Early inoculation with arbuscular mycorrhizal fungi shifts metabolic functions of rhizosphere bacteria in field-grown tomato plants

Abstract Aim The study explores the functional plasticity of rhizosphere microbiomes in response to microbial inoculants, a topic not yet fully explored in open-field agroecosystems. Specifically, it assesses the lasting impact of nursery-stage inoculation with the arbuscular mycorrhizal fungus (AMF) Rhizophagus irregularis and symbiosis-stimulating compounds on the rhizosphere microbiome of Solanum lycopersicum . Methods Tomato seedlings were inoculated with R. irregularis in a commercial nursery. During this period, seedlings were irrigated weekly with strigolactone analogues and the flavonoid quercetin, both with and without AMF inoculation. At harvest, five months post-transplanting, rhizosphere samples were collected for mycorrhizal colonization assessment and predictive metagenomic profiling. Results Nursery AMF inoculation, especially when combined with the strigolactone mimic SL-M2 and quercetin, significantly enhanced mycorrhizal colonization. Although all plants became colonized, early inoculation did not affect bacterial or fungal taxonomic composition at harvest. However, it induced substantial shifts in predicted bacterial metabolic functions, affecting 137 of 154 KEGG modules. These changes, which included key metabolic shifts—such as reduced energy metabolism, increased carbohydrate degradation over lipid or amino acid metabolism, and enriched biosynthesis of stress-responsive metabolites—occurred independently of later colonization or signalling molecule application. Conclusions Early AMF inoculation primes the rhizosphere bacteriome toward a stress-adapted functional state, likely mediated by altered root exudation during early symbiosis. The application of SL-M2 and quercetin further supports their role as prebiotics in sustaining inoculant efficacy. This study provides mechanistic insight into how nursery-stage microbial interventions can shape rhizosphere functionality, offering promising strategies for microbiome-driven improvements in sustainable agriculture. Graphical Abstract