Omics-informed insights into biochar–Trichoderma interactions in plant–soil systems: mechanisms of defense and context-dependent responses

The combined application of biochar and Trichoderma spp. represents a promising strategy for enhancing plant resilience and soil health; however, the molecular mechanisms underlying their synergistic interactions remain poorly understood and inadequately integrated. This review critically synthesizes evidence from transcriptomic, proteomic, metabolomic, and microbiome analyses to elucidate how biochar-Trichoderma interactions modulate plant defense signaling pathways and stress adaptation responses. Transcriptomic analyses reveal context-dependent activation of the jasmonic acid (JA), salicylic acid (SA), and ethylene (ET) signaling pathways. Correspondingly, proteomic and metabolomic datasets demonstrate variable yet recurrent upregulation of pathogenesis-related (PR) proteins, reactive oxygen species (ROS)-scavenging enzymes, and phenylpropanoid-derived metabolites. Notably, accumulating evidence suggests that these molecular responses are highly context-dependent, varying substantially with soil type, biochar physicochemical characteristics, and Trichoderma strain specificity. We critically examine major methodological limitations in existing omics investigations, including inadequate reproducibility under field conditions and insufficient integration of molecular and ecological datasets. Finally, we propose a systems biology framework for designing functionally optimized biochar–microbe formulations and identify research priorities for translating insights into agronomically robust and field-deployable technologies.