Mechanisms by which nitrogen-cycling functional genes enable reduced nitrogen input without yield loss under optimized straw incorporation

This study aimed to clarify how straw incorporation timing reshapes nitrogen (N)- cycling functional processes and regulates N retention and loss in paddy fields under different N fertilization regimes. It also evaluated the effects of these processes on rice yield and N uptake and utilization efficiency in cold-region rice systems, thereby addressing the shortage of field-based evidence from seasonally cold rice-growing regions. A two-year field experiment was conducted with three straw treatments, including no straw incorporation (CK), spring straw incorporation (ST), and autumn wet-harrow straw incorporation (SW). These treatments were combined with conventional N fertilization (N2) and a 20% reduction in N input (N1), resulting in six treatments. Soil environmental variables and metagenomic functional information were integrated to clarify how soil conditions and N-cycling functional genes would drive rice yield and NUE. Autumn straw incorporation by wet harrowing under a 20% reduction in N input (SWN1), maintained rice yield, and improved N recovery efficiency (NRE). The SWN1 significantly increased dissolved organic carbon (DOC) and soil organic carbon (SOC). The sustained DOC supply likely increased microbial oxygen consumption, thereby shifting inorganic N toward the ammonium (NH4+-N) form. The overall downregulation of the nitrification gene amoB/pmoB and the denitrification gene norB weakened the conversion of NH4+-N to nitrate (NO3−-N). Meanwhile, the upregulation of the N fixation gene nifK and the assimilatory nitrate reduction to ammonium (ANRA) related gene nirD may reduce redox-mediated N loss and improve N retention and recycling. These functional shifts helped maintain rice yield and improve NRE under lower N application rates. The SWN1 maintained rice yield and improved NRE by increasing DOC and SOC, favoring NH4+-N accumulation, and reshaping the N cycling functional gene network. These findings provide a mechanistic basis for efficient N fertilization and straw management in cold-region rice systems.