin is a seven-transmembrane retinylidene protein from microbial rhodopsin family. It is a chloride-specific light-activated ion pump found in archaea known as halobacteria. It is activated by green light wavelengths of approximately 578nm. Halorhodopsin also shares sequence similarity to channelrhodopsin, a light-gated ion channel.

<span class="mw-page-title-main">Sulfolobales</span> Order of archaea

Sulfolobales is an order of archaeans in the class Thermoprotei.

<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.

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.

<span class="mw-page-title-main">Pink lake</span> Pink lake phenomenon and examples

A pink lake is a lake that has a red or pink colour. This is often caused by the presence of salt-tolerant algae that produces carotenoids, such as Dunaliella salina, usually in conjunction with specific bacteria and archaea, which may vary from lake to lake. The most common archaeon is Halobacterium salinarum.

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

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.

<span class="mw-page-title-main">Microbial rhodopsin</span> Retinal-binding proteins

Microbial rhodopsins, also known as bacterial rhodopsins, are retinal-binding proteins that provide light-dependent ion transport and sensory functions in halophilic and other bacteria. They are integral membrane proteins with seven transmembrane helices, the last of which contains the attachment point for retinal.

<span class="mw-page-title-main">Gas vesicle</span>

Gas vesicles, also known as gas vacuoles, are nanocompartments in certain prokaryotic organisms, which help in buoyancy. Gas vesicles are composed entirely of protein; no lipids or carbohydrates have been detected.

<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>Halorubrum lacusprofundi</i> Species of archaeon

Halorubrum lacusprofundi is a rod-shaped, halophilic Archaeon in the family of Halorubraceae. It was first isolated from Deep Lake in Antarctica in the 1980s.

<span class="mw-page-title-main">Archaerhodopsin</span> Family of archaea

Archaerhodopsin proteins are a family of retinal-containing photoreceptors found in the archaea genera Halobacterium and Halorubrum. Like the homologous bacteriorhodopsin (bR) protein, archaerhodopsins harvest energy from sunlight to pump H+ ions out of the cell, establishing a proton motive force that is used for ATP synthesis. They have some structural similarities to the mammalian GPCR protein rhodopsin, but are not true homologs.

References

  1. ↑ See the NCBI webpage on Halobacterium. Data extracted from the "NCBI taxonomy resources". National Center for Biotechnology Information . Retrieved 2007-03-19.
  2. ↑ J.P. Euzéby. "Halobacterium". List of Prokaryotic names with Standing in Nomenclature (LPSN). Retrieved 2021-11-17.
  3. ↑ Sayers; et al. "Halobacterium". National Center for Biotechnology Information (NCBI) taxonomy database. Retrieved 2022-06-05.
  4. ↑ "The LTP" . Retrieved 20 November 2023.
  5. ↑ "LTP_all tree in newick format" . Retrieved 20 November 2023.
  6. ↑ "LTP_08_2023 Release Notes" (PDF). Retrieved 20 November 2023.
  7. ↑ "GTDB release 08-RS214". Genome Taxonomy Database . Retrieved 10 May 2023.
  8. ↑ "ar53_r214.sp_label". Genome Taxonomy Database . Retrieved 10 May 2023.
  9. ↑ "Taxon History". Genome Taxonomy Database . Retrieved 10 May 2023.
  10. 1 2 Paterson, Russell; Lima, Nelson (2017). "Bioprospecting". Topics in Biodiversity and Convervation. Topics in Biodiversity and Conservation. 16: 84–91. doi:10.1007/978-3-319-47935-4. ISBN   978-3-319-47933-0.
  11. 1 2 Gontia-Mishra, Iti; Sapre, Swapnil; Tiwari, Sharad (August 2017). "Diversity of halophilic bacteria and actinobacteria from India and their biotechnological applications". Indian Journal of Geo-Marine Sciences. 46 (8): 1575–1587. Retrieved 8 October 2017.
  12. 1 2 Jung, Kwang-Woo; Lim, Sangyong; Bahn, Yong-Sun (30 June 2017). "Microbial radiation-resistance mechanisms". Journal of Microbiology. 55 (7): 499–507. doi:10.1007/s12275-017-7242-5. PMID   28664512. S2CID   8910376.
  13. ↑ SHAHMOHAMMADI, HAMID REZA; ASGARANI, EZAT; TERATO, HIROAKI; SAITO, TAKESHI; OHYAMA, YOSHIHIKO; GEKKO, KUNIHIKO; YAMAMOTO, OSAMU; IDE, HIROSHI (1998). "Protective Roles of Bacterioruberin and Intracellular KCl in the Resistance of Halobacterium salinarium against DNA-damaging Agents". Journal of Radiation Research. 39 (4): 251–262. Bibcode:1998JRadR..39..251S. doi: 10.1269/jrr.39.251 . PMID   10196780.
  14. ↑ Ng, W. V.; Kennedy, S. P.; Mahairas, G. G.; Berquist, B.; Pan, M.; Shukla, H. D.; Lasky, S. R.; Baliga, N. S.; Thorsson, V.; Sbrogna, J.; Swartzell, S.; Weir, D.; Hall, J.; Dahl, T. A.; Welti, R.; Goo, Y. A.; Leithauser, B.; Keller, K.; Cruz, R.; Danson, M. J.; Hough, D. W.; Maddocks, D. G.; Jablonski, P. E.; Krebs, M. P.; Angevine, C. M.; Dale, H.; Isenbarger, T. A.; Peck, R. F.; Pohlschroder, M.; Spudich, J. L.; Jung, K.-H.; Alam, M.; Freitas, T.; Hou, S.; Daniels, C. J.; Dennis, P. P.; Omer, A. D.; Ebhardt, H.; Lowe, T. M.; Liang, P.; Riley, M.; Hood, L.; DasSarma, S. (3 October 2000). "Genome sequence of Halobacterium species NRC-1". Proceedings of the National Academy of Sciences. 97 (22): 12176–12181. Bibcode:2000PNAS...9712176N. doi: 10.1073/pnas.190337797 . PMC   17314 . PMID   11016950.
  15. ↑ Stuart, Elizabeth S.; Morshed, Fazeela; Sremac, Marinko; DasSarma, Shiladitya (15 June 2001). "Antigen presentation using novel particulate organelles from halophilic archaea". Journal of Biotechnology. 88 (2): 119–128. doi:10.1016/S0168-1656(01)00267-X. PMID   11403846.
  16. ↑ Oren, Aharon (July 2010). "Industrial and environmental applications of halophilic microorganisms". Environmental Technology. 31 (8–9): 825–834. doi:10.1080/09593330903370026. PMID   20662374. S2CID   16836957.
  17. 1 2 McCready S, Müller JA, Boubriak I, Berquist BR, Ng WL, DasSarma S (2005). "UV irradiation induces homologous recombination genes in the model archaeon, Halobacterium sp. NRC-1". Saline Syst. 1: 3. doi: 10.1186/1746-1448-1-3 . PMC   1224876 . PMID   16176594.
  18. ↑ Rosenshine I, Tchelet R, Mevarech M (1989). "The mechanism of DNA transfer in the mating system of an archaebacterium". Science. 245 (4924): 1387–9. Bibcode:1989Sci...245.1387R. doi:10.1126/science.2818746. PMID   2818746.
  19. ↑ Papke RT, Koenig JE, Rodríguez-Valera F, Doolittle WF (2004). "Frequent recombination in a saltern population of Halorubrum". Science. 306 (5703): 1928–9. Bibcode:2004Sci...306.1928P. doi:10.1126/science.1103289. PMID   15591201. S2CID   21595153.
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