Transgenerational Dynamics of Endophytic Microbiome in Soybean Seeds

Seeds harbor diverse microbial communities, including endophytes, some of which are vertically transmitted and may contribute to plant health and productivity. However, the temporal dynamics of seed endophytic communities remain poorly understood in many crop species. In this study, we monitored the composition of bacterial and fungal endophytes in soybean (Glycine max) seeds, along with rhizosphere microbiomes, across three plant generations using a culture-independent approach. Our results revealed two key patterns: seed endophytic communities are distinct from those of bulk soil and rhizosphere microbiomes; and the composition of seed endophytes fluctuates over generations, likely influenced by both pre-existing endophytes, environmental factors, and microbial influx from the surrounding soil and rhizosphere, suggesting possible microbial transmission from the rhizosphere into seeds. Interestingly, despite generational variation, the seed fungal endophyte communities consistently maintained higher phylogenetic diversity compared to bacterial endophytes, which showed limited overlap across generations and were composed of fewer, closely related taxa. Analysis of community assembly mechanisms indicated that both seed and rhizosphere microbiomes significantly contributed to the next generation of seed microbiota, primarily through stochastic drift and homogeneous selection processes. Collectively, our findings offer valuable insights into the intergenerational dynamics of seed endophytes in soybean and provide a foundation for future efforts to harness seed-associated microbiomes for improving crop health and productivity.