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Genetic information may lead to advances in cleaning up contaminated soil

DOE/Brookhaven National Laboratory : 27 May, 2006  (Technical Article)
Understanding the genetic makeup of microbes that thrive in polluted environments may one day help scientists engineer bacteria that can clean contaminants from soil. In a step toward that goal, the U.S. Department of Energy's Joint Genome Institute has just released the draft gene sequence of one such toxin-tolerant bug. The bacterium, known as Ralstonia metallidurans, is being deciphered by John Dunn and Geoffrey Hind, biologists at DOE's Brookhaven National Laboratory, in collaboration with scientists in Belgium and others at JGI.
This bacterial strain was first isolated in 1976, from the sludge of a settling tank in Belgium that was polluted with high concentrations of heavy metals. Examination revealed that, in addition to its chromosomal genes, Ralstonia has two large plasmids, genetic material that is separate from the chromosomal genes necessary for ordinary cell function. According to Dunn, these plasmids house genes that make Ralstonia resistant to the harmful effects of a wide array of heavy metals, including zinc, cadmium, cobalt, lead, copper, mercury, nickel, and chromium.

'Having a draft sequence of the Ralstonia genome, which contains some 3,000 genes, will make manipulation of these naturally existing resistance factors much more practicable,' says Dunn. 'Eventually, we'll want to understand how these genes are regulated under a variety of growth conditions and in different environments to see how they might be applied in bioremediation.'

For example, through genetic engineering, scientists might be able to transfer the heavy-metal-resistant genes from Ralstonia into other microbes that decompose organic pollutants. Or alternatively, the scientists might use Ralstonia as a host for other bacterial genes that would enable it to break down a variety of pollutants. In either case, the result would be bacterial strains with a combination of traits, ones that can tolerate heavy metals in a polluted environment while digesting organic contaminants to convert them to harmless forms.

Ralstonia has another benefit in that the heavy metals tend to accumulate on the surface of the cell. 'If you let that happen for a period of time and then remove the bacteria from the soil, you can remove the heavy metal contaminants as well,' says Dunn.

In another potential application, scientists could link Ralstonia's uptake of heavy metals to genes that cause bacteria to glow, or bioluminesce. Then, the bugs could be used to indicate the presence of heavy metals in soil. The higher the concentration of metals, the brighter the glow.

'What we're doing is building on the diversity of biology,' says Dunn. 'Here's a bacterium that potentially could be used as a tool to help us clean up the environment and to monitor how well we're accomplishing that goal.'

Scientists have already developed ways to transfer genes and plasmids to and from the Ralstonia strain. They've also demonstrated that Ralstonia is a good host strain for expressing genes from other bacteria, including genes involved in degrading organic pollutants. 'Because the genes that confer heavy-metal resistance are on a plasmid, it makes our job easier,' says Dunn. 'In nature, plasmids often act as 'shuttle buses' to transport genes from one bacterium to another,' he explains.

The scientists are also working on ways to limit the ability of bacteria to spread genes, so they'll stay in the bacteria where the scientists put them. This can be done by crippling Ralstonia's ability to transfer genes, or by using host strains that don't normally transfer genes, Dunn says.

Ralstonia metallidurans, formerly known as R. eutropha and Alcaligenes eutrophus, is one of 15 bacterial genomes deciphered by JGI researchers this October, during what was called 'Microbial Month.' JGI is a consortium of several DOE laboratories that aims to develop and use new sequencing and computational technologies with the goal of discovering and characterizing the basic principles and relationships underlying living systems. The research on Ralstonia was funded by DOE's Natural Accelerated Bioremediation program.
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