Shifts in seed‐associated endophytic bacterial communities from parental lines to advanced generations in lima bean

Abstract Seeds serve as both carriers of plant genetic material and reservoirs of vertically transmitted microbiota. Understanding how seed‐associated microbial communities change during the advances in generations is essential for developing microbiome‐informed strategies to enhance crop performance. In this study, we investigated the composition of seed‐associated endophytic bacterial communities across successive generations in lima bean ( Phaseolus lunatus L.) from parents (P 1 and P 2 ) to F 2 , F 3 , F 6 , F 8 , and F 9 generations. Using 16S rRNA gene sequencing, we found that the seed bacteriome underwent progressive restructuring with certain taxa recurrently increasing or decreasing across generations, rather than maintaining a stable core microbiome. Statistical analyses revealed a clear separation between early (parental, F 2 ) and advanced generations (F 6 –F 9 ), with F 9 seeds showing the highest richness and divergence. While overall bacterial diversity remained stable, specific phyla were differentially enriched across generations: Firmicutes predominated in F 2 , while Proteobacteria became dominant in F 9 . At the amplicon sequence variant (ASV) level, advanced generations were enriched in genera such as Pseudomonas , Burkholderia , and Lysinibacillus , whereas parental and early lines were associated with Methylobacterium and Anaerobacillus . Complementary analyses confirmed that F 9 seeds harboured the highest number of exclusive and discriminant ASVs, highlighting directional microbial reshaping across generations. These findings suggest that host genotype plays a key role in shaping the seed microbiome and that the advance of generations can unintentionally select for beneficial microbial traits.