Where to look for fungi in a bog? Substrate partitioning reveals hidden richness

Where should one look for fungi in a bog? Historically, fungal diversity in peatlands has been studied primarily in peat itself – understandably, given that peat is the defining feature of these ecosystems – using methods such as sporocarp-based observations and microfungal culturing. These approaches suggested relatively modest richness. In this study, we asked whether that picture changes when we sample multiple contrasting substrates beyond peat. We examined fungal diversity, community composition and structure in a raised bog in northern West Siberia by metabarcoding of 266 environmental DNA samples from key substrates: peat, plant litter, wood and mycorrhizal roots, each partitioned by several inner substrate-related parameters. The metabarcoding data were accompanied and verified by sporocarp monitoring for selected substrate groups. This integrated approach allowed us to capture both the visible and the cryptic components of the fungal community, providing a more complete and robust assessment of diversity distribution. Substrate type emerged as the primary driver of community composition (PERMANOVA F = 10.82, p = 0.001), explaining the strongest dissimilarities in beta-diversity. Plant litter harboured the highest total diversity (7,297 SH), followed by peat (3,590 SH), while wood (1,585 SH) and mycorrhizal roots (1,091 SH) were less diverse. Communities in different substrates showed low species overlap (Jaccard index 0.19–0.42), indicating strong substrate partitioning. The highest number of indicator species was found in mycorrhizal roots (85 SH), reflecting the high specialisation of these communities. In contrast, the apparent low indicator status of litter at the aggregate level masked striking host-specific associations: partitioning litter samples by plant host revealed 40–123 indicator SH per host species. Estimated total fungal richness reached ~ 11,500 SH – far exceeding the 208 species recorded by sporocarp-based methods alone. These results reveal that fungal diversity in a raised bog is not concentrated in peat, but distributed across distinct substrate niches, with plant litter being the richest reservoir and mycorrhizal roots harbouring the most specialised communities. This has implications for understanding carbon cycling and decomposition in peatlands. We conclude that only an integrated, substrate-focused approach can uncover the full fungal richness hidden in these unique ecosystems.