Layered Nitrogen Fertilization Enhances Wheat Productivity by Reshaping Rhizosphere Processes via Root–Metabolite–Bacteria Coupling

Layered nitrogen (N) fertilization has been proposed to improve wheat productivity, yet its rhizosphere mechanisms remain unclear. In a four-year field experiment, we compared layered fertilization (N1–2–1), surface application (N8), and no N input (NCK). Layered fertilization increased grain yield, anthesis-stage N accumulation, root biomass, and soil nutrient availability relative to N8. It also reshaped rhizosphere microbiomes and metabolomes, reducing overall microbial richness but enriching a Flavobacterium -enriched bacterial module. Network and correlation analyses linked this module with key metabolites, particularly β-thujaplicin and Ingenol mebutate, which were associated with yield, root traits, and improved soil fertility. These findings suggest that layered fertilization enhances wheat performance by coordinating root architecture, rhizosphere metabolite signals, and selective bacterial recruitment. The study provides a mechanistic basis for precision N placement to regulate rhizosphere processes and improve wheat productivity under sustainable management.