Partial substitution of chemical fertilizer with organic amendments reduces yield variability by shifting climate to soil-microbe-mediated regulation under equivalent nutrient supply

Intensive agriculture confronts critical challenges of soil nutrient depletion and yield instability under escalating climate variability. To evaluate whether organic material amendments stabilize soil nutrients and enhance agricultural resilience, a five-year field trial (2018–2023) was conducted to compare chemical fertilizer (NPK), chemical fertilizer plus crop straw (NPK+S), and chemical fertilizer plus organic manure (NPK+O) in a wheat–maize rotation on the North China Plain. We monitored inter-annual dynamics of climate, soil nutrients, bacterial communities, and yields, and analyzed environmental-yield linkages via multivariate analyses including partial least squares path modeling. (PLS-PM). The results showed that organic amendments significantly increased soil organic carbon 4.1%–7.7% and total nitrogen 3.9%–6.2%, reduced their inter-annual coefficient of variation (CV) by 12.9%–32.4%, and concurrently lowered crop yield CV by 17.2%–27.7%. Straw return (NPK+S) delayed nutrient mineralization, attenuated precipitation-induced nutrient depletion, and provided synergistic water conservation and nutrient stabilization benefits during droughts. Conversely, whereas NPK + O increased leaching losses under intense rainfall. Phylum-level analysis revealed divergent microbial pathways: straw enriched oligotrophic Acidobacteriota and polysaccharide-degrading Bacteroidota for carbon stabilization, whereas manure triggered an excessive Actinobacteriota bloom while suppressing Proteobacteria , indicating stress-oriented filtering that may weaken functional resilience. PLS-PM demonstrated that the bacterial community mediated the effects of soil nutrients on yield, with the pathway shifting from direct climate-to-yield dominance under NPK to indirect soil-biology-mediated regulation under organic amendments. These findings indicate that straw return is optimal for semi-arid regions with high precipitation volatility to bolster system resilience, while manure supplementation requires strategic irrigation to mitigate nutrient leaching—providing key pathways for climate-smart agriculture.