Deinococcus radiodurans is a bacterium, an organism that lives in extreme environments, and one of the most radiation-resistant organisms known. It can survive cold, dryness, vacuum, and acid, and is called a polyextremophile because it can live in many extreme conditions. The Guinness Book of World Records listed it in January 1998 as the world's most radiation-resistant bacterium or lifeform.

Other bacteria with similar resistance to radiation are known, including some species of the genus Chroococcidiopsis (phylum cyanobacteria) and some species of Rubrobacter (phylum Actinomycetota). Among the archaea, the species Thermococcus gammatolerans has comparable resistance to radiation.

Name and classification

The genus name Deinococcus comes from the Ancient Greek words deinós, meaning "terrible," and kókkos, meaning "berry." The specific name radiodurans is from the Latin words radius, meaning "radiation," and durare, meaning "to survive." This species was once called Micrococcus radiodurans. Because of its strength, it is sometimes called "Conan the Bacterium," named after a strong character from a story.

At first, this bacterium was grouped with the genus Micrococcus. Later, scientists studied ribosomal RNA and other evidence and moved it to its own genus, Deinococcus, which is closely related to the genus Thermus.

Deinococcus is one of three genera in the order Deinococcales. D. radiodurans is the type species of this genus and the most studied member. All known species in the genus are resistant to radiation. These include D. proteolyticus, D. radiopugnans, D. radiophilus, D. grandis, D. indicus, D. frigens, D. saxicola, D. marmoris, D. deserti, D. geothermalis, and D. murrayi. The last two species, D. geothermalis and D. murrayi, can also live in very hot environments.

History

Deinococcus radiodurans was discovered in 1956 by Arthur Anderson at the Oregon Agricultural Experiment Station in Corvallis, Oregon. Scientists were testing if high doses of gamma radiation could sterilize canned food. A tin of meat was exposed to radiation believed to kill all known life, but the meat later spoiled, and D. radiodurans was found in the sample.

In 1999, The Institute for Genomic Research published the complete DNA sequence of D. radiodurans. A detailed analysis of its genome was released in 2001. The genome consists of four parts: two chromosomes measuring 2.65 Mbp and 412 kbp, one megaplasmid of 177 kbp, and one regular-sized plasmid of 46 kbp. The sequenced strain was ATCC BAA-816.

In August 2020, scientists reported that Earth bacteria, including Deinococcus radiodurans, survived for three years in outer space, as shown by experiments on the International Space Station (ISS). These findings support the idea of panspermia, the theory that life exists throughout the Universe and is spread through space dust, meteoroids, asteroids, comets, planetoids, or spacecraft.

Description

Deinococcus radiodurans is a large, round bacterium that measures 1.5 to 3.5 micrometers in diameter. Four cells usually join together to form a group called a tetrad. These bacteria are easy to grow in laboratory conditions and do not cause illness. Under controlled conditions, scientists can observe cells in different shapes, such as pairs, groups of four, or larger clusters. When grown, the bacteria form smooth, rounded colonies that are pink or red in color. The cells are classified as Gram positive, but their cell structure is unique and somewhat similar to the cell walls of Gram negative bacteria.

Deinococcus radiodurans does not produce protective spores and cannot move on its own. It requires oxygen to generate energy from organic materials in its environment. It is commonly found in places with high levels of organic matter, such as sewage, meat, feces, or soil. It has also been discovered in medical equipment, dust, fabrics, and dried food.

This bacterium is highly resistant to radiation, ultraviolet light, drying, and substances that cause chemical damage. Scientists can use PCR tests and fluorescent in situ hybridization (FISH) methods to detect D. radiodurans in natural environments.

The genome of D. radiodurans includes two circular chromosomes, one 2.65 million base pairs long and the other 412,000 base pairs long. It also contains a megaplasmid of 177,000 base pairs and a plasmid of 46,000 base pairs. The bacterium has about 3,195 genes. During its stationary phase, each cell holds four copies of its genome. When growing rapidly, each cell contains 8 to 10 copies of the genome.

Ionizing-radiation resistance

Deinococcus radiodurans can survive very high levels of radiation, such as 5,000 grays (Gy) without losing much of its ability to live, and 12,000 Gy with about 10% of its cells surviving. A dose of 5,000 Gy causes many breaks in the DNA of the organism. Scientists estimate that each gray of radiation causes about 0.005 breaks per million base pairs (Mbp) of DNA. Since the bacterial genome is about 3.2 Mbp, this would result in about 80 breaks if the DNA was haploid. For comparison, a chest X-ray or an Apollo mission exposes a person to about 1 mGy of radiation. A dose of 5 Gy can kill a human, 200–800 Gy can kill E. coli, and more than 4,000 Gy can kill the radiation-resistant tardigrade.

Deinococcus radiodurans resists radiation by having multiple copies of its genome. Studies using scanning electron microscopy show that DNA in D. radiodurans is arranged into tightly packed structures called toroids, which may help repair DNA.

This bacterium can repair both single- and double-stranded DNA damage. When DNA damage is detected, the cell moves the damaged DNA into a special ring-shaped area inside the cell where repairs occur. After repairs, the cell can combine the fixed DNA with DNA from the outside of the compartment.

Deinococcus radiodurans usually repairs chromosome breaks within 12–24 hours using a two-step process.

The bacterium can also take in DNA from other cells through a process called genetic transformation. This DNA is then added to its own genome using a process called homologous recombination. This may help if the DNA in a single cell is not enough to repair a complete chromosome. Natural genetic transformation in D. radiodurans happens under stressful conditions and is linked to DNA repair. When DNA damage, such as pyrimidine dimers, is introduced into donor DNA by UV light, recipient cells repair the damage in the same way they repair damage in their own DNA.

Michael Daly suggested that D. radiodurans uses manganese complexes as antioxidants to protect itself from radiation. In 2007, his team found that high levels of manganese(II) inside the bacterium protect proteins from being damaged by radiation. They proposed that proteins, not DNA, are the main target of radiation in sensitive bacteria, and that extreme resistance in bacteria that store manganese is due to protection of proteins. In 2016, Massimiliano Peana and others studied how manganese(II) interacts with specific peptides in D. radiodurans using techniques like NMR, EPR, and ESI-MS. In 2018, Peana and Chasapis used bioinformatics to identify manganese-binding proteins in D. radiodurans and proposed a model for how manganese interacts with proteins involved in responding to stress caused by reactive oxygen species (ROS).

In 2009, scientists found that nitric oxide plays an important role in D. radiodurans recovery after radiation exposure. The gas is needed for the bacteria to divide and grow after DNA damage is repaired. A gene that increases nitric oxide production after UV radiation was identified. Without this gene, the bacteria could still repair DNA damage but could not grow.

Other mechanisms, such as LEA proteins and the SDBC, are described in the following section.

A question remains about how D. radiodurans evolved such high resistance to radiation. Natural background radiation levels are very low, typically about 0.4 mGy per year. Even in areas with the highest known background radiation, such as near Ramsar, Iran, levels are only 260 mGy per year. This suggests that organisms evolving to resist high radiation levels are unlikely. In the distant past, higher radiation levels existed due to more radioactive elements and natural nuclear reactors, such as those in Oklo, Gabon, which were active about 1.7 billion years ago. However, even if adaptations to high radiation evolved at that time, genetic changes over time would likely have eliminated them if they had no other benefits.

A team of scientists proposed that D. radiodurans may have originated on Mars. They suggested that the bacterium evolved on the Martian surface before being delivered to Earth via a meteorite. However, Deinococcus is genetically and biochemically similar to other Earth-based life forms, which supports the idea that it evolved on Earth.

Valerie Mattimore of Louisiana State University suggested that the bacterium’s radiation resistance is a side effect of a mechanism to survive long periods of dryness. She tested this by showing that mutant strains of D. radiodurans that are highly sensitive to radiation are also highly sensitive to dryness, while the normal strain resists both. She also found that dryness causes DNA breaks similar to those caused by extreme radiation. In addition to DNA repair, D. radiodurans uses LEA proteins to protect against dryness.

The strong cell envelope of D. radiodurans, made up of a protein complex called the S-layer Deinoxanthin Binding Complex (SDBC), also contributes to its resistance. This complex acts as a shield against radiation and helps protect the cell from high temperatures and dryness.

Applications

Deinococcus radiodurans has the ability to be used in many areas of science. Scientists have changed the genetic makeup of D. radiodurans to help clean up polluted environments. It is also useful in medical research and in the development of nanotechnology.

Bioremediation is the process of using living things, such as bacteria, fungi, plants, or enzymes from these organisms, to clean up environments that have been polluted. Many areas of soil, sediment, and groundwater are polluted with radioactive materials, heavy metals, and harmful chemicals. Some bacteria can help remove heavy metals from soil by trapping them, but radiation from nuclear waste often stops other bacteria from working. Because of this, D. radiodurans is a good choice for cleaning up nuclear waste. Scientists have changed D. radiodurans to help it break down harmful solvents and heavy metals in radioactive areas. A gene from Escherichia coli was added to D. radiodurans to help it remove mercury from nuclear waste. Researchers also created a version of D. radiodurans that can remove both mercury and toluene from mixed radioactive waste. Scientists added genes from Salmonella enterica and Sphingomonas to help D. radiodurans remove uranium from water in both acidic and alkaline conditions.

In medical research, D. radiodurans can help scientists study how aging and cancer happen. These conditions are often caused by damage to DNA, RNA, and proteins from harmful molecules called reactive oxygen species (ROS). Scientists are studying how D. radiodurans protects its cells from this damage and repairs its DNA. These discoveries may help develop medical treatments to slow aging or prevent cancer. Researchers are also testing how D. radiodurans' protective systems could help human cells avoid damage from ROS or help cancer cells become resistant to radiation.

In nanotechnology, scientists have used D. radiodurans to create silver and gold nanoparticles. Traditional methods to make these particles are costly and create pollution. Using living organisms to make nanoparticles is a cheaper and more environmentally friendly option. These nanoparticles are useful in medicine because they can kill harmful bacteria, prevent the growth of algae, and damage cancer cells.

Other uses of D. radiodurans include helping scientists build synthetic DNA. Researchers used parts of D. radiodurans' DNA repair system to create a synthetic organism called Mycoplasma laboratorium. In 2003, scientists showed that D. radiodurans could store information in its DNA. They encoded the song "It's a Small World" into DNA segments and successfully retrieved the information after many generations of the bacteria.

Clues for future search of extremophile microbial life on Mars

When grown in labs and exposed to radiation in liquid environments, Deinococcus radiodurans can survive up to 25 kGy. Horne et al. (2022) studied how drying and freezing affect the ability of microbes to survive radiation, focusing on research to return Martian subsurface soil samples for analysis and to identify suitable landing sites for future robotic missions. They discovered that dried and frozen cells could survive a radiation dose 5.6 times higher: up to 140 kGy. They estimated that this survival level might allow microbes to remain alive for about 280 million years at a depth of 33 feet (10 meters) below the Martian surface. However, this time is much shorter than the period since liquid water disappeared from Mars (2–2.5 billion years ago), making it unlikely for microbes to survive long enough to be found by a rover drilling below the surface. Despite this, Horne et al. (2022) suggest that meteorite impacts may have heated parts of the Martian subsurface over time, occasionally melting ice and creating brief opportunities for dormant microbes similar to Deinococcus radiodurans to briefly become active before freezing again. To increase the chances of finding dormant microbes in Martian soil for analysis, future missions like the European Rosalind Franklin rover should aim to collect samples from relatively young impact craters, where microbes might be better protected from deadly radiation.