ABSTRACT Seeds harbor diverse microbial communities important for plant growth and health. During germination, seed exudation triggers intense microbial competition, shaping the communities transmitted to seedlings. This study explores the role of the bacterial type VI secretion system (T6SS)-mediated interference competition in seed microbiota transmission to seedlings. Distribution of T6SS within 180 genome sequences of seed-borne bacterial strains enabled the construction of SynCom with different levels of phylogenetic diversity and T6SS richness. These SynComs were inoculated with Stenotrophomonas rhizophila CFBP13503, a bacterial strain which possesses a T6SS active in vitro and in planta . SynComs compositions were compared in vitro with CFBP13503 wild-type strain or its isogenic T6SS-deficient mutant. Additionally, the effects of T6SS on the whole bacterial community dynamics during seed-to-seedling transmission were examined following seed-inoculation. The T6SS of S. rhizophila CFBP13503 targeted a large number of bacteria belonging to 5 different families The phylogenetic proximity and metabolic overlap of preys with CFBP13503 partly explains the sensitivity phenotype observed. The T6SS of CFBP13503 modulates the abundance of a few specific bacterial taxa during seed-to-seedling transmission depending on seed microbial initial inoculation and plant stage. Depending on the sensitivity of the co-inoculated competitors, the T6SS can provide a competitive advantage to CFBP13503, resulting in an increase in population size. Importance The high prevalence of T6SS in seed-borne bacteria supports the importance of T6SS-mediated competition for seed microbiota assembly. In vitro , S. rhizophila CFBP13503 T6SS exerts a strong impact on bacterial community dynamics. The susceptibility to T6SS increases with the phylogenetic and metabolic proximity of bacteria to CFBP13503, suggesting an influence of interspecies trophic patterns in T6SS-mediated competitions. In planta and in soil, CFBP13503 T6SS influences specific bacterial taxa, leading to shifts in bacterial interactions and distinct community dynamics. T6SS-mediated competition plays a pivotal role in shaping seed bacterial communities and the dynamics of seed-to-seedling transitions.

T6SS-mediated competition byStenotrophomonas rhizophilashapes seed-borne bacterial communities and seed-to-seedling transmission dynamics