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 different hosts or substrates. Recent advances in eDNA technologies enable broad-scale investigations of fungal distributions, but in-depth explorations at finer scales across substrates within specific ecosystems remain scarce. Here, we obtain a comprehensive understanding of fungal diversity and ecology in boreal forests by analyzing fungal communities across 26 different substrates. We show that fungal diversity is highly structured by substrate specificity, with clear community partitioning across boreal forest strata. Nearly half of fungal OTUs occur in only one substrate, implying many specialists. Soils act as reservoirs of fungal diversity, while plants host specialized and less diverse mycobiomes. Aerial and aquatic substrates contain dynamic, likely dispersal-driven communities, while tree-related substrates contribute substantially to ecosystem diversity, including large fractions of unexplored diversity. By characterizing the mycobiome across the boreal forest, we present a novel framework for understanding fungal diversity at the ecosystem level, highlighting the importance of fine-scale and localized patterns. We conclude that maintaining the full breadth of boreal forest niches is key to conserving fungal diversity.