Journey to the Center of the Earth: The Search for Dark Oxygen

The elevator ride down was quicker than he expected.

South Africa has the deepest active mines on Earth. And MBL scientist Emil Ruff and an international team of eight other scientists were headed towards the bottom.

The 9,500 foot (2.9 km) trip down Earth’s deepest single-shaft elevator took only four minutes. Crammed in with dozens of miners headed to their regular shifts, the scientists held on as the metal cage of the elevator rattled when it reached speeds of up to 40 mph. The descent is more than three times the distance of the elevator ride in the Burj Khalifa—the world’s tallest building.

From there, they boarded an underground train that took them hundreds of more meters down into the rock.

Then it was time to walk.

The air was warm, dusty, and stale as the scientists walked the final few hundred meters. The closer you get to the Earth’s core, the hotter it gets, and at the sample site the ambient temperature was well over 80^oF (25°C).

The sample site was in a blind tunnel, where scientists had drilled down another 300 meters into the rock. They attached their specialized sampling containers to a long metal tube, which reaches down to a sealed borehole, and went on the hunt for the salty waters known as brine that they knew were present within these ancient rock fissures.

You might be asking yourself why? What could they possibly be hoping to find?

Molecular oxygen (O₂) requires a lot of energy to be made and is extremely reactive with its environment, which means it really only accumulates where lots of energy is available and O₂ can be produced continuously—places like the sunny surface of Earth. Most of Earth’s O₂ is produced by plants and microorganisms that harvest sunlight through photosynthesis. So it came at a surprise that deep below the Earth’s surface—in groundwater, in mines, in the deep ocean… in places with no light at all—molecular oxygen still exists.

The light-independent process that creates it is called “dark oxygen” production and it’s what our scientists were searching for evidence of. 

“The brine we sampled was, to the best of our knowledge, isolated in the rock for about 1.2 billion years, and yet it contained active, living microbes and oxygen,” said Ruff.

Thriving in the Dark

Dark oxygen is produced without photosynthesis. The South African mine the scientists visited is an active gold and uranium mine and radiolysis (the splitting of water through radioactivity) is one of the possible ways the O₂ is produced without sunlight. But Ruff said the puzzling question isn’t where the oxygen originally came from, but why it’s still present in such high concentrations.

“These waters have been largely disconnected from surface processes for more than 1 billion years,” said Ruff. “So, whether the oxygen is coming from radiolysis or from an ancient atmosphere, the question is why has it not been respired? Just like humans, most microbes  use oxygen and normally if oxygen is present in the environment, somebody is breathing it.”

That’s because oxygen, as an element, loves to interact with other elements and molecules. The oxygen atom really wants electrons from other things, and it is better at attracting electrons than almost any other element. As a gas, it steals electrons from carbons, sulfurs, metals, and many others, oxidizing these elements while itself getting reduced. Basically, that means, if O₂ isn’t continuously being added to an environment (by trees and plants, for example) it eventually disappears.

Confused? Look no further than your car. The atmospheric O₂ dissolved in water reacts with iron atoms to form a new compound—rust (iron oxide). Boom. The gaseous molecular O₂ has turned into a solid metal oxide and is removed from the atmosphere for an exceedingly long time. Luckily, atmospheric O₂ is replenished by trees and other photosynthetic organisms using the energy of the sun. But which process is responsible for replenishing the O₂ in the rock?

To find the source of O_2, the samples from the gold mine are currently at ETH Zurich for oxygen isotope analysis. The hypothesis is that oxygen isotopic signatures can be used to distinguish dark oxygen from atmospheric oxygen. The latter will likely be isotopically “heavier” than the O₂ that is produced in the rocks. So far, the exact isotopic signature of the different dark oxygen producing processes (whether radiolytic or microbial) is unknown, so pioneering experiments and analyses await the team.

“Our hypothesis is that, yes, maybe all of that oxygen comes from radiolysis, but the radiolysis of water is a slow process and it’s possible that in these ecosystems, we’ll also find microbes that produce oxygen, like we did in groundwater. So that’s what we were looking for—this lighter isotopic oxygen and the microbes that might be responsible for its production,” said Ruff.

In 2023, Ruff led a study in Nature Communications that found just that. His team discovered evidence of dark oxygen production by microbes in groundwater samples that were thousands of years old, from deep below the surface in Alberta, Canada.

Ruff is also lead author on a review paper that was recently published in FEMS Microbiology Ecology, which analyzed the isotopic signatures of dissolved O₂ in groundwater and found evidence to support in situ production in about half of the studied groundwater environments.

They also found, when they analyzed previously published metagenomic data, that the enzyme thought to be responsible for dark oxygen production is present in many microbial species in 16 major bacterial lineages and occurs widely in many environments. This suggests that dark oxygen production is likely much more common on our planet than previously thought.

“We find evidence for it in oil reservoirs, in lake sediments, wetlands, in oxygen-depleted zones of the ocean, in the seafloor and many other ecosystems. In all these ecosystems that we thought were free of oxygen, we now find evidence of dark oxygen production,” said Ruff.

Understanding dark oxygen helps scientists understand new possible niches for life on our planet and, perhaps even elsewhere in the universe.

Life Beyond Earth

In astrobiology and exobiology, the detection of O₂ is considered a biosignature. “If you find substantial amounts of O₂ in the atmosphere of an exoplanet, there are few processes that make more sense than life as [its] source,” said Ruff.

“Nobody thought oxygen would be detectable in these underground, extreme environments. Finding it completely changes our idea of the biochemistry and the ecology of the subsurface,” said Ruff, adding that it could upend what we think we know about the original oxygenation of Earth, something that could have “paradigm-shifting implications,” as humans look for evidence of life elsewhere in the universe.