PGPB administration influences the cross-talk and interactions of rhizosphere and endophyte microbial communities in sunflower

Plant Growth Promoting Bacteria (PGPB) represent a promising strategy for sustainable agriculture, offering the potential to modulate plant-associated microbiomes and enhance crop resilience. This study evaluated the impact of three microbial consortia (among <i>Bacillus,</i> Lactobacillaceae and <i>Paenibacillus</i>) on the rhizosphere and root endophytic microbiota of two sunflower (<i>Helianthus annuus</i>) genotypes: a hybrid (LST907 - Olival) and an open-pollinated variety (Peredovick), over two consecutive growing seasons. High-throughput 16S rRNA amplicon sequencing revealed that PGPB inoculation induced significant modulation of microbial communities, with strong genotype- and year-specific responses. Inoculants selectively enriched key beneficial taxa, including Pseudomonadaceae, Streptomycetaceae, Lactobacillaceae, and Comamonadaceae, while depleting others such as Chitinophagaceae and Micromonosporaceae, suggesting a functional shift in microbiome composition. Correlation and co-occurrence across endosphere and rhizosphere niches revealed enhanced connectivity between taxa under inoculated conditions, with stronger and more variable associations observed in Peredovick. Remarkably, several microbial families showed consistent cross-niche associations across years, suggesting robust and reproducible inoculant effects. Principal Component Analysis confirmed clear structural shifts in both rhizosphere and endosphere communities, with specific microbial families acting as key drivers of treatment-related variance. These findings provide evidence that PGPB not only shape microbial diversity at the community level but also influence microbiome assembly dynamics in the root endosphere and rhizosphere niches. Moreover, the sunflower genotype plays a central role in mediating the magnitude and direction of these microbiome shifts. Overall, our results support the development of genotype-adapted microbial inoculants to modulate plant microbiomes with enhanced functional potential, pointing to a perspective for improving crop performance under sustainable management frameworks.