Soil acidification is defined as a decline in soil pH to ≤5.5, affecting about 30% of global ice-free land and imposing significant constraints on crop growth and yield. Most nutrients are optimally absorbed within a neutral pH range (6.5–7.5), whereas abnormal pH conditions reduce nutrient availability and increase toxicity. Acidic soils are commonly associated with deficiencies in phosphorus, magnesium, and calcium, along with elevated aluminum concentrations—factors that collectively inhibit plant development and reduce both yield and quality.

To investigate crop adaptive responses and potential mitigation strategies, we conducted metabolomic and transcriptomic analyses in soybean (Glycine max) subjected to acidic stress. Our metabolomic data revealed substantial accumulation of antioxidant metabolites such as flavonoids, phenolics, and organic acids; transcriptomic profiling showed upregulation of the genes associated with these pathways, indicating genetic-level regulation of antioxidant metabolite biosynthesis under acidic stress. Additionally, some amino acids and dipeptides exhibited significant changes during stress. Exogenous application of certain acid stress–induced metabolites alleviated stress-induced growth inhibition and promoted lateral root development, while also rapidly increasing the pH of the growth medium.

Under acidic stress, supplementation with glutamine (Gln) markedly increased the concentrations of the micronutrients calcium (Ca) and magnesium (Mg) in soybean roots. Pharmacological experiments using EGTA and La³⁺ further demonstrated that calcium signaling plays a key role in Gln-mediated mitigation of acidic stress. Moreover, inhibition of the TOR signaling pathway reduced the growth suppression caused by acidic stress. Multi-omics analyses also showed that Gln treatment reduced the accumulation of stress-induced antioxidant metabolites, indicating mitigation of oxidative stress responses. Transcriptomic data revealed that genes associated with mitochondrial function and photosynthesis were affected by acidic stress, while Gln application decreased this impact and activated genes involved in stress alleviation, highlighting its regulatory role in both metabolism and signaling.

Finally, we found that commercially available protein hydrolysate–based biostimulants can serve as effective acid stress mitigators. Overall, this study elucidates the metabolic and molecular mechanisms by which Gln enhances plant tolerance to acidic stress, emphasizing the interplay between amino acid metabolism and calcium signaling. Our findings deepen the understanding of how acidic soils affect crop physiology and highlight protein hydrolysates as promising biostimulants capable of enhancing crop stress resilience in sustainable agriculture.

東京大学大学院理学系研究科・生物科学専攻・植物生理学研究室