Physiological, Transcriptomic, and Metabolomic Analyses Reveal the Mechanism of Biochar Involved in Manganese Toxicity in Rice Seedlings

Biochar is widely used to remediate heavy metal-contaminated soils, but its effects on rice seedlings under manganese (Mn) toxicity remain unclear. This study aimed to examine the impact of biochar on rice growth under Mn toxicity. Results showed that 800 μmol/L MnCl 2 inhibited seedling growth. Application of 200 mg/L biochar promoted root development under Mn stress, as indicated by root length and root fresh weight significantly increasing by 9.79% and 11.72%, respectively, compared to Mn stress alone. However, combined Mn and biochar treatment led to more severe shoot growth inhibition, reflected by significantly elevated levels of H 2 O 2, O 2 .−, and MDA in leaves by 10.94%, 26.12%, and 17.26%, respectively, relative to Mn stress alone. Integrated multi-omics analysis of plants subjected to combined Mn and biochar treatment identified coordinated enrichment of differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs) in the phenylpropanoid biosynthesis, amino acid biosynthesis, and ABC transporter pathways. Among the top 30 DEGs, 12 in leaves and 26 in roots were positively correlated with growth; similarly, 24 and 21 DAMs in leaves and roots were positively correlated with growth. Interestingly, the DEGs enriched in different pathways might contribute to Mn chelation and also reduce oxidative effects. These findings elucidate biochar's modulatory role in response to Mn toxicity and underscore the need for cautious application in soils with elevated metal concentrations. Further experimental validation of the functional roles of key DEGs and DAMs is warranted.