Rock-eating fungi flourish deep below our feet

ANN ARBOR—Hundreds of feet below Earth’s surface, rocks and water teem with fungi and support complex ecosystems of tiny organisms, according to a University of Michigan study, which finds that fungi are far more abundant deep below ground than researchers previously thought. 

The study, led by U-M doctoral candidate Quinn Moon, is believed to be the first time fungal abundance has been successfully quantified in a deep subsurface site, as far as 1,640 feet below ground. Moon and colleagues identified 689 unique species of fungi, including 13 species that have not been described before, in water samples drawn from gas well sites. 

Using genetic tools and microscopy, the research team found that a single drop of this water may contain as many fungal cells as a drop of ocean water. That equals roughly 250 fungal cells in a single drop—or more than 12 trillion cells in an Olympic-sized pool. 

The researchers also found other complex life forms, including tardigrades—often called “water bears”—and tiny segmented worms. Together, the organisms appear to form a true underground food web. Some organisms likely eat others, while some may live as parasites, according to the study, published in The ISME Journal.

“Our study challenges the idea that it’s inhospitable for more complex life like fungi in the deep subsurface, and under favorable conditions, eukaryotes can actually be quite abundant,” Moon said. “We propose in the paper that we may be meaningfully underestimating the biomass and diversity of fungi on the planet because we’ve never incorporated the subsurface into estimates of global fungal biodiversity.”

Tim James, curator of fungi at the U-M Herbarium and professor of ecology and evolutionary biology, is the senior author of the study. The study was funded by the Canadian Institute for Advanced Research, or CIFAR, which brought together earth scientists and fungal biologists to dig into whether fungi inhabited deep spaces in the Earth. 

Making a living inside ancient rock

To study organisms in the subsurface, the researchers examined the Antrim Shale, a buried rock formation rich in organic material that stretches beneath much of the Great Lakes region. They collected water from gas wells drilled into the shale at depths ranging from 650 to 1,640 feet. The team, which included hydrologists, biologists and geologists, then tested the water to determine its origin.

Using the water samples’ stable isotopes—atoms of the same element that have the same number of protons, but differing number of neutrons—the researchers determined that the water from deep beneath the ground likely came from the melting of ice sheets that covered Michigan at the end of the last Ice Age, and that much of the water “was last in contact with the surface 11,000 years ago,” Moon said.

The abundance of melting glacial water likely carried fungi and bacteria down through porous and fractured rock layers until they settled in cracks of the Antrim Shale, where they began munching on the organic material trapped in the rock. The researchers also studied carbon dioxide and methane in the samples to confirm that the shale itself is the food source at the base of this underground ecosystem. 

“For a long time, there wasn’t evidence that eukaryotes can be abundant in the deep subsurface. People have found traces of them using environmental DNA, but they’ve been chalked up to being transient or dormant,” said Moon, a researcher in James’ lab. 

There are likely similar sites across the world, according to Moon. Deep rock formations that hold reservoirs of oil and gas may also support undescribed communities of fungi and other eukaryotic organisms.

A collection of extreme fungi to understand carbon sequestration in Earth’s crust

The study raises new questions about carbon stored underground. Scientists often think of carbon locked in rock as safely sequestered. But if fungi, alongside bacteria and other organisms, convert some of that ancient material into gas, then underground carbon may be more biologically active than previously thought.

“Regardless of whether these fungi originated in or were introduced to these deep spaces, many fungi possess adaptations that allow them to grow and influence the carbon dynamics deep in the earth,” James said. “Fungi need to be incorporated into models of carbon cycling and sequestration in the subsurface.”

The team isolated and grew more than 200 kinds of fungi from the deep subsurface to help researchers better understand how fungi survive in extreme environments, how underground ecosystems function and what happens to carbon stored in the Earth’s crust. The collection is now the first public collection of deep subsurface fungi, and is stored at the U-M Herbarium.

“The discovery opens a window into a world that is dark, ancient and almost entirely hidden—but is far from lifeless,” Moon said.

The U.S. National Science Foundation and U-M’s Institute for Global Change Biology and Rackham Graduate Program also provided support. 

Study co-authors include U-M researchers Michelle Orozco-Quime, Thomas Derosiers, and Ivan Paciorka; USGS researchers Elliott Barnhart, Matthew Varonka and Elizabeth Tomaszerski; James Schramski and Michael Carley of Riverside Energy Michigan; Northwestern University researchers Bradley Stevenson, Magdalena Osburn and Anurup Mohanty; Amherst College researcher Anna Martini; University of California Riverside researcher Jason Stajich; and University of Arizona researcher Jennifer McIntosh.