Nuclear clean-upHelping improve microbes’ ability to remediate toxic metal contamination

Naturally occurring bacteria in the Gulf of Mexico did a great job helping to clean up 2010’s huge Deepwater Horizon oil spill, but bacteria can do even heavier lifting. Routinely used to help clean up toxic metals at contaminated sites, bacteria and other soil microbes are fed to boost their ability to turn soluble metals into solids that will not leech into streams or aquifers.

UC Berkeley scientists have now dug into the soil of one of these heavy metal contaminated sites to analyze the genes of the underground microbial community in hopes of finding ways to help improve the microbes’ ability to remediate toxic metal contamination.

A University of California, Berkeley release reports that in this week’s issue of the journal Science, Jill Banfield, Kelly Wrighton and their colleagues report the sequencing of nearly 150,000 genes from soil samples at a former uranium mill site along the Colorado River in Rifle, Colorado. They were able to assign most of the genes to eighty separate microbes — bacteria and Archaea — plus a few viruses.

What they learn could also lead to improved methods for stimulating the uptake of carbon from the atmosphere by soil bacteria to reduce greenhouse gases.

“In order to make this goal a reality, it is critical not to just detect the relevant genes in subsurface microorganisms, but to know enough about the lifestyles of the organisms with genes of interest so that manipulation of the system enriches specifically for that organism,” said Banfield, UC Berkeley professor of earth and planetary science and of environmental science, policy and management.

It may be possible, for example, to add nutrients that would create the ideal mix of microbes to immobilize the metals, instead of just feeding all the microbes already present.

“Our study turned upside down what we thought was happening at the bioremediation site,” said Wrighton, lead author and UC Berkeley post-doctoral fellow who specializes in the physiology of microbes. “What these genomes have given us is amazing in terms of being able to look under the hood at the machine of these organisms that we never really knew anything about, except that we saw them in certain types of environments.”

The release notes that the microbes came from groundwater samples taken at a site once used to process vanadium and, during and after the Second World War, uranium. The site borders the Colorado River, which means that rain can carry dissolved metals