Biological nitrification inhibition compromises the soil methane sink

Biological nitrification inhibition (BNI) is a plant-mediated process that suppresses nitrification and is widely considered beneficial for reducing nitrous oxide emissions. Here, we show that methane oxidation is consistently suppressed in soil bioreactor systems containing the BNI-active plant Brachiaria and in methanotrophic pure cultures exposed to representative BNI compounds. Kinetic analyses indicated an uncompetitive-like inhibition pattern, characterized by concurrent decreases in Vmax and Km, while reversibility assays showed that inhibition was not associated with loss of cellular viability. Experiments under copper-replete and copper-depleted conditions further suggested that inhibition is primarily associated with particulate methane monooxygenase. Transcriptomic analyses demonstrated compound-specific responses, including suppression of methane oxidation pathways and altered expression of stress-associated genes. These findings suggest that plant-derived nitrification inhibitors may simultaneously inhibit methane oxidation while reducing N2O emissions, revealing a previously unrecognized trade-off in greenhouse gas regulation. Biological nitrification inhibition compounds suppressed methane oxidation and nitrification, suggesting a link between biological nitrification inhibition and methane cycling, based on soil bioreactor experiments and metagenomic sequencing.