Scientists discover game-changing bacterium that literally eats nuclear waste — here’s how it could protect us from toxins

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There are many types of bacteria in the world. One particular group is called an extremophile, which means it thrives only under extreme conditions such as high or low acidity, temperature, pressure, oxygen, etc. Bacteria consume many sorts of organic nutrients, too, and there are even some that use photosynthesis like plants to create their own. Some bacteria have symbiotic relationships with other creatures as well, like those in our gut, on our skin, or inside plant nodules. Whether they break food down or generate their own, bacteria energy sources to keep them alive, whether under normal or extraordinary environmental conditions. The energy can come from light or breaking down organic molecules (sugars or amino acids), or inorganic molecules (like minerals). But in recent years, scientists have discovered some bacteria that use radioactive materials and are not harmed by them. How is that possible?

How they get energy:

• Plants and some bacteria get energy directly from sunlight to put carbon dioxide and water together to make oxygen and organic compounds that store the energy. Photosynthesis is the name of that process, and it means taking light ("photo") to build ("synthesize") food containing energy.
• Another type of bacteria just digest organic molecules (big sugars, proteins, amino acids, etc.) into smaller sugars that store energy from the original material.
• A final type also digests organic material, but it needs minerals like iron or sulfur to provide some energy that gets incorporated into smaller molecules they store or digest to release that energy. 

In 1956, Arthur Anderson and his research team from the Oregon Agricultural Experiment Station in Corvallis, Oregon were studying how to sterilize canned foods. They hit them with gamma radiation strong enough to kill all forms of life (250 times stronger than what kills ordinary bacteria), but they discovered a bacteria that survived. Soon afterward, similar bugs were found in sausage, fish, and air samples, as well as English soil, granite in Antarctica, animal feces in a zoo, and a shielding pool for cobalt radiation. It's everywhere.

Anderson's bacteria was named Micrococcus radiodurans. "Micro" means small, and "coccus" refers to the spherical shape. It might be found singly, in pairs, or in groups of four. The species name suggests its durability to radiation. Later, this was identified genetically as a new genus, so the name changed to Deinococcus radiodurans, where "deino" means terrible. 

A tetrad of Deinococcus radiodurans (Wikipedia)

Since Anderson's discovery, many other bacteria have been shown to be highly resistant to UV and ionizing radiation. "Highly resistant" needs some clarification. A chest X-ray produces 0.0001 rads of radiation, and humans die when exposed to 500 rads. But D. radiodurans can survive 500,000 rads with no loss of viability, and a third of its population is still around after exposure to 1,500,000 rads (more than what was in the atomic bombs at Hiroshima and Nagasaki)! So, how do they do it?

Gamma rays and X-rays pass through cellular material and cause breaks in one or both strands of the DNA molecule. That can be enough to cause problems in the cells' ability to reproduce.

From Jobilize.com

Virtually all life has built-in mechanisms to protect or repair the day to day damage to its DNA. This daily damage can occur from exposure to sunlight or chemicals in the environment or the body, so it's important for creatures to have an efficient repair system operating. Deinococcus radiodurans, like most bacteria and other creatures, has DNA shaped like a twisted ladder (double helix). However, instead of being assembled in string-like strands or chromosomes, it's in an unbroken circle. 

The DNA repair tools that this bacteria use are similar to the ones in many other life forms, but they work much faster and more efficiently (fixing >100 breaks in one DNA molecule compared to 2 or 3 by other bacteria). Its unique repair system can heal hundreds to thousands of DNA breaks per cell, while regular bacteria can only tackle a few dozen before dying.

Normal repair tools fix problems if one strand in the DNA ladder is damaged. But if both strands of the DNA are damaged, those other tools are needed, but another copy of the DNA is needed to serve as a template to copy the correct broken pieces. Fortunately, D. radiodurans has 4-10 sets of its DNA, more than other bacteria, that it can use in this way.

D. radiodurans not only repairs itself, but it has a protection mechanism as well. Damage from ionizing radiation is lethal mostly because it generates free radicals of oxygen, which cause DNA injury. This is mediated by high concentrations of manganese which D. radiodurans seems to stockpile. The manganese protects the DNA repair proteins instead of the DNA itself.

Put these repair tools and protection mechanism together, and it isn't surprising that D. radiodurans is often called "Conan the Bacterium", suggesting its strength to survive. Look below at a comparison with a common bacteria.

Survival of D. radiodurans vs E. coli against gamma rays (Minton, 1994)

When some bacteria use minerals like iron or sulfur in their metabolism, they change the mineral from one form to another. In the case of iron, they take it from the water, use it, and leave its chemically changed form to settle out on the bottom instead of remaining dissolved. Some bacteria like D. radiodurans can be engineered to do the same thing with radioactive materials. Their natural ability to survive radiation keeps them around for the newly genetically engineered metabolism to operate. Its byproducts settle out and allow for bioremediation in areas where the dangerous minerals like uranium are dissolved in water. Lab experiments, for example, show a 90% removal of uranium in 6 hours in this way.

This process has also been shown to work for other dangerous, non-radioactive materials. For example, D. radiodurans has the ability to survive radiation from uranium, and by splicing into its DNA a gene to tolerate and convert mercury, scientists have been able to clean up waste sites of the mercury. Since a third of the 3,000 waste sites in the U.S. are leaking into the ground, this multi-billion dollar cost can be greatly reduced with such a treatment.

Radiation-resistant bacteria can also be beneficial in another way. They make chemicals called extremolytes (extreme metabolites) like UV protecting proteins for their own survival. Some of these can be used as sunscreens or antioxidants.

The antioxidants made by these special bacteria can be used to improve vaccines, too. Vaccines made by irradiating the virus or bacteria you want to generate an immune response are more effective than those made by heating or chemically treating the bugs. The radiation destroys the bug's DNA, but it can also destroy a protein that generates the desired immune reaction, unless it is protected by adding the antioxidant from a radiation-resistant bacteria.

D. radiodurans manganese protecting vaccine particle (Gayen et al, 2017)

Tough Deinococcus radiodurans has been found all over the Earth, and because of its resistance to radiation, acidity, and drying, some have said it might be one of the earliest organism on the planet. Others suggest it might have been transplanted here from Mars when it was ejected from collisions with meteors. Whatever the case, studying it may help us learn not only what is out there in the cosmos, but also how to protect ourselves from radiation damage.