Ecological drift and host filtering jointly structure foliar endophytes during ecosystem development

Background Foliar endophytes contribute to plant nutrient acquisition, stress tolerance, and pathogen resistance, yet their responses to ecosystem-level processes remain poorly understood. Using a space-for-time substitution design, we investigated bacterial and fungal community dynamics in the foliar endosphere of four phylogenetically distinct plant hosts across a well-characterized successional chronosequence. Results Amplicon sequencing revealed that the ecosystem development stage (site age) significantly influenced endophyte community composition, particularly among fungi, but explained only a small proportion of the total variation. Host plant identity and associated leaf stoichiometry were stronger predictors of community structure, with sampling time within the growing season also contributing significantly. Together, these deterministic factors explained 10% and 11% of bacterial and fungal compositional variation, respectively, and 27% of predicted bacterial functional potential. Null model analyses indicated that remaining variation was mostly consistent with stochastic assembly processes, particularly ecological drift. Endophytic communities were characterized by a few persistent dominant taxa and many rare, transient members with overlapping functional potential, including N 2 fixation, methylotrophy, and denitrification. Conclusions Our findings demonstrate that host identity outweighs ecosystem age in structuring foliar endophyte communities and that stochastic processes play a central role in community assembly. The coexistence of stable dominant taxa and a dynamic rare biosphere may enhance plant responsiveness to environmental changes, while the functional potential of endophytes may remain largely consistent across seasons and successional stages.