Plant nutritional and metabolic responses to drought and elevated CO2 revealed by machine learning-enabled non-targeted metabolomics

Projected atmospheric CO2 rise, coupled with intensification of drought in many regions, impacts the physiology of C3 plants beyond photosynthesis and carbon metabolism. The interaction between CO2 and drought affects the concentrations of many nutrients in crops, often resulting in excessive agrochemical use and less nutritious food production. To address these challenges, we investigated nutrient dynamics in Brachypodium distachyon, a model crop plant, under ambient and elevated CO2, factorially combined with well-watered or drought treatments. Integrative analyses of plant physiology, transcriptomics, and machine learning-enabled non-targeted metabolomics revealed that plant elemental composition and metabolomic responses to elevated CO2 strongly depend on water availability and differ between shoots and roots. Elevated CO2 and drought significantly impaired nitrogen status, with root nitrate uptake being more negatively affected than ammonium uptake. However, elevated CO2 increased iron partitioning in shoots under drought, potentially driven by enhanced carbon availability facilitating chelator synthesis for iron translocation. The high accumulation of sphingolipids in roots under combined stresses suggests a protective role against ionome imbalances. These findings highlight how climate stressors interact to shape plant nutrient dynamics, providing insights that can guide agricultural practices and breeding strategies to optimize nutrient management and foster sustainable agriculture under changing climate.