Searching for ‘Dark Oxygen’ in One of the World’s Deepest Mines

Emil Ruff was about to travel into the center of the Earth. Wearing safety goggles, a protective suit, a helmet, and sturdy work boots, he was crammed in a large metal cage with his colleagues, along with several dozen miners on their morning shift, to descend down the world’s deepest single-shaft elevator. His ears popped as the elevator plunged downward at 60 kilometers per hour (37 mph). The lift made stops along the way. First one kilometer down. Then two. The elevator descended further. The air got hotter.

Finally, at around 3 kilometers (nearly 2 miles), a mere four minutes later, Ruff and his team got off. After a short train ride, they reached a rocky tunnel that looked a lot like Mars, which is exactly what brought Ruff to these depths. He’s a microbiologist at the Marine Biological Laboratory in Woods Hole who studies organisms deep below Earth’s surface as a way to understand the possibility of life in the cosmos. Ruff is particularly interested in how microbes produce so-called “dark oxygen,” or oxygen found in the absence of light. A couple of years ago, he found microorganisms that appeared to have this ability in aquifers in Canada, a couple hundred meters below Earth’s surface. “And so then I was wondering, well, how deep can you go and still find these organisms?” he says.

It was this question that led Ruff to Moab Khotsong, a 3.6-kilometer-deep (2.2 miles) mine and longtime scientific research site. The mine is in the Witwatersrand Basin, located in the northeast corner of South Africa, a region known for its rich gold reserves. Over the course of a century of mining, companies have dug deeper and deeper holes in pursuit of the precious metal. As a result, many of the world’s deepest mines exist here.

But mining in Witwatersrand has also unearthed something else: billion-year-old brine. This fluid is hidden in the cracks of ancient rocks and is the remnants of a shallow sea that existed in the basin long ago. “There’s hardly any other way, or any other place on Earth, where you can go really that deep and also [that far] back into time,” Ruff says. By studying the brine, Ruff and other scientists hope to learn not only more about life in Earth’s early history, but also how it may be able to survive in extreme environments beyond our own planet.

In fact, science and mining have had a long relationship in this part of South Africa. Esta van Heerden, a geochemist in the area, has been working for several decades with mining companies. She describes it as “a symbiotic relationship.” Scientists are able to go to these hard-to-access places to study mysteries like ancient life and seismic activity, while companies could gain data on the risks and remediation of their activities.

The research around microbes at Moab Khotsong, however, originated primarily with one person: the late Princeton University geologist Tullis Onstott, who passed away in 2021. An expert on South Africa’s ancient subterranean water, Onstott was part of an international scientific drilling project investigating active faults in the area. But when drilling in Moab Khotsong intersected a pocket of ancient brine, Onstott organized a different kind of field expedition. In 2018, along with collaborators from Belgium, Japan, and South Africa, he traveled into the mine’s depths to set up infrastructure for an underground laboratory to study the possibility of ancient life. The laboratory includes a series of tubes and hoses that allow researchers to collect samples of the brine.

“It’s a tap you could open, and the water comes out of this borehole,” says Ruff. But getting the water out of these deep tunnels can be hot and strenuous work. “Sometimes we would carry these… basically large containers that can hold up to like, 10 liters (2.6 gallons) of brine,” says Devan Nisson, a postdoctoral fellow at NASA’s Ames Research Center who has worked at Moab Khotsong both with Onstott and on other projects. She recalls often needing the help of mine workers to carry the heavy containers through the tunnels and bring samples back to the surface for further analysis.

Over the years, researchers have started to get a clearer picture of the fluids at Moab Khotsong. For instance, they estimate that the brine is ancient, over a billion years old. It’s seven times saltier than seawater, says Nisson, a characteristic of water that has been isolated for a really long time. The age of the brine is further supported by its levels of argon, which gradually accumulates in the fluid as radioactive elements in the surrounding rock decay. Life, too, is possible in the brine, as Nisson’s recent research has detailed. Coauthor and microbiologist Julio Castillo, at the University of the Free State in Johannesburg, is particularly interested in how these microbes here can produce phosphorus, another element that’s foundational to life as we know it. Other scientists have also found viruses swimming in the mine’s walls.

But one mystery remains: dark oxygen. The Moab Khotsong brine has high levels of oxygen, but no one really knows how it got there. This is what Ruff is looking into. “Oxygen is a powerful molecule,” he says, a way for life to thrive. But reactions that create oxygen, especially without light, are extremely rare.

There are two main hypotheses about how the dark oxygen at Moab Khotsong is produced. First, radioactivity can split water molecules through a reaction called radiolysis, one way dark oxygen can be created—and, in addition to gold, Moab Khotsong is a uranium mine. It was long assumed that this was the source of dark oxygen at the mine, but, says Ruff, “nobody has ever really tested that hypothesis.”

Ruff is interested in the other possibility: that microbes are creating the dark oxygen. “Certain microbes seem to have figured out a sort of very wild chemical reaction to produce oxygen to a point where it seems to actually accumulate in the ecosystem,” he says.

In his past research, Ruff has observed how microorganisms use nitric oxide to make oxygen without the presence of light. He’s currently conducting tests to see if these tiny life-forms, or others, are living in South Africa. During his trip in August, Ruff first sampled a groundwater aquifer at a depth of 1.2 kilometers (0.75 miles), and then the Moab Khotsong brine at a depth of 2.9 kilometers (1.8 miles). He’s now analyzing chemical signatures of the oxygen within the samples for clues about its origin.

Ruff’s work to understand dark oxygen has implications far beyond Earth’s deepest mines. Moab Khotsong’s ancient, hidden ecosystem exists at high temperatures, pressures, and salinity, and has been buried for over a billion years. And yet life persists. This extreme environment is similar to what scientists think exists below the surface of Mars, potentially including water left over from shallow seas in the planet’s deep past.

“If any life ever existed on Mars, it was microbial, and if any of it survived, it was very likely in pockets of brines deep, deep in the rock,” says Ruff, whose research may decipher one of the secrets of life on Earth—and elsewhere.