The Mystery of the Contaminated Mine


Depending on your perspective, this was either Hell or the Garden of Eden.

The place has been known as Iron Mountain since the 1880s, when prospectors first began tunneling into its bowels to extract gold, iron, copper, zinc, and other valuable metals. By the time the mine in northern California was finally abandoned in 1959, not much was left behind—besides a colossal environmental mess.

Highly acidic waters chock-full of dissolved metals had leached into groundwaters, killing off plant and animal life for miles around. Rains sent these contaminated waters cascading into the Sacramento River, causing massive fish kills. The waters drained all the way into San Francisco Bay, whose fish contained metals that could be traced back to Iron Mountain. The Environmental Protection Agency declared Iron Mountain a Superfund cleanup site and supervised construction of an expensive facility to control the damage.
To this not-so-idyllic spot, Katrina Edwards came to do her research. Encapsulated in protective clothing, she ventured into the hot, poorly ventilated, abandoned mine tunnels to collect samples. Dissolving rock crashed and echoed ominously in the mine’s nether regions. Waters inside the mine reached 115°F and were the most acidic found on Earth. On the pH scale, which ranges from 0 (most acidic) to 7 (neutral) to 14 (most alkaline), the Iron Mountain waters measured –3.5. That’s not a typo.

Edwards already suspected that these seemingly unnatural conditions had a perfectly natural cause. The mine was dark, dank, and desolate—but hardly devoid of life.

“Life finds a way, as long as you have water,” said Edwards, who joined WHOI as an Assistant Scientist last year. “Microorganisms can exploit the chemistry and physics of any conditions that exist. Any situation that’s out there, you can bet there’ll be a microorganism wedged right in there, taking advantage of it.”

Simply by living, microorganisms take in, rearrange, make, and release chemicals—catalyzing and regulating reactions that determine the environment we live in, she said. They may be out of sight, but Edwards, a geomicrobiologist, is ever mindful of their dramatic, cumulative effects. Beyond creating our essential atmosphere, they play a critical, overlooked role in dissolving and making rocks, thereby shaping Earth’s surface features, such as the pathways of rivers. They regulate the chemistry of groundwaters, lakes, rivers, estuaries, and ultimately the oceans themselves. Tiny as they are, microorganisms for billions of years were the only living things capable of fundamentally changing our environment. Only recently have human beings achieved this—by producing excess industrial greenhouse gases, for example, or creating mines like Iron Mountain.

The abandoned mine may have seemed God-forsaken, but Edwards knew it was not microbe-forsaken. Iron Mountain had all the creature comforts of home-sweet-home to some microorganisms, which use sulfide minerals in metal ores to generate energy and two nasty byproducts—sulfuric acid and dissolved metal ions.

The idea that microbes can accelerate the dissolution of rocks is not new, and classic textbooks cite two iron-oxidizing bacteria as primary suspects: Thiobacillus ferroxidans and Leptospirillum ferroxidans. Edwards found these two in samples of water taken from drainage streams outside the mine, but surprisingly, they were not present in water from inside the mine. These bacteria were red herrings—Johnny-come-latelies that didn’t acifidy the waters but arrived on the scene only after the waters already had become acidic.

So who were the real culprits?

Edwards expanded her search. She used different culture media that better mimicked environmental conditions inside the mine, and she used new molecular probes that allowed her to isolate and identify different microorganisms. It soon became clear that scientists had been barking up the wrong evolutionary tree. Bacteria weren’t primarily responsible. Instead the mine was rife with a previously unknown organism that came from another of the three domains of life: archaea. Edwards and her colleagues at the University of Wisconsin, where she conducted this research in pursuit of her Ph.D., called the new species Ferroplasma acidarmanus.

“We think this new microbe might be one of the more important players in catalyzing the reactions that cause acid mine damage (AMD),” Edwards said. As soon as long-buried sulfide-rich ore bodies are exposed to air and water by mining, Ferroplasma acidarmanus moves in quickly. Where they come from is an open question. The sulfuric acid they create contaminates not only the immediate area, but also eventually flows to the ocean.

“It is estimated that half of the sulfates that end up in the world’s oceans result from human activities such as mining,” Edwards said. “Once you unearth sulfide minerals at the surface, you’ve opened up a big tap of sulfuric acid and broken off the handle. You can’t stop it.”

Still, discovering Ferroplasma acidarmanus may be a first step to understand, prevent, and mitigate AMD—or to “mine” in more economical and less environmentally damaging ways. For example, industrialists are already trying so-called bio-leaching reactors—harnessing microbial activity to dissolve low-grade ores and extract metals from them.
Further, Ferroplasma acidarmanus’s ability to thrive in such toxic, acidic conditions once again forces scientists to re-examine preconceived notions about the evolution of life on Earth and the possibility of life on other planetary bodies.

“Most bacteria have membranes and cell walls to hold their interior structures and fluids, while protecting them from the environment and giving the cell rigidity and shape,” Edwards said. “These archaea have only one membrane and no cell wall. We at first assumed that F. acidarmanus must be really hardy, with some sort of armor around them to sustain such conditions, but we found that they are separated from their highly acidic environment by a single flimsy membrane.”

How does this peculiar cellular architecture work? What possibly unknown enzymes or biochemical processes does this microorganism use to oxidize metal sulfides? This discovery of F. acidarmanus opens up new avenues of potential discovery and proves, once again, that life—wherever you find it and however you define it—is full of surprises.