Healing Nature with Nurture

It sounds too good to be true, like a Discovery Channel infomercial: Mushrooms transform devastated, polluted creeks into vital, healthy ecosystems. Environmentally friendly white-rot fungi conquer DDT and PCBs effortlessly. Harmless organisms make mincemeat out of vinyl chloride twenty feet deep. Just call 1-800-BIOREMEDIATION.
Bioremediation is the use of natural organisms—bacteria, fungi, and plants—to break down toxins in water or soil. It could happen in our backyard if logic triumphs over legal and bureaucratic logjams at a Richmond site slated for restoration. The technology got a boost this summer when Nature magazine reported the discovery of a tough little bacterium dubbed BAV1 that breaks down vinyl chloride, a toxic, difficult-to-dispose-of compound that contaminates groundwater throughout the world.
But bioremediation has also promised more than it’s delivered, and its very “naturalness” has made it a quagmire of patents, claims, and counter-claims. At stake is the fate of hundreds of thousands of sites that would benefit, including an estuary in Richmond where fungi and plants might break down contaminants that have poisoned the area for generations.
No story better illuminates bioremediation’s difficult path than Steven Aust’s. An award-winning professor of chemistry and biochemistry at Utah State, during the mid-’90s Aust demonstrated that common “white-rot” wood fungi could break down some of the nastiest chemical pollutants known to humanity, including 2,4,6-trinitrotoluene, DDT, and a host of other persistent organic chemicals. The idea of using fungi that had evolved to chew through tough substances like the lignin in wood to neutralize manmade pollutants took the environmental and biochemical communities by storm. With the blessings of Utah State, Aust founded a company called Intech One-Eighty, which itself was heralded as an innovative way to commercialize academic research. Intech One-Eighty licensed its technology to a small firm called EarthFax Engineering, which developed pilot studies to remediate sites contaminated by such chemicals as creosote.
But a series of business missteps, regulatory changes, and interpersonal disconnects have left Intech mostly dormant, and Aust and key EarthFax personnel are no longer on speaking terms. “We were the first lab to show that white-rot fungus could handle DDT,” says Aust. “But the EPA took over the project, got awards, and ran it into the ground. They’re political animals, but they’re just incompetent at the science.”
Aust explains that political wrangling at the EPA helped bioremediation fall out of favor at the agency.
And although they are at odds on many other issues, Richard Lamar, director of research and applications at EarthFax Development Corporation, a former affiliate of EarthFax Engineering, agrees that the shift in attitude at many agencies has been a biotech-killer, especially given the huge expense associated with developing and proving new technologies. “There was a power struggle at EPA, and our guy lost,” he says.
That wasn’t the only political battle white-rot technology forfeited. “We had a site where we did a pilot study using white-rot, and it was successful,” Lamar says. “We thought we were going to get the go-ahead [to do the whole project], and then we were told that they were going to be allowed to just pave it over.” The result? Contaminants will stay in the soil, probably for decades.
The two men also agree that their field has been plagued by what bioremediation proponents admit was “over-promising” payoffs that never materialized. “Lots of money has been wasted on white-rot fungus…and on bioremediation grants in general,” says Aust. But, he argues, when businesspeople who don’t understand the technology get involved with nascent invention, it’s a recipe for disaster. “People who have no understanding of the science have even patented [bioremediation methods]. When a million people jump into an area and don’t know what they’re doing, it’s highly likely to fail,” he says.
And as businessmen don’t know science, scientists don’t know business. Putting together pilot projects takes years, and then comes the work of commercializing the technology, something few scientists are able to see through to a successful product. These problems have stalled bioremediation technology for the last ten years, at least in the United States. “We’ve gotten better reception overseas, especially in Australia and New Zealand. Here it’s pretty bleak,” says Lamar.
Aust says, “I still have some hope that my technology will be resurrected. Just recently, a guy contacted me who was concerned that his work might infringe on my patent. I’d like to maybe license it to him, because this man knows fungus, and if anyone can grow it, he can.”
That man, Paul Stamets,  is perhaps fungi’s most passionate advocate. Founder of Fungi Perfecti, a company near Aberdeen, Washington, that pioneered the mushroom “kits” sold in catalogs and gardening magazines, his clean rooms and storage areas house hundreds of exotic fungi. He’s the author of two respected books, The Mushroom Cultivator and Growing Gourmet and Medicinal Mushrooms, as well as a new book, Mycelium Running, out this coming spring from Ten Speed Press. Much of this ex-logger’s knowledge is self-taught, which makes his acceptance by academic bright lights like Aust even more remarkable.
One of Stamets’ early remediation projects involved “mycofiltration” at his own farm in Olympia, Washington. Stamets wanted to eliminate E. coli bacteria from wastewater, so he designed a system in which the water, contaminated with animal feces, had to pass through successive bands of fungi before it entered a stream near his property. Within a year, he says, the coliform count had almost disappeared. After that success, Stamets experimented with different kinds of fungi to see which might break down chemical contamination.
His results have been breathtaking. In a test that he conducted with Battelle, a big corporate player in bioremediation, oyster mushroom mycelia that Stamets had collected from old-growth forests in the Pacific Northwest broke down 95 percent of the hydrocarbons at a Washington Department of Transportation site in just eight weeks. The test was deemed nothing short of miraculous, compared to the years or decades that it usually takes to dig out soil, treat it, then put it back.
But Stamets says that the ultimate benefit of mycoremediation is that fungi pave the way for other forms of life, as they may have done near the dawn of land-based life. “Often, after the primary colonizers—such as the bacteria and the fungi—get started, a balance is restored, and you get a cascade of biological communities that spontaneously re-green the site. Insects lay eggs, larvae develop, then the birds come in, and you get an oasis where the toxics were, thanks to millions of years of adaptation and evolution.” That’s what happened at the DOT site: Fungus gnats attracted birds, which attracted other wildlife. Soon, the area was indistinguishable from uncontaminated land.
That experiment led Stamets to combine bioremediation techniques into what he calls a “three-kingdoms” approach that uses bacteria, fungi, and plants to do what they’ve always done: break down and convert complex molecules into other chemicals. The difference now is that the complex molecules are manmade.
“We all feel a little funny about saying that we ‘discovered’ this,” says Stamets. “We’ve really only rediscovered that which nature has forever known.”
Stamets is optimistic that bioremediation techniques will allow restorers to clean up chemicals that earlier were difficult or impossible to remove. “In the early days, we had one string,” he says. “Now we have a piano.” He says he’d hoped to use his “piano” to remove toxics from a 150-acre UC Berkeley site at a marsh in Richmond, near Meeker Slough. “It’s right in front of EPA’s [regional] headquarters, so they could look out their windows and see it,” he says. Since the late 1800s, the site has had a long history of contamination due to everything from a nearby railroad to an explosives manufacturer named California Cap Company. But Stamets has become discouraged by what he says was a chilly reception from UC Berkeley.
UC environmental health specialist Anna Moore says Stamet’s plan is still under consideration, but the university can’t go ahead during critical nesting or breeding times for the endangered marsh-dwelling California clapper rails. Moore is intrigued by Stamets’ approach because she’s concerned that if soil is dug out to treat it, exotic hybrids of the cordgrass that grows nearby could become more established, ultimately out-competing the natives. It doesn’t require digging out existing flora, and so might offer a way to get rid of the toxics with virtually no disturbance of the soil and water.
Stamets faces other problems—leave it to the profit motive to make the simply elegant almost unworkable. The rush to patent biological organisms and processes has meant that practitioners can easily infringe each others’ patents or trespass onto others’ intellectual property, even though the biological processes involved are natural and fortuitous.
“You can do a remediation that starts with bacteria or fungi to get rid of a particular toxic and someone else can say you inadvertently broke down this other chemical, and the landowner got some benefits, so you’ve violated my patents,” Stamets says. “ That’s probably why this technology hasn’t advanced as far as it could have. And if it turns out that there’s no money in it because of legal liabilities, then lawyers will have destroyed the technology that could have saved us.”
As Stamets points out, sites near human habitation usually have layers of different types of contamination, so the most effective approaches might well involve a multitude of organisms, each using or breaking down a different toxin. While combining approaches might be a boon to the clean-up crews, it could be a disaster from a legal standpoint.
“We absolutely have to smooth out the intellectual landscape,” says Stamets. “Because if you do mycoremediation right, you get a cascade of diverse, thriving biological communities that restore natural systems, and you’ll probably stumble onto someone else’s patented technology.”
Even worse, that someone is probably not in your field. Bioremediation usually requires small armies of specialists to cooperate and work together. “These are very smart people, but they’ve usually had no interdisciplinary training,” says Oak Ridge National Laboratories anthropologist Amy Wolfe. Stamets says it more succinctly: “We need to put our egos aside and just get the job done.”
And all this before you talk to the neighbors. “The general public believes that bacteria are generally bad, so sometimes they’re scared or they don’t believe that this will help,” says Georgia Tech environmental engineer Frank Loeffler. As a researcher at Michigan State University, he discovered how to grow and apply naturally occurring BAV1 to attack vinyl chloride underground.
“But when you talk to them in person, and explain what you want to do and how it’s going to work, it’s very different,” he continues. “A lot of teams don’t do that. They figure they’re not paid directly by the community, so they don’t take the time to work with the community.”
Loeffler and his team called a meeting so neighbors of the Oscoda, Michigan project—removing vinyl chloride in cold, wet soil twenty feet down—could understand the rationale. “We explain that it’s a lot better than pump-and-treat, which often goes on for decades and usually doesn’t even get rid of the contamination, it just removes some of it,” says Loeffler. “Bioremediation takes months to a few years, and then it’s over, and the land can be used again.”
Lately, in the face of a growing assault on sensitive ecosystems by invasive non-native species, communities worry about introducing an alien organism that might have unintended consequences. That’s why most bioremediation efforts lately—such as Loeffler’s and Aust’s—focus on manufacturing, feeding, and inoculating the site with the same organisms already present. “We surveyed the site and found the same bacteria already there, so we aren’t introducing anything new,” says Loeffler.
But the most critical hurdle the newest wave of bioremediation faces is a dwindling supply of its naturally occurring “tools.” Stamets worries that just as bioremediation is getting a new lease on life, the very strains of fungi that could prove most useful are disappearing.
“The [fungal] genome needs to be protected,” he explains. “We’re finding there are thousands of fungi that we didn’t know about, and they can often be specific to a particular site. We used to think that the organisms that live in hot-spring geysers were pretty much the same, but now we know that they’re totally different across the world. We’re destroying so much that the [fungal] genome is plummeting in its biodiversity.”
Stamets says that governments need to make preserving fungal environments a priority, so that as new toxins are developed, they’ll have the right fungus to solve the new problems. “It was recently discovered that there’s a fungus that actually breaks down VX nerve gas. But it only grows in old-growth forests. I think that George Bush needs to protect these environments as a matter of national security.”
Could it be that the future of biotechnology is as cloudy as that of old-growth forests? Perhaps there’s still hope for both, if each can survive the next few years. Otherwise, in the words of Paul Stamets, we might learn firsthand “what threshold we have to cross in environments before it all unravels.”

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