Hundreds Of Feet Underground, Fungi Are Feasting On Ancient Rock

Deep Beneath Michigan, Fungi Are Quietly Feeding on Buried Carbon

For decades, scientists assumed the dark, pressurized world deep beneath Earth’s surface was essentially a fungi-free zone. Bacteria and archaea, ancient single-celled organisms that thrive without oxygen, were thought to run the show down there. A new study is blowing that assumption apart. Researchers sampled water from actively producing gas wells drilled into rock hundreds of feet underground in northern Michigan and found fungi present in surprisingly large numbers, including potentially novel lineages that remain uncharacterized by science, alongside tiny animals like tardigrades and segmented worms.

“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,” said lead author Quinn Moon, a doctoral candidate at the University of Michigan.

What makes this discovery hit harder than a typical “life found somewhere unexpected” story is what these fungi may be doing. Researchers propose that fungi may help turn ancient carbon, locked in rock for hundreds of millions of years, into compounds that methane-producing archaea can use. That connection is a hypothesis the study raises rather than one it directly tested or demonstrated.

Researchers from the University of Michigan and collaborating institutions, publishing in the ISME Journal, collected water from wells drilled into a buried rock formation in the Michigan Basin known as the Antrim Shale, between roughly 650 and 1,640 feet down. It formed more than 350 million years ago and is one of the largest sources of naturally produced methane gas underground. What scientists did not know was whether fungi lived there at all.

Fungal Cells Found at Levels Rivaling the Ocean

Water samples were pulled directly from wellheads at actively pumping gas wells, with 80 liters of ancient trapped water collected from each. The team combined fluorescent dyes viewed under microscopes to count individual cells, genetic sequencing to identify which organisms were present, and lab cultures grown from filtered water to raise the fungi in a controlled setting.

Fungal cell counts ranged from roughly 4,200 to 6,800 cells per milliliter, meaning a single drop of this ancient water may hold as many fungal cells as a drop of ocean water, or roughly 250 cells. Scaled up, that is more than 12 trillion cells in a volume the size of an Olympic swimming pool. By biological mass, the team found roughly one part fungus for every 4.7 parts bacteria, a real chunk of the microbial life down there, though the math leaned on formulas built for ocean fungi that have not yet been tested on deep rock formations.

689 Fungal Types and 13 Potential New Species Underground

Genetic analysis identified 689 distinct fungal types across six major groups. Among the most frequently detected were Agaricomycetes and Dothideomycetes, known at the surface for breaking down resistant organic matter, including wood and, in some cases, coal and rock. Finding them in such abundance underground hints they may be doing something similar down there.

Beyond detection, the team grew 205 live fungal cultures and identified 67 distinct groups. Thirteen fell outside the similarity threshold used to match any known species, marking them as candidate new taxa rather than confirmed new species. One isolate, Teichospora sp. QM01, underwent deeper genetic analysis and was clearly separated from all known relatives in its group, whose closest identified member decomposes woody plant material at the surface.

“Prolonged physical isolation over millennia, or tens of thousands of years in the examined Antrim Shale, may strongly select for diverse fungal lineages that are uncommon aboveground,” the authors write, noting this work likely represents the first direct isolation of novel fungi from the terrestrial subsurface.

All cultures are now preserved and accessible through the University of Michigan Herbarium, described as the first public collection of deep subsurface fungal cultures of its kind.

Ancient Carbon, Methane, and a Food Web Nobody Expected

To understand the broader chemistry of this underground world, the team also analyzed the gases produced from each well. Dissolved methane made up between 86% and 97% of the total gas content, and its carbon signature pointed to a microbial origin, meaning living organisms were converting ancient carbon from the rock rather than heat and pressure doing it alone.

Water chemistry suggests conditions underground may have remained relatively stable since the Late Pleistocene, when glacial meltwater could have carried surface microbes into the shale.

Bacterial data from the same samples revealed a mix dominated by organisms adapted to salty, oxygen-poor environments, including groups capable of producing methane. One fungus known for breaking apart tough plant materials, Irpex cf. lacteus, was detected in every well, and fungi known from the ocean also turned up, prompting comparisons between the underground water and the open ocean.

Roughly 90% of Earth’s organic carbon is stored underground. Earlier research estimated that erosion tied to Late Pleistocene glacial retreat physically released as much as 88% of the methane once stored in parts of the rock, a geological process distinct from any fungal contribution.

“A more comprehensive understanding of the taxa and mechanisms involved in organic carbon conversion can refine predictive geochemical models and guide efforts to manage greenhouse gas emissions,” the study concludes.

“Fungi need to be incorporated into models of carbon cycling and sequestration in the subsurface,” said senior author Tim James, curator of fungi at the University of Michigan Herbarium. Fungi have long been left out of models of how deep underground carbon moves and transforms. This study suggests they deserve a seat at that table, even though it did not measure any effect on methane emissions or climate.

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