Unveiling microbial-plant interactions via multi-omics: A nitrogen-fixing agent enhances Astragalus mongholicus growth and medicinal properties for sustainable culture

Astragalus mongholicus is a key medicinal plant, but its cultivation faces challenges in soil fertility and microbial interactions. PGPR can affect the secondary metabolism of host plants by regulating the level of phytohormones in medicinal plants, thus affecting the growth of medicinal plants and the accumulation of medicinal components. This study investigates the impact of a nitrogen-fixing bacterial agent on root physiology, metabolite profiles, gene regulation, and microbial communities to enhance agricultural sustainability. Integrative multi-omics analyses revealed that mixed nitrogen-fixing bacterial agent inoculation shifts microbial community, marked by produce plant hormones to promote plant growth, regulate host secondary metabolism and enhance host stress resistance, suggested synergistic microbial plant interactions. Genes linked to secondary metabolism, stress tolerance, plant hormone signal transduction, and nitrogen metabolism were up-regulated in A. mongholicus . Key metabolites, including succinic acid and flavonoids, showed significant increases, correlating with enhanced medicinal compound accumulation. This work demonstrates that microbial interventions can modulate root metabolism and microbiome composition, offering a sustainable strategy for improving A. mongholicus yield and quality. The findings highlight the potential of bioactive microbial agents in precision agriculture. • Synthetic PGPR bacterial agent significantly increased the yield of A. mongholicus . • Sixty-three differential metabolites were increased after bacterial agent inoculation. • Genes related to flavonoids biosynthesis were significantly up-regulated after treatment. • The agent alter root endophytic microbiota to regulate host growth and secondary metabolism.