A rich fungal community lives hundreds of metres below Michigan

Fungi in water from deep rock

Fungi are not confined to soil, litter and dead wood. A study published on 29 July 2026 in The ISME Journal describes fungal communities in Antrim Shale formation waters from Michigan, collected at depths of 247–556 metres. Quinn Moon and colleagues combined cell counts, sequencing, cultivation and geochemical analyses. The results suggest that eukaryotes, including fungi, may be more significant in this habitat than an exclusive focus on bacteria and archaea would imply. Read the open paper.

Samples came from wells producing gas and associated formation water. This is not a discovery of an underground cavern filled with mushroom caps. Much of the reported life is microscopic, and accessing it required sampling a particular geological system. The shale contains ancient organic material, providing the background for questions about the underground carbon cycle.

Cells, sequences and cultures offer different evidence

The researchers recorded approximately 4,200–6,800 fungal cells per millilitre of water. Bacterial cells were much more numerous. Biomass calculations suggested a smaller disparity, because fungal cells are larger. However, the conversion factors came from marine systems. Applying them to a substantially different environment introduces uncertainty, so the estimate should not be treated as a direct weighing of all the fungi present.

DNA-marker analyses identified 689 fungal operational taxonomic units across six phyla. A sequence-based unit does not automatically correspond to a formally described species. Similarly, the thirteen candidate novel taxa found among cultured isolates do not amount to thirteen completed taxonomic descriptions. Further comparison and documentation are needed before that stronger claim can be made.

Cultivation yielded 205 strains. These provide living material for follow-up experiments investigating what particular organisms can do. Detecting DNA establishes the presence of genetic material; growing an isolate enables additional questions about metabolism. Neither method, on its own, describes the functioning of the entire subsurface community or measures every organism’s contribution to it.

Ancient carbon and unresolved roles

Methane isotope signatures pointed to microbial transformation of fossil carbon. Dominant fungal groups included lineages whose surface relatives can break down resistant organic compounds. The authors therefore identify fungal involvement in related underground processes as a plausible subject for further work. They did not measure each fungal taxon’s individual contribution to gas production.

This distinction avoids an overly simple story about fungi “eating rock”. Rock can supply both a habitat and organic substrates, while different microorganisms perform successive steps in transforming those materials. Demonstrating a community is not the same as balancing every carbon flow through it. The wider chemical and microbial context remains essential to interpreting the finding.

For mycology, the work expands the range of habitats worth investigating. For a field observer, it illustrates the distance between visible surface diversity and the organisms revealed by specialised sampling. A single formation does not establish that every deep geological environment contains similar fungal abundances or the same taxa. Its importance lies in opening a well-supported research question about a part of fungal life that ordinary mushroom surveys cannot reach.