Mining bacteria’s appetite for toxic waste
Researchers try to clean nuclear sites with microbes
David Perlman, Chronicle Science Editor. July 14, 2003.
DEANNE FITZMAURICE / SFC
Criddle holds a solution of uranium in a lab at
Stanford University. The environmental engineer hopes that after
bacteria consume radioactive waste, the uranium can be separated from
water like sand and be gathered like a common mineral. The process is
called “bio-remediation.” Chronicle photo by Deanne Fitzmaurice
Scientists are experimenting with some unusual species of bacteria
that can thrive by cleaning up radioactive wastes left over from the Cold War
when nuclear weapons plants across the country were running full blast.
The problem exists wherever uranium has been mined, processed and made into
nuclear bombs. Almost 500 billion gallons of groundwater — enough to supply 1.
5 million homes for a year — remain contaminated with uranium and other toxic
chemicals in 36 states, the U.S. Department of Energy estimates.
Another 800 million gallons of waste from uranium mines and weapons plants
lie buried in landfills, trenches and unlined tanks. More than 2 billion cubic
feet of contaminated sediments remain to be cleaned — a mountain of
radioactive and toxic dirt 2,000 times larger than Egypt’s Great Pyramid at
For many years, scientists have known about the unusual appetites of some
microbes, including the ability of certain strains to consume uranium and
other deadly poisons. Now researchers are starting to exploit that ability as
a way to clean up nuclear sites, a process called “bioremediation.”
STANFORD ENGINEER’S STUDIES
Among the experimenters is Craig Criddle, a Stanford University
environmental engineer. He is working with several classes of microbes that he
believes can turn a soluble form of uranium into an insoluble form. The
uranium can precipitate out of the water like sand and be gathered like a
common mineral, he believes.
Next week, Criddle will pursue an experiment at the Oak Ridge National
Laboratory in Tennessee, which produced the uranium for the infamous atom bomb
dropped on Hiroshima, killing almost 80,000 people.
The lab has another legacy. “The nitric acid and uranium oxide waste, a
witch’s brew, was dumped into unlined pits there for 31 years and then covered
by a parking lot,” Criddle said.
The waste ate its way down into layers of saprolite, a claylike rock, so
that more than 99 percent of it is deep in the soil, he said. The remaining
uranium has contaminated groundwater, a long-term threat to human health,
because the uranium is soluble and moving steadily toward nearby Bear Creek,
which flows through the area.
A complex community of microorganisms thrives by “breathing” oxides of
sulfur, iron, aluminum and even more hazardous compounds like the uranium and
other radioactive elements. As the microbes obtain their oxygen from soluble
uranium oxide, for example, they transform it into a highly insoluble form
At Oak Ridge, Criddle will be working with several bacteria, including
members of a genus called Desulfovibrio, which numbers more than 30 distinct
Heavy metals such as chromium that were used during the bomb-making era
also pose a human health problem. Similar techniques mobilizing bacteria to
remove chromium, a cancer-causing metal, are also being tested in the Oak
Ridge experiments by a team from UC San Diego’s Scripps Institution of
Oceanography, led by marine biologist Bradley Tebo.
Criddle’s uranium experiments involve lowering the acidity of the microbes’
environment and nourishing them with ethanol to “get them all happy,” as
Criddle says. Doing so encourages them to go to work on the uranium by
reducing oxides of the radioactive uranium and thereby rendering them
Like other researchers in bioremediation, Criddle has support from the
Department of Energy. The agency’s program manager, microbiologist Anna
Palmisano, is a former member of the astrobiology group at NASA’s Ames
Research Center in Mountain View, seeking microbial analogues on Earth for
possible life on other planets. “There are wonderful microbes that could
be able to help us,” Palmisano said. “But the radioactive elements that
are moving into the water are soluble, and to get them out, they must be
URANIUM DRIFTING TOWARD RIVER
Along the Colorado River, about 200 miles west of Denver, is the small town
of Rifle, whose two mines and mills produced almost 17 million tons of uranium
oxide, known as “yellowcake.” When the mines shut down about 30 years ago,
they left almost 3 million tons of contaminated uranium tailings. Uranium
dissolved in the water beneath the tailings is moving gradually toward the
Colorado River. Internet maps warn of the Rifle mill site: “No well drilling
or use of groundwater.”
After more than a decade of laboratory work, microbiologist Derek Lovley of
the University of Massachusetts at Amherst has built a field site for testing
the ability of a class of microbes, called Geobacters, to attack the uranium
waste problem at the old Rifle mines. Two weeks ago, he began new and large-
scale tests there.
In effect, Lovley and his colleagues have discovered that the Geobacter
bacteria can live or “breathe” in environments where uranium oxides dominate.
They are focusing on the old Rifle mill site to see if they can reduce the
uranium-polluted water to radioactivity levels well below the government’s
The genes of Lovley’s Geobacter species already have been sequenced by the
Institute for Genomic Research in Rockville, Md., founded by famed scientist
Craig Venter, who raced government scientists to sequence the entire human
genome, and at the Energy Department’s Joint Genome Institute, operated in
Walnut Creek by the University of California.
Understanding those genes, according to Lovley, could enable scientists to
engineer new strains of Geobacter even more capable of transforming the water-
soluble forms of uranium into insoluble forms that could be filtered from
streams and underground aquifers.
OTHER MICROBES IN SPOTLIGHT
Still other strains of microbes are under investigation.
One unique bacterium bears the intriguing name of Deinococcus radiodurans,
meaning “strange berry that withstands radiation.” It was discovered by Oregon
radiation researchers in 1956 in a can of meat that had spoiled even after the
meat was sterilized experimentally by intense radiation beams, and it is by
far the most radiation-resistant organism in the world.
Gene-splicers are experimenting to see if the genes of D. radiodurans can
be engineered to produce a new “superbug” that could decontaminate the most
intensely radioactive wastes on Earth — wastes much more deadly than the
uranium that scientists such as Criddle and Lovley are hoping to clean up.
E-mail David Perlman at firstname.lastname@example.org.
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