Biochar and Trichoderma viride co-application boosts industrial soybean performance under continuous cropping stress via rhizosphere metabolic reprogramming

Continuous monoculture of soybean, a key industrial crop for bio-based products, faces severe yield and quality declines due to soil degradation and microbial dysbiosis. Here, we investigated whether biochar and Trichoderma viride co-application (BT) can synergistically alleviate continuous cropping stress in soybean by integrating multi-omics and industrial quality assessments. BT significantly increased grain yield by 18.5% compared to the control, outperforming single amendments of biochar (B) or Trichoderma viride (T). Metabolomic and metagenomic analyses revealed that BT uniquely reprogrammed rhizosphere metabolism (upregulating defensive metabolites like β-Lapachone and Lupulone, while alleviating flavonoid suppression) and restructured microbial assembly towards enhanced bacterial cooperation and fungal competition. Root transcriptomic profiling demonstrated that BT integrated biochar-mediated basal metabolic homeostasis with Trichoderma -induced hormone signaling, activating defense-related pathways including phenylpropanoid biosynthesis and sphingolipid metabolism. Crucially, beyond yield, BT substantially improved seed industrial quality. It increased oil content and protein content, leading to 20.3% and 17.1% increases in oil and protein yields, respectively, and raising the comprehensive Industrial Value Index (IVI) from 1.82 (CK) to 2.08. Structural equation modeling (SEM) confirmed soil properties as upstream drivers, indirectly regulating yield and quality via root transcriptional reprogramming. Collectively, biochar- Trichoderma synergy overcomes continuous cropping barriers by establishing a positive feedback loop among soil habitat, microbiome, and plant adaptive responses, offering a sustainable strategy to secure both productivity and industrial feedstock quality of soybean.