Integrated multi-omics profiling reveals effects of exogenous plant growth regulators on tobacco rhizosphere under Vulpia myuros rotation

Soil degradation poses a significant threat to agricultural sustainability. The integration of plant growth regulators (PGRs) with cover cropping systems represents a promising strategy for enhancing soil health and plant resilience. However, the synergistic effects of PGRs and cover crops on soil microbial communities and plant metabolism remain poorly understood. Exogenous PGRs under Vulpia myuros rotation were linked to distinct restructuring of tobacco rhizosphere microbiomes and metabolic networks. High-throughput sequencing of 16 S rRNA and ITS regions revealed that NaHS was associated with enhanced fungal diversity, promotion of beneficial saprotrophic taxa, and activation of phenylpropanoid and lignin metabolism. VB₁-based treatments modulated bacterial communities, enriched cooperative Firmicutes–Proteobacteria clusters, and drove sphingolipid, coenzyme, and amino acid pathways, while multivitamins promoted synergistic microbial clusters and stimulated phenolic antioxidant and secondary metabolite production. Glutamate maintained overall microbial diversity but induced rare taxa, reshaping lipid and ceramide metabolism and activating neurotransmitter and amino acid pathways. Integrated metabolomics–microbiome analysis revealed treatment-specific microbial–metabolite interactions, including lipid remodeling, pollutant degradation, and phenolic activation, linking microbial shifts with metabolic reprogramming. Network analyses demonstrated that PGRs differentially modulate microbial co-occurrence, enhancing cooperation, centrality, or competitive partitioning, collectively optimizing rhizosphere ecological functions and plant stress adaptation. Our findings demonstrate that exogenous PGRs differentially reshape rhizosphere microbial communities and metabolic networks, enhancing plant stress adaptation in a cover crop system. These results provide a mechanistic basis for optimizing PGR-cover crop synergies to improve soil health and crop resilience.