Ecosystem Sequencing of the Boreal Forest Mycobiome Reveals High Substrate Specificity

Fungi are key players in nearly all ecosystems, contributing to ecological dynamics through diverse ecosystem services. They are versatile and can have complex life cycles across hosts or substrates. Although environmental DNA approaches have advanced our understanding of fungal distributions at broad spatial scales, in-depth explorations at fine spatial scales across substrates within ecosystems remain scarce. Here, we provide a comprehensive assessment of fungal diversity and ecology in boreal forests by characterising fungal communities across 26 substrates spanning major ecological compartments such as soil, plant tissues, fungal sporocarps and aquatic habitats in three forests. Fungal community composition is highly structured by substrate, with comparatively weaker effects of geographic site, resulting in clear community partitioning across boreal forest strata, from forest floor to canopy. Nearly half of the detected fungal taxa were restricted to a single substrate, implying a high degree of specialisation. Soils act as reservoirs of fungal diversity, while plants host less diverse but more specialised fungal communities. Aerial and aquatic substrates supported dynamic, likely dispersal-driven fungal assemblages, while tree-related substrates contributed substantially to overall ecosystem diversity, including large fractions of unexplored diversity. By characterising the mycobiome across a wide range of substrates, we provide an ecosystem-level perspective on fungal diversity in the boreal forest, highlighting the importance of considering the full breadth of fungal diversity beyond well-studied substrates to accurately assess and conserve fungal biodiversity.