The Big Idea: Accelerated Bioremediation

Genetically engineering bacteria to eat our most toxic Superfund sites for dinner.

Published October 21, 2005 11:10AM (EDT)

Erin Brockovich used the law to take on toxic waste. Today, she'd want a microbiologist in her corner, too.

Using bacteria and plants to neutralize contaminants in polluted areas is a decades-old practice known as "bioremediation." But naturally ocurring organisms can't mop up all our toxic messes. Evolution simply hasn't had enough millennia to produce organisms that can effectively decontaminate all the waste dished out by chemical, oil and nuclear weapons production facilities. Many contaminated sites contain multiple toxins, so while an organism may be able to stomach one, another kills it off. Oil spills, like the many that Hurricane Katrina caused, might require dozens of enzymes to fully degrade.

Enter "accelerated bioremediation" and genetic engineering, which scientists such as Dr. David Ackerley of Stanford University's Matin Laboratory are using to speed up evolution in the lab -- turning living organisms into better toxic-fighting machines. In one dream scenario, an organism feeds off the toxic sludge in a Superfund site, then disappears when its cleanup work is done.

Of course, some critics have raised concerns that genetically modified organisms could have myriad unintended effects. But their release into the environment is tightly regulated by the Environmental Protection Agency, and the government has a big vested interest in getting it right. The U.S. Department of Energy funds labs like the one at Stanford where Ackerley works, through its Natural and Accelerated Bioremediation Research program, with the hopes of using their breakthroughs to clean up its own contaminated sites.

Ackerley, who will be continuing his research at Victoria University of Wellington in New Zealand next year, told Salon how microbiologists are speeding up evolution in the lab to take on toxic waste.

Why do we need genetic engineering to help clean up contaminated sites?

The whole industrial revolution, the Cold War and the arms race, particularly nuclear weapons production, produced a huge number of massively contaminated sites, in particular heavy-metal contamination. What you're seeing for the first time in the history of the planet are compounds that would not arrive in nature. So there has never been any natural selection for bacteria to evolve a way of detoxifying these compounds.

We're trying to find ways of evolving enzymes to actually reduce and degrade these compounds. Our lab uses a set of techniques called "directed evolution" to try to mimic evolution in a test tube. We're asking: What would have happened if there had been this selective pressure, either on bacteria or on individual molecules? How would they have adapted to actually confront this problem?

What's an example that you're working on?

In our lab, we work on hexavalent chromium, which you might remember being the toxic nasty in the Erin Brockovich case. In that case, PG&E was using chromate as a rust inhibitor in their cooling towers. They were dumping it in unlined pools, and it's incredibly soluble. So even though it was a couple of miles away from this little township, it was able to leach its way through subterranean waterways into the township's water supply.

The natural form of chromium in the environment is chromium-3. But the toxic form is chromium-6, and that's the form that is generated by a wide range of industries, including nuclear weapons production.

How do you take it on?

We broke down bacteria, and all of its constituent proteins, to try to find one protein -- an enzyme -- that was able to turn chromium-6 into chromium-3. We actually found one of these enzymes. What we're doing now is introducing a whole range of mutations into this enzyme, so basically just mimicking what would have happened through evolution. We've taken it out of the whole living cell, which is a really complicated system, and put just this one enzyme into the test tube, focusing on its ability to reduce chromate.

Normally when you have a selective pressure in evolution, it gets complicated by the fact that you have millions of other proteins and genes floating around inside the cell. So if you improve one quality, a lot of the time it's not going to make enough difference. A lot of positive changes will be lost throughout evolution. But here in a test tube we're focusing on just one gene, one protein and one activity. So, you have a lot more ability to select for the things that you really want. The simple view of evolution is that it happens through mutation in individual genes. So, you're basically accelerating the rate of evolution.

What are some of the toxins that biotechnologists are trying to engineer new approaches to now?

Some of the toxins that are being worked on are associated largely with nuclear weapons production, and these heavy metals like chromium and uranium. A lot of times what you're looking at is containing these compounds, because they can be highly soluble and they can spread through soil and waterways. So, if you can at least make them insoluble and contain them, you've won a large part of the battle.

Another common problem is arsenic, which is used in the tanning and timber industries. Then, there are a whole pile of these things like dioxins or polyaromatic hydrocarbons, which are produced through a huge range of industries, like coal and oil.

Why is this field growing right now?

For a long time, people thought that with nuclear waste it was fine to just dig a big hole in the ground and dump it in. But now people are realizing that the subterranean environment is a very dynamic environment. Just because you've covered something up, and you can't see it anymore, doesn't mean that it doesn't have a way of spreading and causing massive environmental damage. I guess we're trying to play catch-up for our previous lack of understanding over the last 50 years.

I have friends in Greenpeace who really can't make up their mind whether I'm a good person or a bad person, because I'm trying to clean up the environment, but I'm doing it with genetic engineering.

By Katharine Mieszkowski

Katharine Mieszkowski is a senior writer for Salon.

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