Credit: Drake et al. 2017

Nuclear waste repositories are not known for curb appeal. Yet they are unpleasant necessities for enlightened nations seeking to stow the waste of one of the only relatively carbon-neutral fuels on Earth.

As a result, engineers have often sought to bury the stuff. In the United States, some of our radioactive waste has found its (hopefully) eternal resting place in a salt bed over 2,000 feet deep near Carlsbad, New Mexico, where it will eventually be swallowed by flowing salt.

Sweden has also begun exploring the geological solution to nuclear pollution by probing its own bedrock. At nearly 2,500 feet below ground at Test Borehole KLX09, about a mile from the Baltic Sea in southeastern Sweden, engineers and geologists recently encountered something that must have shocked them.

In a core sample – a slender cylinder of stone extracted by drill – they found a small cavity inside a vein of quartz. Inside was a brownish powder mingled with crystals of calcite and cowlesite. When they examined the powder under the microscope, they came to a startling conclusion: it was the half-fossilized remains of fungi. They had found a moldy pocket of rock. Generally speaking, rock isn’t supposed to mold (lichen fiestas notwithstanding).

When I was in college, my microbiology professors were just beginning to report that there might be life in the deep crust. Scattered reports from gold mines were hinting that bacteria might not just survive but thrive in hot, wet fissures deep underground.

Now we know that bacteria permeate cracks in Earth’s crust, feeding off hydrocarbons and other foods trapped within. Even relatively large animals (for the subsurface) called nematodes have been discovered in mines at depths of over two miles.

That got microbiologists thinking: if bacteria are abundant down there, why not fungi? Fungi have been found growing pretty much everywhere we have looked. They have also shown themselves to be capable miners, tunneling through rock by secreting acid from their growing tips.

Searching for truly subterranean fungi (and not just drifters from above) is difficult and expensive, though, generally involving engineers with drill rigs rather than a eager biologists with a net or box. As a result, the world that remains unseen and unsampled is profound: scientists estimate that up to 19% of Earth’s biomass is contained in the deep continental subsurface. That’s a fifth of all life on Earth!

A handful of studies have turned up underground fungi or suggested they live there indirectly, but such studies are "surprisingly rare", write the Swedish and German authors of the paper describing the fungal pocket in Nature Communications in July.

The fungi hypothesized to live in deep fractures are presumed to survive without oxygen (there being no ready source nearby), but we know little about anaerobic fungi as they are scarce in habitats above ground. There is one place that we have found and studied anaerobic fungi in detail, however: the rumen of cattle. Inside this hot, dark digestive bag where cud is produced, fungi generate hydrogen, a fuel that tiny microbes living there can use to make organic chemicals that benefit the entire community.

The pocket from the Swedish borehole is, according to the authors, the first discovery of fungi grown in place in deep bedrock. They were partly fossilized and partly organically preserved, itself a rare finding. Under the microscope, the scientists could see a network of entangled branching and fusing filaments, a pattern characteristic of fungi. Fungus-like microbes called actinobacteria never fuse, and fungal mimics called oomycetes (the most famous of which caused the Irish potato famine) fuse only when reproducing.

a)Organically preserved fungal filament 10 micrometers in diameter next to a mineralized hypha of the same diameter. b) Mycelium-like structures partly overgrowing cowlesite. c) Branching and anastomosing mineralized hyphae. Credit: Drake et al. 2017

The filaments in the pocket also contained a mineralized central strand -- a common feature of fossilized fungi -- grew in a mat resembling a biofilm, and appear to have carved channels into rock which they contacted just as fungi near the surface sometimes do.

Yet fungi, unlike bacteria and plants, cannot make their own food. They must feed on the waste products or remains of other organisms. So what were they eating in this tiny crack a half a mile from the surface?

The scientists could not see any direct evidence of bacteria or other life in the fissure. However, pyrite crystals found among the fungal filaments were enriched in a form of sulfur preferred by microbes called sulfate-reducing bacteria -- one of the very same groups that grow with anaerobic fungi inside cattle.

If this was indeed the case, both organisms would have benefited each other: bacteria could have fed on the hydrogen and organic waste products made by the anaerobic fungi, while the fungi fed on sugars and other organic chemicals produced by the bacteria. 

Together, the combination of fossilized filaments and isotope-skewed pyrite suggests, they claim, that the deep biosphere in continental rocks may be “a neglected vast fungal habitat.”

If true, this surfeit of subsurface fungal life could pose a long-term threat to our plans for deep disposal of toxic and radioactive waste, the very thing the drillers were pursuing when they encountered the moldy rock. Both anaerobic fungi and their bacterial cohorts could dissolve or corrode barriers between waste and rock if it served their purposes. That includes leading contenders like zeolite barriers for high-level radioactive waste and copper canisters for spent nuclear fuel. We might want to take that into consideration in future designs.

It is melancholy for me, however, to think of life under these conditions, radioactive waste or no. These fungi will never know the kiss of rain, the sparkle of sunshine, or the freshness of a gentle breeze. All these things would assuredly kill them. They life they know – the only life they will ever know – might as well be on another planet, eternally dark, eternally hot, and eternally lonely, trapped under pressure in a tiny fissure half a mile from Earth’s surface.


They, on the other hand, are probably as happy as pigs in a waller.



Henrik Drake, Magnus Ivarsson, Stefan Bengtson, Christine Heim, Sandra Siljeström, Martin J. Whitehouse, Curt Broman, Veneta Belivanova, Mats E. Åström. Anaerobic consortia of fungi and sulfate reducing bacteria in deep granite fractures. Nature Communications, 2017; 8 (1) DOI: 10.1038/s41467-017-00094-6