Berkeley Pit lake, in Butte, Montana, holds 37 billion gallons of deadly poison — and an unknown number of mutated microorganisms. *
Photo: Chris Muller * Berkeley Pit Lake is about a mile long and half again as wide, rimmed by naked rock walls that gleam white under the sun of big-sky country. The water is oxblood red at the surface, stained by manganese and iron; deeper down, heavy copper compounds turn it the color of limeade. It will burn your eyes, stain your clothes, and desiccate your skin. If you drink it, it will corrode your gullet before it poisons you. A dozen years ago, 342 snow geese made the mistake of overnighting at the lake. They were dead the next morning.
No fish live in the lake; no grass, reeds, or bushes grow along its fenced-off shores. Not even a mosquito buzzes through the air. Aside from a couple of Gatorade empties tossed onto a nearby gravel slide and seven scraggly trees barely visible beyond the lip of the crater, there's nothing — just a toxic teardrop in the middle of a Montana wasteland.
This used to be a copper mine. For more than a century, workers pulled ore from the ground here. Then, in 1982, the Anaconda Mining Company shut down Berkeley Pit and turned off the pumps that kept out the groundwater. The 3,900-foot-deep hole began to fill up — 7.2 million gallons a day at first, flowing in from aquifers and from 10,000 miles of abandoned mine shafts, stopes, and tunnels beneath the city of Butte. The water is still rushing in today.
The effects have been catastrophic. Pyrite minerals in the rock oxidized in the water, transforming the pit into a giant cauldron of dilute battery acid spiked with metals. Today, Berkeley Pit contains 37 billion gallons of contaminated water and is part of the biggest contiguous Superfund site in the US, stretching 120 miles from Butte to just outside Missoula.
A decade ago, Don and Andrea Stierle, researchers at Montana Tech, received a gift from a colleague: a stick covered with green slime. Their friend had spooned it from Berkeley Pit when he noticed its texture. Andrea portioned the goop onto a few petri dishes, which yielded a relatively common species of protist , the first living thing ever discovered in the lake.
Berkeley Pit, it turns out, isn't entirely sterile. The Stierles have identified more than 100 types of microbes in the lake — bacteria, algae, and fungi that manage to survive in the unique, noxious ecosystem. Natural selection has had its way with many of them — some of these organisms apparently live nowhere else on Earth.
And they're more than merely unique — these creatures are also potentially miraculous. They have produced more than 50 different compounds that the Stierles have isolated and tested against enzymes present in diseased human tissue. An extract from a newly discovered species of Penicillium from the lake attacked ovarian cancer cells in lab tests. Another Berkeley Pit Penicillium shows promise in treating lung tumors. Whatever lets these bits of biology thrive in the noxious waters has a side effect: It makes medicine, too.
In the early years of the 20th century, more than 100,000 people lived in Butte; Anaconda employed 14,500 of them as miners, and when they weren't extracting the raw materials of the industrial age from the ground, they lived in cottages steps away from the shafts. Today, downtown Butte is dotted with 13 ghostly, derrick-like structures called gallus frames, aboveground hoists for dropping miners a mile deep into holes with names like Molly Murphy, Wake Up Jim, Never Sweat, and Orphan Girl.
In 1955, Anaconda switched to open-pit mining, blasting and digging out a progressively wider and deeper hole. Trucks brought out the ore, driving up "haul roads" carved into the sides of the pit. The new method kept Butte prosperous but created an environmental monstrosity. A century of mining had already contaminated the Clark Fork River system from Butte Hill almost all the way to Missoula, but now mountains of waste rock and tailings were heaped around the Berkeley Pit crater and beyond.
The smelter closed in 1980. The mine closed two years later, and five years after that, the Environmental Protection Agency put Berkeley Pit on the Superfund National Priority List. Naked, rolling dunes surrounded a lake filled with millions of gallons of acidic water. The government simply contained it, since cleanup would cost too much.
Real estate values plunged, and businesses closed. The Berkeley Pit mess made it impossible for Butte to reinvent itself as a nature preserve or a summer getaway for rich urbanites. Instead, the sturdy, turn-of-the-20th-century banks, union halls, and hotels where the city once conducted business and raised hell quietly emptied out. The company was abandoning the company town.
The Stierles married the same year the smelter shut down — Don was a natural-products chemist who had just finished a postdoc at the Scripps Institution of Oceanography in La Jolla, California, and Andrea eventually became a bioorganic chemist. They were both ocean lovers who were interested in isolating medicines from nature and hoped to find potential pharmaceuticals in the plants and animals of the seas.
Water samples from the old mine yielded colonies of bacteria and fungi. Compounds from these microbes appear to fight cancer.
Photo: Chris MullerLandlocked Butte wasn't a natural destination, but Montana Tech offered Don a tenure-track job in the chemistry department. He and Andrea moved into a pale green craftsman-style home on Butte Hill, and by the mid-'80s, they were spending their summers off the coast of Bermuda, investigating a bacterium that grows in sponges and, in the lab at least, appears to halt the spread of HIV. Then a team they organized found a fungus that produces taxol, an extract effective in treating several kinds of cancer. (Taxol is usually purified from the bark of yew trees, but industry needs a more ready source.) The Stierles and a colleague were granted several patents for finding the fungus, which they named after Andrea: Taxomyces andreanae.
In 1996, the money ran out. "It was very depressing," Andrea says. "We decided it was time to start a new project, but we weren't able to launch a trip to the Philippines or South America to look for interesting plants in the rain forest." They were stuck in Butte with no funding.
That's when they shifted their focus back to those petri dishes of Berkeley Pit slime. There was a chance that medically useful life-forms dwelled just next door (and just below the surface). Andrea asked Ted Duaime, the Montana Bureau of Mines and Geology hydrogeologist in charge of monitoring the pit water, to ask his inspectors for a sample; what came back was a jar of the limeade- looking, copper-saturated stuff from 200 feet below the surface. Andrea smeared some of the water on a bunch of nutrient-coated petri dishes and let the colonies grow. Soon they had isolated three microbes — fungi from Berkeley Pit. And each was able to produce at least one substance that had never been seen before. Anywhere.
Berkeley Pit Lake has a pH between 2.5 and 3.0, as acidic as vinegar. That means anything that lives there has to be tough and adaptive, what scientists call an extremophile. Most of the microbes that lived in Berkeley Pit before it flooded, or the ones blown onto the lake today by the wind, die. But those that don't keel over right away? That which does not kill them makes their offspring stronger. Like their cousins in Earth's other preposterously harsh environments — dry, frigid Antarctica, say, or boiling, smoky undersea thermal vents — the extremophiles of Berkeley Pit have evolved biological tricks to help them get by. These tricks can be useful to humans: Bacteria living in hot springs produce a heat- tolerant enzyme that researchers use for polymerase chain reaction, a high- temperature lab technique that amplifies tiny amounts of DNA into a larger sample.
Andrea separates the Berkeley Pit Lake extremophiles into two categories: survivors, which can't get out of the pit but manage to reproduce — slowly — in its acid waters, and thrivers, which embrace the environment and flourish there. At Berkeley Pit, nature and humankind have collaborated in the creation of a unique toxic soup that shares one thing with other extreme environments: No one expects anything to live in such a hellhole, and common creatures rarely do. But something uncommon — and useful — almost always does.
The Stierles had a new project, and it came with unlimited raw material. "Maybe we couldn't go to Tahiti, Bermuda, or Africa," Andrea says. "But we had something nobody else had — our very own toxic waste dump." They turned their expertise in finding cancer-fighting microbes toward Butte Hill.
Photo: Chris MullerThe most expensive part of bringing a new drug to market is research and development. And in the past quarter century, advances in computer electronics and automation have revolutionized the search for new drugs. One key technology is a method called high-throughput assay, which in the richest laboratories uses robot arms and vast libraries of chemicals to test a huge number of possible medicines against a huge number of diseases. Researchers inject tiny amounts of compounds into hundreds of small wells in giant gridded plates. Target cells sit at the bottom of the wells — if the compound kills enough of them, software flags the hit. The technique can be used with both natural and synthetic compounds, and the procedure also works in reverse: Researchers can test a target against an array of chemicals to see which ones will attack it. High-throughput assays have transformed a hit-or-miss process into a practical research strategy.
But all that tech is useless without a compound to test. That's the front end of drug discovery, where the Stierles are situated. They're finding the microbes that make the compounds to test in those grids — an unlikely pursuit for scientists working in a little lab at a tiny college in a nearly derelict mining town whose onetime pride and joy is now a punch bowl filled with poison. Funding to run the lab (and pay their salaries) comes hard: When they first applied to the National Science Foundation for a grant, the couple came up empty. "On the East Coast, all they have are abandoned quarries," Don says. But rock quarries filled with water don't generally turn toxic. "So they don't really understand when you tell them about a source of micro organisms that's the size of Berkeley Pit."
The Stierles tried again and failed — many times. Andrea came to wonder whether anyone was reading the proposals at all. One reviewer, she says, even commented that their proposal ignored "one crucial part of the equation — the fish."
So they started on their own, growing cultures in the lab, extracting chemical compounds from them, and driving 180 miles round-trip every week to Montana State University, in Bozeman, to analyze the extracts with the mass spectrometer there. They ran out of money, dipped into their savings, wrote more grant proposals, and struggled forward until 2002, when the US Geological Survey, interested in bioremediation and the unique geochemistry of the pit, funded them for four years. Then, in 2004, they competed for and won $150,000 per year for five years from a National Institutes of Health program targeting small states without prestigious research universities that nevertheless somehow come up with good science.
Today, the Stierles grow their microbes in petri dishes and flasks arranged about their two-room lab — 142 different creatures stacked in plastic hockey pucks, displaying colors ranging from DayGlo chartreuse to gumbo brown. The researchers wait for the microbes to produce chemical products and then extract and purify them — all by hand.
Once they have a microbial extract, they prescreen it with an enzyme assay kit, testing it against an enzyme produced by tumor cells. The Stierles don't have robots. "I'm the automation," Don says. If the extract blocks enzymatic activity, they send it to the NIH to be tested against a 60-cell-line screen maintained by the National Cancer Institute, living samples from eight different solid tumor cancers. If they get another hit at the NCI, they write up the research and publish it. To their knowledge, they're the only researchers doing drug discovery in toxic waste dumps. "Each year, we see about 80 percent of the same things we saw the previous year," Andrea says. "But it's a changing ecosystem, and any time you look, you have the possibility of seeing stuff that nobody's seen before."
Their first big hit, berkeleydione, came from a Penicillium species they found in a pit-water sample in 1998. It inhibited the growth of non-small cell lung cancer. That gave them enough credibility to keep at it. Then, in 2002, they found a Penicillium species that, like berkeleydione, was unique to Berkeley Pit. A compound it made worked against the enzymes in their assay kit and in the NCI 60-cell assay, where an extract from the stuff attacked cells from OVCAR-3, an ovarian cancer. "With the first compound, the reaction was like, ‘Well, OK, that's interesting,'" Andrea says. "But when we did it again, it was, ‘Wow! Maybe there's more to these pit microbes than we thought.'" Don and Andrea named the extract berkelic acid.
So why aren't the Stierles world-famous cancer researchers? Finding a chemical that is "active against" or "inhibits the growth of" tumor cells is a triumph — but only the beginning. "Most anticancer compounds are basically poisonous chemicals," Andrea says. "We are trying to show proof of concept — that by identifying compounds that inhibit particular enzymes, we can find compounds with selective anticancer activity."
Of course, the Stierles have no idea whether anything they find will actually lead to a medicine. "What you wait for is a partner," Andrea says. "We don't have a big enough lab to do large-scale fermentation." It will be up to bigger, richer enter prises — Big Pharma — to shepherd berkelic acid through all the research-and- development hoops. That's who will replicate the Stierles' findings on a large scale. That's who will do "mode of action" studies, watching the compound under a microscope to see how it works. That's who will conduct fermentation experiments to determine how to produce the gallons of compound necessary for tests. And then there will be the trials — on enzymes and animals first, and perhaps eventually on people. Is it safe? Does it do what the Stierles' work suggests that it might? The Stierles have neither the infrastructure nor the money to even begin this process.
They're creeping into their fifties now, and while they still speak fondly of past research summers spent skin-diving off Hawaii and Bermuda, that phase of their lives is probably over. For better or worse, they are wedded, like the city of Butte, to Berkeley Pit. In town, the upper floors in the big old buildings are boarded up. Lower floors have become storefront shops selling "antiques" that probably came from the upper floors. Local businesses are shutting down, replaced by megastores crouched near freeway on-ramps. And up on Butte Hill, Berkeley Pit continues to percolate, and the samples keep coming to the Stierles' lab. Andrea says she and Don have found more "compounds of interest," and as they publish their results the buzz will grow. Funding will rush into their lab like water into Berkeley Pit Lake, benefitting the Stierles and their university as the mine provides a new kind of raw material for the next technological revolution.
Guy Gugliotta (guygugliotta@yahoo.com) is a writer in New York.
