Plant Exposure to Agrochemicals in the Soil Has Transgenerational Impact on the Seed Microbiota in Tomato

Seed-associated bacterial communities are crucial for plant health, yet the impact of agrochemicals on them remains largely unexplored. This study investigated the effects of repeated soil applications of nine different agrochemicals (four synthetic and five biopesticides) on the seed microbiome of tomato (Solanum lycopersicum L.) plants. They represent major plant protectant categories in current agricultural use. The results showed that abamectin (R² = 21.9%), chitosan (R² = 24.7%), fosthiazate (R² = 11.8%), imidacloprid (R² = 27.2%), ningnanmycin (R² = 19.3%), and wuyiencin (R² = 22.1%) significantly (P < 0.05) altered the composition, diversity, and abundance of seed-associated microbial communities comprising 33 bacterial phyla and 445 genera. Among these, abamectin increased bacterial richness while simultaneously reducing key beneficial taxa such as Streptomyces and Rhizobium, which are known to be crucial for plant health. In contrast, kasugamycin, moroxydine hydrochloride, and sodium nitrophenolate exhibited negligible impacts, likely due to their non-bacterial targets or rapid degradation. Our study suggests that pesticide-induced microbiome shifts extend beyond direct effects and are associated with influencing seed endophyte selection by the host, as indicated by the depletion of Streptomyces and Rhizobium under specific treatments. Other treatments promoted taxa such as Pseudomonas, suggesting ecological trade-offs. These findings highlight the need to incorporate seed microbiome considerations into pesticide risk assessments and to develop agrochemical strategies that protect the functional integrity of plant-associated microbial communities.