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Mysterious fungi: Researchers pinpoint hotspots of 'dark taxa' across Earth's underground ecosystems

Mycorrhizal fungi help regulate the Earth's climate and ecosystems by forming underground networks that provide plants with essential nutrients, while drawing carbon deep into soils. Scientists and conservationists have been racing to find ways to protect these underground fungi, but they keep finding dark taxa—species that are known only by their DNA sequences that can't be linked to named or described species.

It is estimated that only 155,000 of the roughly 2–3 million fungal species on the planet have been formally described. Now, a review in Current Biology shows that as much as 83% of ectomycorrhizal species are so-called dark taxa.

The study helps identify underground hotspots of unknown mycorrhizal species occurring in tropical forests in southeast Asia and Central and South America, tropical forests and shrublands in central Africa, Sayan montane conifer forests above Mongolia, and more. This discovery has serious implications for conservation.

Names are important in the natural sciences. Traditionally, once a species is described, it is given a binomial—a name made of two Latin words that describe the species and genus. These names are used to categorize fungi, plants, and animals, and are critical identifiers for conservation and research.

Most mycorrhizal fungi in the wild are found using environmental DNA (eDNA)—genetic material that organisms shed into their surroundings. Scientists extract fungal eDNA from soil and root samples, sequence that DNA, and then run those sequences through a bioinformatics pipeline that matches a sequence with a described species. For dark taxa there are no matches—just strings of As, Gs, Cs, and Ts.

"We are a long way out from getting all fungal DNA sequences linked to named species," says lead author Laura van Galen, a microbial ecologist working with the Society for the Protection of Underground Networks (SPUN) and ETH University, Switzerland.

"Environmental DNA has enormous potential as a research tool to detect fungal species, but we can't include unnamed species in conservation initiatives. How can you protect something that hasn't yet been named?"

Ectomycorrhizal fungi are one of the largest groups of mycorrhizal fungi and form symbiotic partnerships with about 25% of global vegetation. Ectomycorrhizal fungi facilitate the drawdown of over 9 billion tons of CO₂ annually (over 25% of yearly fossil fuel emissions) and help Earth's forests function by regulating nutrient cycles, enhancing stress tolerance, and even breaking down pollutants.

The researchers' work has uncovered that dark taxa of ectomycorrhizal fungi are not spread evenly across Earth. "There are hotspots of high dark taxa around the globe, but particularly they are concentrated in tropical regions in Southeast Asia and parts of South America and Africa," says van Galen.

"Most of the research on ectomycorrhizal fungi has been focused in the north, but mid-latitude and southern-hemisphere regions show signs of being home to many unknown species. This means there is a mismatch in resources and funding. We need to bridge this gap and facilitate more tropical researchers and those from southern-hemisphere regions to focus on identifying these super-important fungi."

The researchers have suggestions of how we can start bringing these fungi out of the shadows. "One way to reduce the dark taxa problem is to collect, study and sequence mushrooms and other fungi," says co-author Camille Truong, a mycorrhizal ecologist at SPUN and research scientist at the Royal Botanic Gardens Victoria in Australia.

"Conversely, there are mushrooms that have been sitting for decades in collections of botanical gardens. These should be urgently sequenced so that we can, hopefully, start matching them up with some of these dark taxa."

Many of the unidentified fungal species are associated with plants that are themselves endangered. "We're at risk here," says van Galen. "If we lose these host plants, we might also be losing really important fungal communities that we don't know anything about yet."

The technology is available—what's missing is attention. "We really need to pay so much more attention to fungi in the soil so that we can understand the species and protect them and conserve them before we lose them," says van Galen.

The team hopes that conservation organizations will use the information to protect hotspots of underground biodiversity, even if these species remain nameless.