Temporal and spatial niche partitioning in plant microbiomes: Divergent assembly processes shape floral and foliar microbial communities in spring-flowering trees

Abstract Spring-flowering trees present distinct microbial habitats across their floral (anthosphere) and foliar (phyllosphere) organs, yet the spatiotemporal dynamics of their microbiome assembly are not fully understood. Here, we combined high-throughput amplicon sequencing (16S rRNA/ITS) and trait-based analyses across six Prunus species to characterize how organ identity, seasonal progression, and host functional traits were associated with microbiome structure. Bacterial α-diversity declined markedly from flowers (highest) to summer leaves (lowest; P < 0.05), governed predominantly by deterministic processes—heterogeneous selection in flowers versus homogeneous selection in leaves. In contrast, fungal phyllosphere communities maintained stable α-diversity but displayed pronounced compositional turnover, shifting from more stochastic assembly in spring to deterministic selection in summer. Co-occurrence network analysis revealed distinct interaction patterns: floral microbiomes formed highly connected networks with low modularity, whereas leaf microbiomes, especially in summer, exhibited more compartmentalized structures. Several plant functional traits (e.g. flower/leaf moisture content) were significant predictors of microbial community composition. Our study delineated the spatiotemporal patterns and assembly processes of tree microbiomes, highlighting how divergent ecological forces shaped microbial communities in different plant organs. These insights contribute to a framework for understanding microbiome assembly in perennial plants.