FungalGO_data.and.code.zip

Plant-microbe interactions are critical in shaping forest dynamics, yet molecular functions through which foliar endophytic fungi (FEF) influence seedling survival and coexistence remain unresolved. Combining FEF transcriptomics with seedling dynamics in a subtropical forest, we tested whether FEF molecular functions regulate seedling survival via host fitness differences and niche differentiation under modern coexistence theory. We found FEF transcripts diversity strongly associated with host divergence time and maximum height, and FEF functions significantly enhance seedling survival through fitness-related and niche-related processes. Among these FEF functions, gene ontology (GO) terms with high host-phylogeny dependence enhance seedling survival through fitness differences associated with stimulus responses and multi-organism interactions, and those with high host-trait dependence enhanced seedling survival through fitness differences related to basic life processes. For GOs independent to host-phylogeny and host-trait, they enhance seedling survival via increased niche differentiation. Our findings bridge microbial functional genomics with modern coexistence theory in natural forests.