Hidden highways

Mycorrhizal fungi are the unsung heroes of our planet’s terrestrial ecosystems. Nearly all plants form symbiotic associations with mycorrhizal fungi, which create vast underground networks to find, transport and exchange nutrients in the soil.

These fungal ‘superhighways’ physically connect plants underground, enabling nutrients such as carbon, phosphorous, nitrogen and water to move where they’re needed. There’s even some evidence that the networks can help trees detect threats that other plants are facing – insect attacks, for example – and can enable other microorganisms such as bacteria to commute between different root systems underground.

This 450-million-year-old symbiotic relationship helped early terrestrial plants survive on land, pre-dating the evolution of terrestrial plant roots, and plays a vastly important role in global carbon sequestration – drawing approximately 13 billion tonnes of CO2 into the soil each year. Despite this, mycorrhizal fungi are often overlooked in climate change strategies, conservation initiatives and restoration efforts.

The Society for the Protection of Underground Networks (SPUN), is an international group of scientists hoping to change this. It is working to map the intricate mycorrhizal networks that regulate the Earth’s climate and ecosystems, while advocating for their protection and driving innovation in underground science. Using almost three billion fungal DNA sequences from samples collected across 130 countries, SPUN has created high-resolution maps to predict mycorrhizal fungal biodiversity at a 1km² resolution across the entire planet. 

Dr Bethan Manley, the society’s lead computational biologist, works at the intersection of field biology and big data. She coordinates the sequencing and computational work that’s helping to identify fungal species from the biological noise found in SPUN’s global soil-sampling efforts

How well do we understand biodiversity and biodiversity loss in underground fungi?

Our understanding is still in its infancy compared with the comprehensive baselines we have for many groups of plants and animals. Just 0.2% of global conservation funding goes to studying fungi, even though we estimate there are around two million species of fungi, most of which are undescribed.

SPUN recently published work showing that just 9% of predicted mycorrhizal richness hotspots – areas where large numbers of species of mycorrhizal fungi exist – are found in protected areas. This means that the areas where the highest concentrations of mycorrhizal fungi live are not currently being protected.

Like other species, the main threats mycorrhizal fungi face globally are habitat loss, pollution and climate change. Tillage from intensive agriculture, deforestation and land-use change are direct threats, where soil disturbance literally rips apart these delicate hyphal networks. Excessive application of synthetic fertilisers can cause plants to reduce their reliance on fungal partners, leading to a decline in the mycorrhizal fungi found in agricultural soils; and changes in temperature and rainfall can directly affect the distributions of mycorrhizal fungal species, especially highly specialised or endemic ones.

Essentially, we’re losing species we haven’t even described, which compromises the resilience of the ecosystems they support.

On top of their crucial symbiosis with plants, what other ecological functions do these underground networks provide?

Mycorrhizal fungi are a gateway, linking the carbon that is fixed and stored in plant biomass during photosynthesis to the soil. Carbon flows from plants into the soil through mycorrhizal networks and fungal biomass is a massive, often underestimated, long-term carbon sink. SPUN collaborated on research that estimates that the equivalent of roughly 40% of annual energy-related emissions are drawn into the soil by mycorrhizal fungi each year.

On top of this, mycorrhizal fungal hyphae produce compounds, particularly glomalin, that physically bind soil particles together. This reduces the amount of soil that is physically washed or blown away, an issue that leads to flooding or desertification in many parts of the world. The extensive hyphal networks dramatically increase the capacity of their plant partners to absorb water from soil, acting as a buffer against drought, and helps soils hold on to soluble nutrients.

Restoration practices that don’t consider the soil microbiome, including mycorrhizal fungi, have been found to have lower success rates than those that do consider below-ground biodiversity.

Mapping these delicate and complex underground networks on a global scale sounds so difficult. How is it done and what tools and technologies make this possible now where it would have been impossible in the past?

The first step involves working with local scientists to collect thousands of soil samples from all over the world in a standardised manner. We extract DNA from these soil samples and use DNA metabarcoding to identify which species are present in each soil sample. This enables us to identify all traces of mycorrhizal fungi in the soil, rather than relying on visible mushrooms, which is especially important as a majority of mycorrhizal fungi don’t form mushrooms or any above-ground structures at all.

We combine this biological data with vast geospatial layers (climate, soil type, plant cover, land use) and train machine learning algorithms to predict fungal biodiversity and endemism in the many places we haven’t sampled, using the data from the areas that we have sampled. This enables us to generate the high-resolution global maps that predict where the planet’s hotspots of mycorrhizal fungi are. This can be explored by anyone using our Underground Atlas (spun.earth/underground-atlas). Users can browse where high numbers of mycorrhizal fungi are and where rare species likely exist. 

Who is helping collect samples and how do you choose where to sample?

Working with and supporting local scientists is one of SPUN’s core principles. Our data collection is built on a foundation of collaboration. Traditional ecological knowledge from local and indigenous communities is indispensable, offering site-specific context that our global models can’t capture. This ensures our science is ethical and responsible, and directly informs local conservation strategies. We’ve carried out collaborative projects with indigenous communities in Ecuador and Chile, involving long-term discussions and the development of scientific and policy concepts.

We also have an initiative called the Underground Explorer’s Program, which funds scientists from all over the world to carry out projects studying the mycorrhizal fungi in their ecosystems of interest. This means that geographical gaps in mycorrhizal data are filled, and the people with the specific expertise in a particular environment are working to generate data in the areas that they most care about and understand. 

Essentially, we’re losing species we haven’t even described, which compromises the resilience of the ecosystems they support

What factors help predict mycorrhizal diversity? What are the above-ground signs that an area might be a mycorrhizal biodiversity hotspot?

A species-rich plant community generally supports a diverse array of mycorrhizal fungal partners. However, SPUN’s research has identified that there can be mismatches between hotspots for plants and hotspots for mycorrhizal fungi. Varied landscapes create microclimates and niches that support greater specialisation and endemism for mycorrhizal fungi, as well as other organisms.

Mycorrhizal fungi are a wide group of organisms, though, and some areas of the planet are hotspots for their different functional groups. Ectomycorrhizal fungi (those that form a sheath, net or sleeve around root tips) tend to form symbioses with temperate and boreal tree species, so their hotspots tend to be in northern forests. Hotspots for arbuscular fungi (those that form intracellular structures within plant roots) tend to be in the tropics.

Our models have identified hotspots of fungal diversity in biodiverse ecosystems such as the Brazilian Cerrado and Guinean forests of West Africa, but also hotspots of rare mycorrhizal fungi in many northern tundra ecosystems. Luckily, we have Underground Explorer grant awardees in many of these locations actively researching the fungal communities there. 

In recent years there’s been a mainstreaming of interest in fungi and their importance, thanks to books such as Entangled Life and major documentaries such as Fantastic Fungi. Is that translating into more grants, philanthropic interest and more boots on the ground studying underground networks?

We are very excited by growing enthusiasm and understanding of fungi in general – and specifically mycorrhizal fungi. Public interest is vital and is certainly generating attention from the media and policymakers. It does seem to be translating into tangible action and we have seen an increase in philanthropic interest and private funding specifically targeting fungal conservation and research.

Governments and large NGOs are beginning to include fungi in conservation agendas and climate strategies, moving beyond the traditional plant and animal focus. Notably, the 3Fs movement (adding ‘funga’ to ‘flora and fauna’) spearheaded by the Fungi Foundation has had an impact on the consideration of fungi in policy initiatives by the Chilean and UK governments.

The challenge now is to convert this enthusiasm into sustained, large-scale and long-term funding that properly reflects the ecological importance of mycorrhizal fungi.

How do you hope researchers will use all this new data on Earth’s underground biodiversity?

We hope that the Atlas will shift focus to below-ground conservation. Most conservation and restoration initiatives don’t use fungal data in their surveys or biodiversity data layers, so they miss an enormous part of the ecosystem, one that is fundamental for supporting above-ground biodiversity. A better understanding of the total biodiversity in a system will surely enable greater success in its conservation.

We also want our data to be used by policymakers to advocate for greater funding and adoption of mycorrhizal data in global policies. This data can also play an important role in climate modelling. Mycorrhizal fungi are a crucial carbon store that is not currently considered in models of carbon cycling and future climate scenario predictions.

Find out more at spun.earth

Dr Bethan Manley is SPUN's lead computational biologist