Long-term nitrogen fertilizer improves nitrogen use efficiency and wheat yield by regulating the interactions of rhizosphere soil-root-microbes

Nitrogen (N) fertilizer is widely used in agroecosystems to maintain and improve soil fertility while affecting soil microbial communities. The ability of root to absorb nutrients is critically mediated by these soil microbial communities, ultimately determining crop growth and yield formation. Thus, comprehensively understanding the rhizosphere root-soil-microbe interaction mechanism is critical for synergistically regulating nitrogen use efficiency (NUE) and yield. Here, a 13-year field experiment in a wheat-maize rotation system was conducted to explore the effects of N fertilizer on soil physicochemical properties, root parameters and rhizosphere microorganisms. Compared with N0 (0 kg ha −1 ), moderate N application (180–240 kg ha −1 ) optimized soil nutrient availability, as evidenced by increasing available nitrogen (AN) and ammonium-N (NH 4 + -N) by 17.42 %–27.33 % and 12.24 %–6 2.49 %, respectively, and enhanced root morphology, with root vessel diameter (RVD), root length density (RLD), and root weight density (RWD) rising by 5.12 %–21.57 %, 14.17 %–65.77 %, and 3.46 %–62.10 %, respectively. Consequently, N uptake and metabolic enzyme activities were significantly boosted. These root modifications, in turn, reshaped the rhizosphere microbiome by enriching beneficial bacterial and fungal taxa, Pseudomonadota and Basidiomycota increased by an average of 20.93 % and 73.28 %, facilitating efficient N cycling and organic matter decomposition. Structural equation model (SEM) revealed that soil N and root enzyme activity mediated microbial community compositions and diversity, which collectively enhanced both yield and NUE. Overall, our findings highlight the critical role of root-microbe feedback in driving N efficiency and propose that optimizing N inputs can sustainably enhance crop productivity by leveraging soil-plant-microbial synergies. • A 13-year experiment clarified the synergistic regulation of wheat yield and NUE by rhizosphere soil-root-microbe interaction . • Optimal N fertilization enhanced soil nutrient availability and root traits, improved root N metabolic enzyme activities. • Rhizosphere microbiomes promote N cycling and organic matter decomposition via beneficial taxa. • SEM revealed soil and root traits mediated microbial community characteristics, collectively enhancing wheat yield and NUE.