Canopy Height and Epiphytic Bryophytes Shape Fungal Communities in a Temperate Rainforest

Fungal communities contribute to plant ecology and evolution in forested ecosystems. Their diverse interactions with associated host plants can vary along abiotic and biotic gradients, but these gradients are poorly understood in complex natural ecosystems. Given the high diversity of epiphytic plants in many ecosystems, forest canopies offer a unique and underexplored system for studying plant-associated microbial diversity and distribution. We explored both abiotic and biotic factors structuring arboreal fungal communities. Specifically, we hypothesized that bryophyte-associated fungal communities are structured by the vertical height gradient within host trees (from the ground to high in the canopy), vary across host plant species, and that living bryophytes host distinct fungal communities compared to dead bryophyte matter. To test these hypotheses, we sampled living and dead bryophytes (mosses and liverworts) across three different bryophyte host species and four heights, ranging from the forest floor to 18 m above the ground. We characterized the fungal community composition in each sample using metabarcoding. Fungal communities showed significant variation across substrates: bryophytes collected from the ground exhibited 17% greater Shannon diversity and 34% higher taxonomic richness than epiphytic bryophytes, while living bryophytes had 15% higher diversity and 30% greater richness than dead tissues. This pattern suggests that the diverse microhabitats within living bryophytes may drive microbial diversity. Community analysis identified a core fungal community across living bryophyte samples, but rare taxa accounted for a majority of reads, driving differences in community composition between different heights and bryophyte species. Synthesis: Epiphytic bryophyte-associated fungal communities show high heterogeneity across different substrates and heights, which provides insight into the structuring of the forest microbiome and epiphyte ecology. These results demonstrate the importance of exploring canopy-associated microbes to better understand microbial diversity and function in forest ecosystems.