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 BNI compounds also inhibit methane oxidation by methanotrophic bacteria, revealing a previously unrecognized trade-off in greenhouse gas regulation. Across soil bioreactor systems and pure cultures of both Type I and Type II methanotrophs, BNI compounds consistently suppressed methane oxidation activity. 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 showed that inhibition is predominantly associated with particulate methane monooxygenase (pMMO). Transcriptomic analyses demonstrated compound-specific responses, including suppression of methane oxidation pathways and differential regulation of stress-associated genes. These findings suggest that BNI-mediated inhibition of methane oxidation may offset reductions in nitrous oxide emissions, with implications for predicting net greenhouse gas fluxes in agricultural and wetland ecosystems. Incorporating BNI effects into biogeochemical models will be critical for accurately evaluating their role in the global methane budget.