Decade-long nitrogen fertilization differentially alters microbiome-mediated nitrification and denitrification in...

The intensive use of nitrogen fertilizers in agriculture, while boosting crop yields, has triggered severe environmental consequences including greenhouse gas emissions and groundwater pollution through disrupted N-cycling. Understanding how fertilizer regimes interact with soil types to govern microbially-driven nitrogen transformations is critical for developing sustainable intensification strategies, yet remains poorly characterized particularly in contrasting soil matrices under identical climatic conditions. This knowledge gap hinders the formulation of soil-specific fertilizer management practices to reconcile agricultural productivity with environmental protection. Through a decade-long field experiment employing split-plot design (soil types: black soil vs. sandy soil; N rates: 0, 168, 312 kg N ha^-1), we deciphered the microbiome-mediated mechanisms underlying nitrification (NP) and denitrification potentials (DP) using qPCR, high-throughput sequencing, and gas inhibition methods. Nitrogen fertilization significantly altered functional gene abundances (AOA-amoA, AOB-amoA, nirS, nirK, nosZ), reshaped microbial community structure, and induced divergent diversity responses between nitrification and denitrification processes. Structural equation modeling revealed that N addition alters microbial diversity, thereby enhancing NP(4.1 %), whereas stimulated DP(72.6 %) via gene abundance regulation. These soil-dependent microbial adaptation patterns provide mechanistic evidence for optimizing N application strategies: Black soils benefit from moderate N inputs maintaining higher NP, whereas sandy soils require stricter N controls to mitigate denitrification-derived DP. This study provides a theoretical basis for improving nitrogen use efficiency and reducing environmental risks, while offering new insights into the microbial drivers of sustainable agricultural intensification.