Plant growth-promoting rhizobacteria mitigate N2O emissions via divergent nitrification-denitrification synergies in contrasting agricultural soils

Abstract: Aims Nitrous oxide (N2O) from agricultural soils is a potent greenhouse gas and a dominant ozone-depleting substance, underscoring an urgent need for sustainable mitigation strategies. Plant growth-promoting rhizobacteria (PGPR) represent a promising bio-based solution, given their dual role in enhancing plant productivity and regulating soil N cycles. Methods This study explores the soil-specific mechanisms by which PGPR regulate N2O emissions, with research sites located in two contrasting soils in China: Wuxi, Jiangsu (paddy-upland rotation soil), and Dezhou, Shandong (upland-upland rotation soil). The experiment employed PGPR inoculation treatments to investigate their regulatory effects on N2O fluxes. Quantitative real-time PCR (qPCR) was used to quantify the absolute abundances of critical nitrogen-cycling functional genes, and high-throughput sequencing was performed to analyze the shifts in soil microbial community composition. Correlation analysis, Mantel tests and Random Forest modeling were further applied to identify the core microbial taxa driving N2O flux variations. Results PGPR efficacy was found to be co-determined by native soil properties and strain functional traits. In Wuxi soil, effective PGPR strains suppressed nitrification gene abundance (AOA-amoA, AOB-amoA) while enriching key denitrifiers such as Rhodanobacter, thereby constraining N2O production and enhancing its reduction. In contrast, in Dezhou soil with upland-upland rotation, successful mitigation involved optimizing the microbial consortium to favor a synergy between low-N2O-yield ammonia oxidizers (e.g., Nitrososphaeraceae) and efficient denitrifiers. Furthermore, we identified and validated key microbial taxa (e.g., Lysobacter and Vicinamibacteraceae) whose abundances strongly correlated with N2O flux. These findings provide a mechanistic framework for tailoring PGPR inoculants to specific soil environments, advancing their application as a precise and sustainable tool for mitigating agricultural N2O emissions. Conclusions The nosZ-carrying strain YSQ030 exhibited stable robust, cross-soil N2O mitigation performance.