Genotypic Variation in Rice Root Exudates Controls Biological Nitrification Inhibition Efficiency in the Rhizosphere

Abstract

Nitrification in agricultural soils drives significant nitrogen fertiliser losses and nitrous oxide (N2O) emissions, particularly in intensively fertilised rice systems. Biological nitrification inhibition (BNI), mediated by plant-derived compounds, offers a promising nature-based strategy to mitigate these losses, but the factors controlling BNI potential remain poorly understood. In this study, BNI mechanisms across five rice genotypes were investigated by combining plant physiology, soil nitrification dynamics and exudate metabolomics. Nitrifier suppression was strongest in the rhizosphere and declined with distance from the root, indicating a spatially localised effect. BNI efficiency varied significantly among genotypes and selectively targeted nitrifiers with little effect on the broader microbial community. Ammonia-oxidising archaea (AOA), the dominant nitrifiers in this acidic flooded soil, were more inhibited than ammonia-oxidising bacteria (AOB) in soil and in exudate-amended culture assays. However, BNI preferentially altered AOB community diversity, whereas AOA diversity remained comparatively stable. Plant physiological traits, rather than the exudate metabolome, were more strongly associated with BNI efficiency. High-BNI genotypes exhibited greater shoot biomass, higher shoot N accumulation and increased exudation, together with a higher relative abundance of N-butyldodecan-1-amine (NBDA) in their exudates. Metabolomic analyses identified a novel rice-derived BNI compound, NBDA, which strongly inhibited diverse nitrifier cultures, reduced soil N2O emissions and showed no detectable off-target effects on non-nitrifying bacteria. Together, this study demonstrates that plant traits and the abundance of BNI-active compounds within the root exudate metabolome regulate BNI efficiency in the rhizosphere, advancing a predictive framework for mitigating nitrification in rice agroecosystems.