How Do Microbes Remove Radioactive Waste?

Jan. 17, 2023

Radioactive elements emit a spectrum of ionizing emissions that hurt humans. 
Thankfully, numerous genera of environmental microbes possess an array of biophysical and biochemical defenses that can help. These defenses allow certain microorganisms to withstand radioactive emissions and protect us from radiation poisoning, cancer and other maladies that manifest from human exposure to radioactive waste. Taking a look at the sources and characteristic properties of radioactive waste will help explain the mechanisms by which these bacteria face the elements and shield us from illness.

Harmful effects of radioactive emissions on humans.
Harmful effects of radioactive emissions on humans.

Properties and Sources of Radioactive Waste

Radioactive waste is discharged from many sources, including military operations (such as nuclear weapons manufacture) uranium mining, power plant effluents and medical and research laboratories. Radioactive waste is filled with persistent unstable elements or radionuclides, which emit ionizing radiation as they decay. Radioactive elements have no stable isotopes, high molecular weights and fall into groups such as the actinides. They are unstable because their atoms spontaneously disintegrate, emitting both particles and energy as they transform into more stable forms. For example, over billions of years the radioactive elements uranium (U) and thorium (Th) decay into radium (Ra) and radon (Rn), respectively. During this decay process radioactive elements emit ionizing radiation. The energy released from this process is so strong that it rips electrons from atoms and molecules, ionizing them. In high enough doses, this ionizing radiation causes cell damage to living tissue and organs.

Illustration of molecules labeled with categories of ionizing radiation.
Categories of ionizing radiation.

Although these compounds have many beneficial uses in research, medicine and industry, radioactive waste can be highly destructive if not properly isolated and disposed of or contained.

Bacterial Bioremediation

While there are numerous ways to dispose of radioactive waste, biological methods, specifically bioremediation by bacteria, are desirable as they are more environmentally friendly than other methods.

Given their billion-plus years on the planet, bacteria have evolved masterful and diverse approaches to mineralize, metabolize and otherwise transform harmful compounds to innocuous byproducts. Since the harmful ionizing radiation emanates from the atomic element itself, conversion of a radioactive compound to a different molecule will not eliminate the deleterious effects. Still, a garrison of microbial genera have been isolated from radioactive waste sites. How do they survive?

Microorganisms used for bioremediation of radioactive waste demonstrate tolerance or resistance to radioactivity and can even disarm the toxic effects of radioactive waste by sequestering radioactive elements through biosorption and biomineralization processes, or through direct and indirect redox transformation.

Illustration of the 4 strategies used by microorganisms to remediate radioactive waste. 1. bioreduction 2. biomineralization (bioprecipitation) 3. biosorption 4. bioaccumulation.
The 4 strategies used by microorganisms to remediate radioactive waste. 1. bioreduction 2. biomineralization (bioprecipitation) 3. biosorption 4. bioaccumulation.
Source: Wikipedia

Bioreduction of Radionuclides

Through the common metabolic process of reduction, problematic, radioactive elements, like plutonium or uranium, in the target waste can be precipitated to make them easier to collect and dispose. Microorganisms inactivate some radionuclides by adding electrons to them and converting the radionuclides from a soluble to insoluble state. The precipitated radionuclide is still radioactive, but it is not transported into solutions, i.e., ground water, as easily as its soluble counterpart.

In oxic environments, oxygen is used as the electron acceptor in microbial respiration, generating H2O. However, microbes use alternative electron acceptors, including radioactive elements, for respiration when growing in an anoxic environment. This type of respiration uses energetically favorable electron acceptors in a sequence dictated by the redox potential in their environment. This is also how different radioactive elements are used by bacteria. Oxidized forms of a radioactive element are reduced by becoming electron acceptors for microbes using anaerobic respiration.

Three categories of reduction will be described here: direct, indirect and genetically bioengineered reduction.

Direct Reduction

Adding electrons by direct reduction occurs when a microorganism uses the oxidized form directly as an electron acceptor in anaerobic respiration. For example, the microbes Geobacter metallireducens GS15 and Shewanella oneidensis reduce oxidized soluble plutonium Pu(VI/V) to the reduced insoluble form Pu(IV).

Indirect Reduction

Indirect reduction occurs when a microorganism uses a non-radioactive element as an electron acceptor, but the reduced element resulting from this anaerobic respiration provides electrons for the subsequent reduction of a radioactive element within that micro niche. For example, ferric Iron [Fe(III)]-reducing bacteria G. metallireducens and S. oneidensis reduce uranium U(VI) indirectly via anaerobic growth. Insoluble forms of radionuclides are then easier to process for chemical and physical waste disposal technologies as they reduce the total volume of the waste.

Genetically Engineered Bioreduction

Deinococcus radiodurans, a radiation-resistant microbe (Transmission Electron Micrograph [TEM]).
Deinococcus radiodurans, a radiation-resistant microbe (Transmission Electron Micrograph [TEM]).
Source: Wikipedia
Radiation-resistant bacteria can be genetically engineered to metabolize radioactive waste. Deinococcus  radiodurans can resist extremely high concentrations of radioactivity, due to potent antioxidants and an enhanced DNA repair mechanism. This makes D. radiodurans an attractive candidate to develop for remediating repositories of radioactive waste. For example, the microbe has been engineered to express the Escherichia coli merA gene, which encodes a mercuric ion reductase. By expressing this reductase, D. radiodurans can convert toxic mercuric [Hg (II)] ions to elemental mercury, which is less harmful to humans and easier to process in waste disposal. Such strategies are applicable for other contaminants that are intermixed with radioactive waste, as well as the radionuclides themselves.


Bacteria can also remove radionuclides from their solution environment by biomineralization/bioprecipitation. In this context, biomineralization refers to the insoluble crystallization of metals, a process of metal precipitation with ligands, such as sulfides, carbonates, phosphates and hydroxides, that are enzymatically generated within the microbial cell wall.

In one study, D. radiodurans strain was reconstructed with phoN, a Salmonella enterica gene that encodes a nonspecific acid phosphatase, which liberates inorganic phosphate from complexed phosphates on the cell surface. The liberated phosphates can subsequently mineralize uranium. In fact, the recombinant D. radiodurans strain was able to precipitate over 90% of uranium from a uranyl nitrate solution in 6 hours, providing the basis for scaled-up remediation of radioactive waste in contaminated water bodies. 

Gram-negative facultative anaerobes, such as Serratia spp., and other microbial genera isolated from natural environments, including uraniferous soils, can also biomineralize and precipitate uranium. Finding naturally occurring microorganisms that have the capacity to biomineralize radionuclides provides more choices for biotechnological refinements via molecular tools.


Biosorption, the third strategy that microbes use to remediate radioactive waste, involves surface adsorption and an extracellular complexation process that, unlike biomineralization, can be reversed. This may allow for the release of the collected waste into a repository.

The bacterial cell surface is coated with various negatively charged groups (e.g. phosphates, sulfides) that attract and remove radioactive metals from an environment. Through this process, certain strains of Pseudomonas can sequester uranium and thorium ions intracellularly. Biosorption of radionuclides at the microbial cell surface facilitates the removal of radionuclides from waste and prevents radioactive leakage and migration of nuclear waste to groundwater. Low-concentration radioactive metallic wastes found in effluents downstream from industrial and research facilities are amenable to biosorption-style remediation.


Tucking substances into micro pockets on a microbial "coat" is one way to view bioaccumulation, the fourth strategy for bioremediation of radioactive waste. Bioaccumulation involves the build-up of radioactive waste inside the bacterial cell. Some metal ions, including radioactive ones, are structurally similar to the essential elements for bacterial growth.

An advantageous side-effect of this molecular mimicry is that microbes take up radioactive ions from the environment. For example, some Pseudomonas species accumulate uranium as uranyl phosphates. Since uranium has no known physiological function within the cell, this uranium uptake is likely due to its natural membrane permeability. Other microbes, like Arthrobacter nicotianaeMicrococcus luteusCitrobacter sp. N14 and Bacillus megaterium, are also radioactive waste bioremediators via bioaccumulation (e.g., M. luteus, B. subtilis and B. megaterium accumulate Th when grown in a Th and U solution).

Table of strategies used by species/genera of microbes to bioremediate radionuclides.
A summary of the strategies used by various species and genera of microorganisms to bioremediate radionuclides.
Source: Vandana et al./Microbial Rejuvenation of Polluted Environment, Jan. 2021 and Natarajan et al./Environmental Science and Pollution Research, March 2020

Repurposing Radioactive Waste

Since some radioactive elements take a long time to decay (the half-life of uranium-238 is approximately 4.5×109 years) it is desirable to reuse the radioactive waste that is collected through bacterial concentration of these elements. Approaches for repurposing radioactive waste are still in the early stages of research, but one method relies on the surface layer, or S-layer, of Bacillis sphaericus.

S-layers are para-crystalline surface structures present on most bacteria and almost all archaea. S-layer proteins typically comprise up to 15% of all proteins of a cell, although B. sphaericus subspecies contain an even higher S-layer protein content—up to 20%. B. sphaericus isolated from uranium mining waste reversibly binds radioactive metals within its S-layer, and scientists have discovered that the extra surface coat is capitalized for both the remediation and re-use of radionuclides for alternate forms of energy. 

To optimize this strategy, microbiologists developed a filter that integrated B. sphaericus S-layer to trap uranium ions from soil and aqueous radioactive waste. The uranium and other collected metals are then repurposed for use for nanotechnology and novel catalysts.

Leveraging Microbial Strategies

Microbes are superbly adept at cleaning up radioactive waste, and scientists are leveraging this potential to improve our methods of removing the persistent, insidious material from the environment. Waste sites that have ongoing remediation efforts include U.S. DOE Rifle site, Colorado, U.S. DOE Oak Ridge site, Tennessee and U.S. DOE Hanford site, Washington. Relevant research includes conducting metagenomics studies of uncultured microorganisms growing in sites contaminated with radioactive waste to determine the abundance and identity of the genes encoding the enzymes responsible for the microbial strategies that sequester radioactive elements.

New advances in omics also reveal microbial physiology and metabolic function of the microbial communities at these sites. Omics includes metagenomics, transcriptomics and metabolomics studies, coupled with state of-the-art, high-performance sequencing tools. Computational analysis of microbial ecology data, along with the use of bioreactor designs, can facilitate development of methods to help remediate a diverse range of radioactive waste sites.

Taken to the field, microbial bioremediation uses integrated techniques, which combine physical and chemical approaches, and a blend of technologies (i.e., phyto and myco remediation) to improve the remediation of a diverse range of radioactive waste sites.

Bioremediation is an environmentally friendly and cost-effective technology for radioactive waste removal. Discovering more of the mechanisms used by nuclear waste site bacteria will capacitate microbiologists to channel these bacterial allies towards removing and repurposing radioactive wastes.
The unique adaptability of microbes to take harmful materials and convert them to usable products extends beyond the bioremediation of radioactive waste, and scientists are eager to harness this adaptability to inform sustainability issues. Learn more about the circular economy and microbial infability hypothesis in this next article about research being conducted by environmental microbiologist Arpita Bose, Ph.D.

Author: JeanMarie Calvillo, Ph.D.

JeanMarie Calvillo, Ph.D.
JeanMarie Calvillo, Ph.D., worked as a research microbiologist at the University of Washington, Seattle in the civil and environmental engineering department.