Deterministic recruitment limitation during soybean pod development shapes seed-transmitted microbiota assembly.

The transgenerational inheritance of plant microbiota is fundamental to host fitness, however the ecological rules governing microbial assembly during the transition from flower to seed remain poorly understood. Therefore, we characterized the spatiotemporal dynamics of the soybean microbiota across developmental stages from vegetative to reproductive growth, and identified the specific seed-pod stages that drive a critical deterministic bottleneck for the recruitment of seed endophytes. Although the floral stage serves as a high-diversity recruitment keystone taxa dominated by stochastic processes, pod enclosure imposes rigorous host-mediated filtering and dispersal limitation, shifting the community toward a specialized "guardian" microbiota. By employing functional characterization and defined microbial community assays, we demonstrated that keystone taxa utilize niche partitioning and functional complementarity to provide collective resilience. The consortium may contribute to the reduction of salinity stress by stabilizing photosynthetic efficiency and suppresses Phytophthora sojae infection through synergizing direct antagonism with compensatory growth. Anatomical evidence suggests the soybean endocarp acts as a physical interface and ecological reservoir, facilitating the redistribution of maternal microbes into the maturing seed. Our findings define a precise "transmission window" for microbiota-based interventions, providing a roadmap for engineering more resilient crop-microbe associations across generations.