A hidden ecosystem beneath Michigan contains abundant fungi and other complex life that may affect underground carbon.
Far beneath Michigan, water trapped inside ancient rock contains a dense and unexpectedly diverse community of fungi. A University of Michigan study suggests that these organisms are far more abundant in the deep subsurface than scientists once assumed, forming ecosystems hundreds of feet below the surface.
Led by University of Michigan doctoral candidate Quinn Moon, the research is believed to provide the first successful measurement of fungal abundance at a deep subsurface site, reaching 1,640 feet underground. Water collected from gas wells contained 689 distinct fungal species, including 13 that had never been formally described.
Genetic analysis and microscopy revealed that a drop of this underground water may hold about as many fungal cells as a drop of seawater. Researchers estimated roughly 250 cells per drop, which would amount to more than 12 trillion fungal cells in an Olympic-sized swimming pool.
The samples also contained other complex organisms, including tardigrades, commonly known as “water bears,” and tiny segmented worms. Evidence suggests that these organisms form an underground food web in which some consume other species and some may survive as parasites. The findings were 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, senior author of the study, is a professor of ecology and evolutionary biology and curator of fungi at the University of Michigan Herbarium. The Canadian Institute for Advanced Research, or CIFAR, funded the work and brought together Earth scientists and fungal biologists to investigate whether fungi could inhabit deep regions of the planet.
Ice Age water may have carried life
The researchers searched for subsurface organisms within the Antrim Shale, an organic-rich rock formation buried beneath much of the Great Lakes region. They collected water from gas wells extending between 650 and 1,640 feet into the shale. Hydrologists, biologists, and geologists then worked together to determine where the water originated.
Their investigation relied on stable isotopes, forms of the same element that contain equal numbers of protons but different numbers of neutrons. The isotope patterns indicated that much of the underground water probably came from ice sheets that melted across Michigan near the end of the last Ice Age.
The analysis also suggested that much of the water “was last in contact with the surface 11,000 years ago,” Moon said.
As the glaciers melted, water may have transported fungi and bacteria downward through porous and fractured layers of rock. The organisms apparently settled into cracks within the Antrim Shale, where they began consuming organic material preserved inside the formation.
Measurements of carbon dioxide and methane provided additional evidence that this ancient material in the shale supports the base of the 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.
Deep fungi could alter carbon models
Moon said similar ecosystems may exist in deep rock formations around the world. Geological layers that contain oil and gas reservoirs could also shelter undocumented communities of fungi and other eukaryotes, organisms whose cells contain nuclei.
Their presence could change how researchers think about carbon stored below ground. Carbon enclosed within rock is often treated as securely sequestered, but fungi, bacteria, and other organisms may transform part of that ancient material into gas. If so, subsurface carbon could be more biologically active than current estimates recognize.
“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.”
A public collection preserves hidden diversity
Researchers isolated and cultivated more than 200 types of fungi recovered from the deep subsurface. Studying these organisms could reveal how fungi endure extreme conditions, how hidden ecosystems operate, and how biological activity affects carbon stored within Earth’s crust.
The specimens now form the first publicly available collection of deep subsurface fungi and are preserved at the University of Michigan Herbarium.
“The discovery opens a window into a world that is dark, ancient, and almost entirely hidden—but is far from lifeless,” Moon said.
Reference: “Deep subsurface organic-rich shale supports abundant, diverse, and novel fungi” by Quinn S Moon, Elliott P Barnhart, Matthew S Varonka, Elizabeth J Tomaszewski, Michelle Orozco-Quime, Thomas Desrosiers, Ivan Paciorka, Michael Carley, James Schramski, Bradley S Stevenson, Magdalena R Osburn, Anurup Mohanty, Anna M Martini, Jason E Stajich, Jennifer C McIntosh and Timothy Y James, 29 July 2026, The ISME Journal.
DOI: 10.1093/ismejo/wrag184
The U.S. National Science Foundation and U-M’s Institute for Global Change Biology and Rackham Graduate Program also provided support.
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