Ecosystem-specific controls of denitrifier gene abundance and community composition on potential nitrous oxide emissions in upland and paddy soils

Abstract

Agricultural soils are major contributors to atmospheric nitrous oxide (N₂O), yet the microbial and environmental determinants of denitrification-driven N₂O emission potential remain poorly understood across contrasting agroecosystems. We combined a regional field survey of paired upland and paddy soils with anaerobic incubations to disentangle how denitrifier abundance, community composition, and soil properties regulate potential N₂O emissions. Results revealed consistently higher abundances of four key denitrifier genes (nirK, nirS, nosZ I, nosZ II) in upland soils, whereas paddy soils, despite lower gene copy numbers, displayed roughly fourfold greater potential N₂O emissions and elevated capacity for both N₂O production and reduction. Across all sites, variation-partitioning and structural equation modeling identified community composition, rather than gene abundance or alpha diversity, as the strongest predictor of potential emissions. Ecosystem-specific analyses revealed that in upland soils, denitrifier abundance explained up to 88% of the variance in potential N₂O flux, whereas in paddy soils neither microbial abundance nor community traits showed significant predictive power, and soil physicochemical factors exerted only weak indirect effects. These results suggest that robust prediction of soil N₂O emissions therefore requires ecosystem-specific frameworks that integrate microbial abundance, community assembly, and key environmental constraints. Such context-aware approaches can advance mechanistic understanding of N₂O fluxes and guide targeted mitigation strategies for upland and flooded agricultural systems.

Graphical abstract

Keywords

nitrous oxide emissions / denitrifying microorganisms / community structure / upland soils / paddy soils

Highlight

	● Regional survey links denitrifier traits to N2O potential in upland and paddy soils.
	● Paddy soils emit more potential N2O despite lower denitrifier gene abundance.
	● Community composition, not gene abundance, predicts N2O emissions across systems.
	● Upland soils show strong gene-flux correlations; paddy soils show weak predictors.
	● Ecosystem-specific frameworks are essential to forecast and mitigate soil N2O flux.

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