The interplay between plant genotype and nutrient management affects rhizodeposition, which in turn modulates the rhizosphere-microbiome and microbe-mediated functions. Substituting mineral nitrogen (N) with an N-fixing inoculant reduces reliance on N fertilizer while supplying N to crops. We evaluated the effectiveness of integrating maize near-isogenic lines (NIL 1 and NIL 2) with the biological nitrification inhibition (BNI) trait into management practices aimed at optimizing N provisioning. Management strategies included mineral N inputs (0 and 67 kg ha⁻¹) with and without an N-fixing inoculant. Our approach synthesized insights from amplicon sequencing data and evaluated nitrification rates, rhizosphere N content, maize N uptake, and N use efficiency (NUE). Genotypes and management structured prokaryotic communities, while the developmental stages of genotypes further refined both fungal and prokaryotic communities. The N-fixing inoculant increased N availability, triggering the BNI capacity without increasing the nitrification rate. This was reflected in lower NO₃⁻ and higher NH₄⁺ levels in BNI-NIL leachate compared to B73, suggesting improved N retention. NIL2, characterized by distinct fungal biomarkers, exhibited higher N content (72.3 kg ha⁻¹) and superior NUE compared to NIL1 (65.0 kg ha⁻¹). NIL2’s enhanced N uptake was associated with a robust microbial network, featuring Archangium (prokaryote) and Trichoderma (eukaryote) as keystone taxa. Notably, Archangium was linked to rhizosphere N dynamics Synergizing BNI with diazotroph inoculants reduces N fertilizer reliance and increases maize N supply for sustainable agroecosystems.
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