| Deinococcus marmoris | |
|---|---|
Scientific classification  | |
| Domain: | Bacteria |
| Phylum: | Deinococcota |
| Class: | Deinococci |
| Order: | Deinococcales |
| Family: | Deinococcaceae |
| Genus: | Deinococcus |
| Species: | D. marmoris |
| Binomial name | |
| Deinococcus marmoris Hirsch 2004 | |
Deinococcus marmoris is a Gram-positive bacterium isolated from Antarctica. [1] As a species of the genus Deinococcus , the bacterium is UV-tolerant and able to withstand low temperatures. [2]
Deinococcus marmoris type strain AA-63T (DSM 12784T) was isolated from a marble sample in Antarctica by Peter Hirsch and colleagues in 2004, and the specific strain PAMC 26562 was isolated in the King George Island in Antarctica from a sample of lichen species called Ursnea. [3] [1] The isolates from antarctic marble were isolated in PGYV broth, a mineral salt solution containing peptone, glucose, yeast, and vitamin solution, at neutral pH and incubated at a range of 9 to 18 degrees Celsius. [1]
Deinococcus marmoris is a part of the domain Bacteria, phylum Deinococcota , class Deinococci, order Deinococcales, family Deinococcaceae, and genus Deinococcus . [4] This bacterium was isolated along with six other related species, among which are its closest relatives, D. frigens and D. saxicola . [1] The bacterium is in close phylogenetic proximity to Deinococcus radiodurans , which has become well understood in terms of its metabolic functions and radiation tolerance. [5] [6] D. marmoris is also related to thermophiles from the genera Thermus and Meiothermus . [3] The phylogenetic relationships were determined using 16S ribosomal RNA analyses. [3] [5]
With respect to the ecology of the genus Deinococcus most of the species are able to live under increased levels of radiation and desiccation. [1] Deinococcus have also shown the ability to precipitate heavy metals and toxins from nuclear waste in order to make removal easier. [7] Most of the species are able to live under increased levels of radiation and desiccation. Deinococcus have also shown the ability to precipitate heavy metals and toxins from nuclear waste in order to make removal easier. [7] It is known that the growth optimum of Deinococcus marmoris is psychrophilic at 15 degrees Celsius, and it is also known that the organism was isolated from a marble slab. [1] Currently, the only known location of Dienococcus marmoris is in Antarctica where it was originally sampled. [1]
The complete genome of Deinococcus marmoris [DSM 12784T] has been sequenced using Illumina Hiseq 2000 and Illumina Hiseq 2500, which are techniques that fragment the DNA of interest and record fluorescence with each individual base of the fragment. [8] This type of sequencing technique gathers small fragments of overlapping DNA sequences called contigs. [9] The contigs gathered from Illumina were then delivered to the DOE Joint Genome Institute (JGI), where the whole genome sequence was recorded and published. [8] Nikos Kyrpides added the genome assembly on March 1, 2012, using an assembly method through JGI Gold Analysis Project, though it was modified on August 5, 2014. [8] The Deinococcus marmoris genome was found to contain 4,800,021 base pairs and a G+C content of 64.4 percent. [1] [10] [11] Of the total sequence, 4,145,112 of the base pairs code for DNA. [8] There are 4,688 total genes and 4,620 protein coding genes. [8] [12] In addition, the genome contains 68 RNA genes and 252 scaffolds. [8] The genome includes genes for restriction endonuclease activity as well as a plasmid. [1] Among the 1,046 protein-coding genes associated with KEGG pathways, Deinococcus marmoris contains genes involved in the citric acid cycle such as pyruvate dehydrogenase, phosphoenolpyruvate carboxykinase, pyruvate kinase, and citrate synthase. [8] The D. marmoris genome also contains genes necessary for the glycolysis and gluconeogenesis pathways, including glucokinase, phosphoglucomutase, phosphofructokinase, and enolase. [8] D. marmoris is able to utilize the pentose phosphate pathway with genes that encode enzymes such as ribokinase, phosphopentomutase, and ribose-5-phosphate isomerase. [8] In its oxidative phosphorylation pathway, the organism uses a multi-subunit NADH-quinone oxidoreductase, genes encoding succinate dehydrogenase and fumarate reductase subunits, genes encoding cytochrome c oxidase subunits, and a V/A-type H+ ATPase enzyme. [8] It has been found that the organism is auxotrophic for synthesis of amino acids such as L-lysine, L-phenylalanine, L-tyrosine, L-tryptophan, L-histidine, L-cysteine, L-leucine, L-isoleucine, L-valine, and L-serine. [8] The organism is able to synthesize (and thus is prototrophic for the synthesis of) the following amino acids: L-alanine, L-glutamate, L-asparagine, L-glycine, and L-glutamine. [8]
Deinococcus marmoris is a Gram-positive, non-motile bacterium that is UV-tolerant and grows in aerobic conditions. [1] The bacterium is coccus, or circle shaped, and its colony color ranges from pink to orange. It grows best in oligotrophic conditions, with high oxygen concentration and few nutrients from plant inhabitants.[ citation needed ]
Researchers have found that D. marmoris grows best with little salt concentration and at low temperatures; it was cultured using a PYGV agar, which is composed of 20 mL of mineral salt solution along with yeast extract, peptone, and distilled water. [2] Due to the organism's psychrophilicity, researchers used a temperature of 15 °C for optimal growth conditions, and the optimal pH for growth of D. marmoris is neutral at 7.5.[ citation needed ]
The metabolism of Deinococcus marmoris has not been researched extensively therefore must be inferred from known relatives in the same genus. The main carbon source for Deinococcus radiodurans is fructose which undergoes several catabolic reactions to eventually the TCA cycle and produces the molecules NADH and FADH for its electron transport chain and the eventual production of ATP. [6] A byproduct of the production of ATP is O
2 which can be either endogenously or exogenously induced to create a reactive oxidative species (ROS). [6] The induction of O
2 into a ROS is by gamma irradiation which can be reduced with an abundance of Mn(II) inside the cell as the reduced form of Mn(IV). [6] Mn(II) is able to reduce the amount of ROS in Deinococcus radiodurans because it acts as an antioxidant and assists other enzymatic reactions that reduce the total amount of ROS allowing the organism to survive in environments of high exposure to radiation. The metabolism of Deinococcus marmoris at this point in time is limited to the research that has been completed; however, what is currently known is that as part of the Deinococcus taxa the species must be radioactively resistant with similar mechanisms to reduce the amount of ROS inside the cell. [6]
The genus Deinococcus is renowned for being the most radioactive resistant bacteria. [13] They have the ability to absorb ionizing and UV radiation and withstand damage from a range of sources, which can include desiccation and oxidative stress. [13] These characteristics and the ability to resist harsh environments has proved to be useful to researchers. [13] Deinococcus has been applied to the task of cleaning and removing nuclear waste. [13] They have shown the ability to precipitate heavy metals and toxins from nuclear waste in order to make removal easier. [13] According to an experiment from Appukuttan et al. published in 2006, [13] a Deinococcus species was introduced to a 0.8 mM uranyl nitrate solution. After 6 hours, 90% of the uranium was bioprecipitated out of the solution. According to this study, this will provide an efficient and eco-friendly solution to nuclear cleanup and waste removal. Due to continued research and genomic sequencing of Deinococcus, its ability to be used as a model organism instead of Escherichia coli and Saccharomyces cerevisiae. [13] This allows for researchers to have another diverse organism to experiment with.
When measuring the G+C content Junghee Kim and colleagues concluded that it was 64.1% which is high for an organism. This raises the question though as to why if Deinococcus marmoris has a high G+C content that its growth optima is at 15 degrees Celsius? [1] This could be useful for studying the other purposes of the G+C content or what factors could be leading to Deinococcus marmoris not being able to survive higher temperatures as its growth optima as its G+C content would suggest. Other reasons why we should pay particular attention to Deinococcus marmoris is because it has a similar sequence size to Escherichia coli. This can be particularly useful because it opens the opportunity of Deinococcus marmoris to becoming a model organism for environmental conditions that call for low temperatures and high radiation. The sole reason that it could be considered for use as a model organism is based on the fact of its small genome size like that of E. coli, however, more research must be done on its sequence to fully understand the organism before manipulating its genome.[ citation needed ]
An extremophile is an organism that is able to live in extreme environments, i.e. environments with conditions approaching or expanding the limits of what known life can adapt to, such as extreme temperature, radiation, salinity, or pH level.
Deinococcota is a phylum of bacteria with a single class, Deinococci, that are highly resistant to environmental hazards, also known as extremophiles. These bacteria have thick cell walls that give them gram-positive stains, but they include a second membrane and so are closer in structure to those of gram-negative bacteria.
Radioresistance is the level of ionizing radiation that organisms are able to withstand.
Deinococcus radiodurans is a bacterium, an extremophile and one of the most radiation-resistant organisms known. It can survive cold, dehydration, vacuum, and acid, and therefore is known as a polyextremophile. It has been listed as the world's toughest known bacterium in The Guinness Book Of World Records.
Deinococcus is in the monotypic family Deinococcaceae, and one genus of three in the order Deinococcales of the bacterial phylum Deinococcota highly resistant to environmental hazards. These bacteria have thick cell walls that give them Gram-positive stains, but they include a second membrane and so are closer in structure to Gram-negative bacteria. Deinococcus survive when their DNA is exposed to high doses of gamma and UV radiation. Whereas other bacteria change their structure in the presence of radiation, such as by forming endospores, Deinococcus tolerate it without changing their cellular form and do not retreat into a hardened structure. They are also characterized by the presence of the carotenoid pigment deinoxanthin that give them their pink color. They are usually isolated according to these two criteria. In August 2020, scientists reported that bacteria from Earth, particularly Deinococcus bacteria, were found to survive for three years in outer space, based on studies conducted on the International Space Station. These findings support the notion of panspermia, the hypothesis that life exists throughout the Universe, distributed in various ways, including space dust, meteoroids, asteroids, comets, planetoids or contaminated spacecraft.
Chroococcidiopsis is a photosynthetic, coccoidal bacterium. A diversity of species and cultures exist within the genus, with a diversity of phenotypes. Some extremophile members of the order Chroococidiopsidales are known for their ability to survive harsh environmental conditions, including both high and low temperatures, ionizing radiation, and high salinity.
Deinococcus geothermalis is a non-pathogenic, sphere-shaped, Gram-positive, heterotrophic bacterium, where geothermalis means 'hot earth' or 'hot springs'. This bacterium was first obtained from the hot springs of Agnano, Naples, Italy and São Pedro do Sul, Portugal.
Deinococcus ficus strain CC-FR2-10T is a recently discovered gram-positive bacteria which plays a role in the production of nitrogen fertilizer. It was originally isolated from a Ficus plant, hence its name.
Deinococcus frigens is a species of low temperature and drought-tolerating, UV-resistant bacteria from Antarctica. It is Gram-positive, non-motile and coccoid-shaped. Its type strain is AA-692. Individual Deinococcus frigens range in size from 0.9-2.0 μm and colonies appear orange or pink in color. Liquid-grown cells viewed using phase-contrast light microscopy and transmission electron microscopy on agar-coated slides show that isolated D. frigens appear to produce buds. Comparison of the genomes of Deiococcus radiodurans and D. frigens have predicted that no flagellar assembly exists in D. frigens.
Deinococcus saxicola is a species of low temperature and drought-tolerating, UV-resistant bacteria from Antarctica. It is Gram-positive, non-motile and coccoid-shaped. Its type strain is AA-1444T.
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.
Rubrobacter xylanophilus is a thermophilic species of bacteria. It is slightly halotolerant, short rod- and coccus-shaped and gram-positive, with type strain PRD-1T. It is the only true radiation resistant thermophile. It can degrade xylan and hemicellulose. The first strain of the genus Rubrobacter was isolated from gamma-irradiated hot spring water samples by Yoshinaka. This organism was found to be extremely gamma-radiation resistant, with a higher shoulder dose than the canonical radiation resistant species of the genus Deinococcus. The organism stained Gram-positive and was slightly thermophilic with an optimum growth temperature of about 60 °C.
Deinococcus deserti is a Gram-negative, rod-shaped bacterium that belongs to the Deinococcaceae, a group of extremely radiotolerant bacteria. D. deserti and other Deinococcaceae exhibit an extraordinary ability to withstand ionizing radiation.
Xenophilus azovorans is a bacterium from the genus Xenophilus which has been isolated from soil in Switzerland.
Microbacterium radiodurans is a Gram-positive, heterotrophic and strictly aerobic bacterium from the genus Microbacterium which has been isolated from the Gobi desert in China. Microbacterium radiodurans is resistant against UV radiation.
Halomonas meridiana is a bacterial species discovered in 1990 in the hypersaline lakes of Vestfold Hills, Antarctica.
Endozoicomonas gorgoniicola is a Gram-negative and facultative anaerobic bacterium from the genus of Endozoicomonas. Individual cells are motile and rod-shaped. Bacteria in this genus are symbionts of coral. E. gorgoniicola live specifically with soft coral and were originally isolated from a species of Plexaura, an octocoral, off the coast of Bimini in the Bahamas. The presence of this bacterium in a coral microbiome is associated with coral health.
Deinococcus aerius is an anaerobic bacterium that can be found in the atmosphere above the island of Japan. Living in such conditions makes these bacteria highly resistant to desiccation, UV-C, and gamma radiation. Although previously unidentified as strain TR0125, this bacterium was determined to be Deinococcus aerius by 16S rRNA sequencing.
Arthrobacter bussei is a pink-coloured, aerobic, coccus-shaped, Gram-stain-positive, oxidase-positive and catalase-positive bacterium isolated from cheese made of cow´s milk. A. bussei is non-motile and does not form spores. Rod–coccus life cycle is not observed. Cells are 1.1–1.5 µm in diameter. On trypticase soy agar it forms pink-coloured, raised and round colonies, which are 1.0 mm in diameter after 5 days at 30 °C The genome of the strain A. bussei KR32T has been fully sequenced.
The species Rhizorhabdus wittichii, formerly Sphingomonas wittichii, is a Gram-negative, rod-shaped motile bacterium, with an optimum growth temperature at 30 °C. It forms a greyish white colony. It has been found to have a 67mol% of DNA G+C content.