Fly agaric mushrooms partner with trees. Magnus Binnerstam/Shutterstock

If you walk through a forest and look down, you might think you’re stepping on dead leaves, twigs and soil. In reality, you’re walking over a vast underground patchwork of fungal filaments, supporting life above ground.

These are mycorrhizal fungi, which form partnerships with the roots of nearly all plants. Found everywhere from tropical rainforests to boreal forests and farmland, these underground fungi sustain life above ground, often without us realising they’re even there.

A recent academic review argues that up to 83% of ectomycorrhizal (ECM) fungi species, which form partnerships with trees, may be unknown to science.

Mycorrhizal fungi grow around root tips and form webs between root cells or penetrate root cells, then make structures inside them. They scavenge nutrients such as phosphorus and nitrogen from the soil and, in return, receive carbon from their host plants.

Traces of these unidentified fungi are often found in soil DNA. The researchers surveyed global DNA databases to see how many DNA traces that seemed to belong to ECM fungi matched to a species. Only 17% could. Scientists call these “dark taxa” – organisms that have been detected, but not formally described, named or studied.

Many of these fungi produce large fruiting bodies such as mushrooms and are foundational to forest ecosystems.

One example is the fly agaric (Amanita muscaria) which produces the iconic red and white spotted toadstools often linked to folklore and can have a range of host trees. It typically associates with birch, pine and spruce, especially in colder climates, helping trees survive in nutrient-poor soils.

Porcini fungi, (for example Boletus edulis), produce delicious mushrooms prized for their rich, nutty flavor, are ECMs too. These fungi grow with pines, firs and oaks. And the chanterelle is highly sought-after by mushroom collectors and often found near oaks, beech and conifers.

Chanterelles thrive in undisturbed, healthy forests. Their presence often signals a well-functioning forest ecosystem. They have a fruity, apricot-like scent that may attract insects to help spread spores.

Chanterelle mushrooms are highly sought after.
Nitr/Shutterstock

The new report shows how little we know about the world beneath our feet. This ignorance has important implications. Entire landscapes are being reshaped by deforestation and agriculture.

But reforestation efforts are happening without fully understanding how these changes affect the fungal life that underpins these ecosystems. For example, in the Amazon, deforestation for farming continues at an alarming pace with 3,800 square miles (equivalent to 1.8 million football fields) of tropical rainforest destroyed for beef production in 2018-19 alone.

Meanwhile, well-meaning carbon offset schemes often involve planting trees of a single species, potentially severing ancient relationships between native trees and their fungal partners. This is because the mycorrhizal fungi in these area will have developed in partnership with the native plants for many years – and may not be compatible with the tree species being planted for these schemes.

Although not all trees have specific fungal partners, many ECM fungi will only form symbioses with certain trees. For example, species within the Suillus genus (which includes the sticky bun mushroom) are specific to certain species of pine.

Introducing non-native plantation species may inadvertently drive endemic fungi, including species not yet known to science, toward extinction. We may be growing forests that look green and vibrant, but are damaging the invisible systems that keep them alive.

The problem isn’t limited to ECM fungi. Entire guilds (species groups that exploit resources in a similar way) of mycorrhizal fungi, remain virtually unexplored.

These dark guilds are ecologically crucial, yet most of their members have never been named, cultured or studied.

Ericoid Mycorrhizal Fungi (ERM)

These fungi form symbioses with many ericaceous shrubs, including heather, cranberry and rhododendrons. They dominate in some of the world’s harshest landscapes, including the Arctic tundra, the boreal forest (also known as snow forest), bogs and mountains.

Research suggests ERM fungi not only help plants thrive in harsh environments but also drive some of the carbon accumulation in these environments, making them potentially part of an important carbon sink.

Despite their abundant coverage across some of the most carbon-rich soils on Earth, the ecology of ERM fungi remains somewhat mysterious. Only a small number have been formally identified. However, even the few known species suggest remarkable potential.

Their genomes contain vast repertoires of genes for breaking down organic matter. This is important because it suggests ERM fungi are not just symbionts living in close interaction with other species but also active decomposers, influencing both plant nutrition and soil carbon cycling. Their dual lifestyle may play a critical role in nutrient-poor ecosystems.

Mucoromycotina fine root endophytes (MFRE)

MFRE are another group of enigmatic fungi that form beneficial relationships with plants. Long mistaken for the arbuscular mycorrhizal (AM) fungi until distinguished in 2017, MFRE are also found across a range of ecosystems including farmland and nutrient-poor soils and often live alongside AM fungi.

MFRE appear to be important in helping plants access nitrogen from within the soil, while AM fungi are more associated with phosphorus uptake. Like ERM fungi, MFRE appear to also alternate between free-living and symbiotic lifestyles.

As researchers begin to uncover their roles, MFRE are emerging as important players in plant resilience and sustainable agriculture.

These fungi frequently appear in plant roots. They are characterised by darkly pigmented, segmented fungal filaments, or hyphae, but their role is highly context-dependent.

Some DSEs appear to enhance host stress tolerance or nutrient uptake. Others may act as latent pathogens, potentially harming the host plant. Most DSEs remain unnamed and poorly understood.

Time is running out

Many of the ecosystems connected to these dark guilds of fungi are among the most vulnerable on the planet. The Arctic and alpine regions which are strongholds for ERMs, DSEs and potentially MFREs, are warming at two to four times the global average.

Peatlands have been drained and converted for agriculture or development while heathlands are increasingly targeted for tree-planting initiatives meant to sequester carbon.

Planting fast-growing, non-native species in monocultures may improve short-term carbon metrics above ground, but it could come at the cost of soil health and belowground biodiversity. Many fungi are host-specific, co-evolving with native plants over millions of years.

Replacing those plants with non-native trees or allowing invasive plants to spread could lead to local extinctions of fungi we’ve never had the chance to study. Soil fungi also mediate processes from nutrient cycling to pathogen suppression to carbon sequestration.

We are changing landscapes faster than we can understand them and in doing so we may be unravelling critical ecological systems that took millennia to form.

Katie Field receives funding from the European Research Council, the Biotechnology and Biological Research Council and the Natural Environment Research Council.

Tom Parker receives funding from The Scottish Government’s Rural and Environment Science and Analytical Services Division and Natural Environment Research Council