The present study investigated the interactions among nitrogen transformation and soil bacteria along the direction of diffusion of hole-applied urea. To this end, a lab incubation trial was conducted on sandy loam and silty loam soils. Soil bacterial communities were analyzed via 16S rRNA high-throughput sequencing, and soil chemical properties were measured at 8, 20, and 60 d after urea application. The treatments were the fertilizer point and 0–4 cm, 4–8 cm, 8–12 cm, and 12–16 cm horizontally distant from the fertilization point. They were designated FP, 0–4, 4–8, 8–12, and 12–16, respectively. The pre-culture and pre-incubation soil sample was used as a control. Soil NH₄⁺ concentration was the key factor influencing the soil bacterial community. For the sandy loam, the FP and 0–4 treatments reduced the putative abundance of amoA by 38.9–83.4% and 40.7–67.6%, amoB by 38.9–83.4% and 40.6–67.6%, and amoC by 41.1–84.1% and 43.6–69.9%, respectively, compared with the control group. For the silty loam, the FP and 0–4 treatments reduced the putative abundance of amoA by 85.0–87.3% and 28.9–82.6%, amoB by 84.6–87.2% and 29.1–82.5%, and amoC by 81.9–87.1% and 27.5–82.7%, respectively, compared with the control group. The fertilizer core region was 60 d, which strongly inhibited nitrification. Overall, the fertilizer core region slowly released nitrogen and inhibited nitrification. For these reasons, hole application of urea may serve as a long-acting nitrogen fertilizer.

Root-zone nitrogen fertilization (RZF) can increase crop N uptake and yield, yet the underlying rhizosphere N-cycling functional mechanisms remain insufficiently resolved. In a field experiment with winter oilseed rape (Brassica napus L.), RZF was compared with conventional fertilization (CF) under the same N input rates, alongside a zero-N control (N0). Compared with CF, RZF significantly increased seed yield (by 0.44 t ha⁻¹) and aboveground N uptake (by 20.45 kg ha⁻¹), while simultaneously enriching rhizosphere mineral N pools (NH₄⁺–N and NO₃⁻–N by 54.50% and 56.02%, respectively). Shotgun metagenomics revealed that RZF reprogrammed rhizosphere N-cycling functional potential, characterized by enhanced nitrogen fixation, reduced nitrification and denitrification, and a tendency toward increased assimilatory nitrate reduction. These module-level shifts were supported by concordant changes in key functional genes, indicating greater genetic potential for N retention and assimilation (nifD, glnA, gltB, nasA, napB, nrfA) and reduced potential for nitrification- and denitrification-driven N losses (amoB/C, narI, nirK, norB). Taxonomic composition analysis showed enrichment of Bradyrhizobium and suppression of key nitrifier taxa (Nitrosospira and a Nitrososphaeraceae-affiliated taxon) under RZF. Rhizosphere pH exhibited the strongest Mantel correlation with multiple N-cycling modules, and rhizosphere available N (AN; sum of NH₄⁺–N and NO₃⁻–N) was positively associated with plant N traits and yield. Structural equation modeling supported a pathway in which a functional balance index (retention/assimilation vs. loss/oxidation) increased AN (0.22), and AN strongly promoted yield (0.90). Collectively, these results elucidate a rhizosphere-centered mechanism whereby localized N placement strengthens soil–plant N coupling and enhances crop productivity through reprogramming microbial N-cycling functional potentials, positioning rhizosphere N processes as a key mechanistic bridge for microbiome-informed optimization of root-zone fertilization.