U.S. Department of Energy 

Office of Science

Using Nature’s Own Toolkit to 

Clean up the Environment

Summary 

Microbes can thrive in the most inhospitable environments on earth, including highly contaminated waste sites, and can even use toxic wastes as sources of food and fuel. In the case of 

organic wastes, environmental engineers are already using bacteria as chemical factories for 

cleanup. Recent advances in genomics and proteomics may allow us to use microbes to change 

the chemical properties of radioactive metals to make them less soluble in water, reducing their 

ability to migrate and to threaten plants, animals, or human beings. 

Microbes have been found living, even thriving, 

in every conceivable and inhospitable environment on earthfrom boiling thermal vents in 

the depths of the oceans to the ice floes of the 

artic to some of the most heavily contaminated 

sites. This remarkable ability of microbes to 

survive in extreme environments can be used to 

solve some of our most intractable problems, 

including cleanup of sites contaminated with 

radionuclides. 

The concept of bioremediation is simple: certain 

microorganisms recognize toxic contaminants as 

food or energy sources and either consume them

outright or make them insoluble in water and 

thus unavailable to humans, animals, or plants. 

Our challenge is to figure out how to get 

microbes to work for us. The tremendous 

advances in genomics and proteomics over the 

last decade will be key to this endeavor. These 

advances have given us new insights into the 

workings of biological systems from an 

organism’s genetic instruction manual, its DNA 

sequence, to its full repertoire of protein 

products, the cell’s working molecules. Using 

these advances, we can begin to understand the 

mechanisms by which microbes survive in the 

environment—how and what they “eat” and 

“breathe,” how they recognize and travel to 

sources of food or energy, and how they

“socialize” or colonize. 

The DOE weapons complex presents some of 

the most daunting cleanup challenges over 

3000 waste sites, 50% of which have soils/ 

sediments or groundwater contaminated with 

radionuclides or metals. Today’s technology of 

excavation and treatment is not only cost 

prohibitive, it is frequently ineffective. 

The use of methods to clean up contaminants in 

place (in situ technologies), especially methods 

that “use” the microbes already living in these 

contaminated sites, could have a huge impact on 

our ability to remediate sites in a cost-effective 

manner. 

Bioremediation has already been used effecttively for several years to clean up organic 

contaminants such as oils or solvents. Certain 

microorganisms recognize these toxic chemicals 

as “food” and “eat” them. However, radioactive 

contaminants (a unique problem at DOE waste 

sites) and metals present another challenge 

altogether. 

Metals and radionuclides cannot be “eaten,” i.e., 

broken down or converted into entirely different 

chemical forms, by microbes or even by harsh 

chemical treatments. But microbes can change 

For more information on the Office of Science visit our website: 

www.science.doe.gov 
U.S. Department of Energy 

Office of Science

the chemical properties and thus the solubility of 

metals and radionuclides in water causing them

to precipitate as solids in their underground 

locations, thereby reducing their availability to 

humans, animals, or plants, and making them

effectively nontoxic. 

For this reason, the Office of Science’s Natural 

and Accelerated Bioremediation Research

(NABIR) program focuses on understanding the 

capabilities of naturally occurring microbes that 

could be used to control the movement of metal 

and radionuclide contaminants. Thus, the focus 

of the NABIR program is on native microbes, 

what they can already do on their own, and what 

we can do to stimulate them (possibly by adding 

additional nutrients) to clean up the surrounding

metals and radionuclides. 

Microbes can only contain the contaminating 

metals and radionuclides by making them

insoluble in water, but these contaminants are 

not destroyed. This presents several scientific 

and social challenges. How can we be sure that 

these contaminants won’t be reconverted from

an insoluble to a soluble form at some time in 

the future10 years, 100 years, 1000 years

and then become a health risk again? This is not 

only a technical issue but a social one as well 

and the NABIR program is addressing both. 

The NABIR program supports a broad range of 

fundamental scientific research aimed at making 

bioremediation an efficient, safe, and costeffective reality. 

NABIR research is intricately linked to ongoing 

DOE research in genomics, structural biology, 

and microbial biochemistry. It also relies heavily

on DOE cleanup research in the Environmental 

Management Science Program (EMSP). EMSP 

focuses on characterizing the forms and movement of contaminants in the subsurface at DOE 

sites. It develops technologies needed for the 

long-term monitoring of these contaminants, 

strategies for long-term stewardship of waste 

sites, and models that can be used to predict the 

movement of contaminants in the subsurface 

environment. 

Another tool for bioremediation research is the 

national scientific user facility, the William R. 

Wiley Environmental Molecular Sciences 

Laboratory (EMSL), located at Pacific Northwest National Laboratory. EMSL provides 

cutting-edge molecular tools needed to develop 

a molecular and cellular level understanding of 

the challenges and possibilities of bioremediationfrom microbial genetics and cellular 

interactions to characterization of field samples 

and subsurface transport modeling. 

These new tools will also be used to remediate 

for mining and industrial wastes around the 

world, as well as for new purposes, such as 

selective separations of metals. 

For further information on this subject contact: 

Dr. Ari Patrinos, Director 

Office of Biological & Environmental Research 

301-903-3251

Ari.Patrinos@science.doe.gov 

For more information on the Office of Science visit our website: 

www.science.doe.gov