Keystone Bacterial Taxa Drive Denitrification and N2O Emission via Adaptive Genomic and Metabolic Strategies in Contrasting Agricultural Soils

Abstract

Soil denitrification mediated by microbial communities is a major driver of nitrous oxide (N2O) emissions, yet the regulatory roles of keystone taxa remain largely unexplored, particularly under distinct edaphic conditions. Black soil (BS) and fluvo-aquic soil (FS), two representative agricultural soils in China, exhibit contrasting N2O emission potentials, providing a unique model system for disentangling microbial mechanisms underlying soil-specific denitrification dynamics. Here, we integrated microbial co-occurrence networks, metagenomics, and functional phenotyping to identify and characterize keystone bacterial taxa involved in denitrification across the above mentioned two contrasting agricultural soils, BS and FS. Structural equation modeling (SEM) and correlation analyses revealed that keystone taxa are significantly associated with soil denitrification rates and N2O emission patterns. Among these, Ramlibacter ASV104 was identified as a conserved keystone in both soils, exhibiting genomic potential for key denitrification genes (nirK/nirS/norB/nosZ) to mediate N2O turnover. In contrast, Ensifer ASV205 was a FS-specific keystone taxon, exhibiting strain-level niche specialization. Comparative genomics revealed that variations in denitrification gene composition and carbon-nitrogen metabolism enable different Ensifer strains to function either as N2O sources or sinks. This functional divergence was linked to their genomic plasticity and growth strategies under nutrient-rich conditions. Our findings demonstrate that soil-specific denitrification processes and N2O emissions are governed by keystone taxa through adaptive genomic and metabolic strategies shaped by environmental filtering. This study improves our understanding of the microbial mechanisms driving N2O emissions and provides a foundation for future strategies targeting microbial taxa to mitigate N2O emissions in agricultural soils. IMPORTANCEThis study provides new insights into the ecological complexity underlying soil N2O emissions by integrating strain-level diversity, genomic attributes, and microbial interaction networks. Key microbial taxa involved in denitrification and N2O emissions were identified in black soil and fluvo-aquic soil. By combining network-based ecological modeling and functional assays, it is revealed that taxa such as Ramlibacter ASV104 and Ensifer ASV205 play significant roles in regulating N2O emissions. Strain-level functional diversity within the keystone taxa of Ensifer ASV205 highlights their varying contributions to nitrogen cycling. Our findings provide a deeper understanding of the microbial mechanisms governing N2O emissions, offering valuable insights for developing microbial-based strategies to mitigate N2O emissions in agricultural soils in the future.