Distinct Yet Coordinated: Pattern of Leaf and Root Fungal Endophyte Communities in an Alpine Meadow

Leaf and root fungal endophytes (LFEs and RFEs) represent essential yet distinct components of the plant holobiont, but their ecological relationships remain poorly understood. Here, we investigated the community structure of LFE and RFE across 45 plant species in an alpine meadow ecosystem using high-throughput sequencing. We found that the richness of RFEs was significantly higher than that of LFEs whereas their diversity showed no significant difference. The community composition of RFEs significantly differed with LFE communities and indicator analysis revealed that Aureobasidium, Didymella, and Mycosphaerella enriched in leaves and Mucor, Candida, and Trichoderma dominating roots. Fungal endophytes form a complementary functional network that supports plant growth, defense, and resource utilization. Plant functional traits rather than phylogenetic distance shaped the structure of both LFE and RFE communities. Despite their compositional divergence, LFEs and RFEs shared a large number of taxa and showed a coordinated assembly pattern. The coordinated variation between leaf and root functional traits, coupled with the fluxes of LFEs and RFEs, is a critical driver of this pattern. Overall, our results provide integrated evidence that LFE and RFE communities constitute ecologically distinct yet interconnected components of the plant holobiont, jointly contributing to plant performance and ecosystem functioning.