Transcriptomic and metabolomic analysis reveals the role of Piriformospora indica in enhancing strawberry alkaline tolerance

Soil alkalinity severely limits the productivity of strawberry, a high-value horticultural crop. The root endophytic fungus Piriformospora indica enhances plant stress resilience, yet the systemic mechanisms underlying its promotion of alkaline tolerance remain poorly understood. This study employed an integrated transcriptomic and metabolomic approach to elucidate these mechanisms in strawberry under alkaline stress. Inoculation with P. indica significantly alleviated stress-induced growth inhibition, improving biomass accumulation and leaf development. Metabolomic profiling identified 1,352 DAMs, predominantly flavonoids and phenolic acids. Transcriptome analysis revealed 19,689 DEGs enriched in oxidoreductase activity, hormone signaling, and secondary metabolism. Multi-omics integration highlighted coordinated changes in the metabolism of pyruvate,alanine, aspartate and glutamate. P. indica maintained the balance of carbon and nitrogen allocation in strawberry under alkaline stress, an effect linked to the downregulation of argG, asnB, and GLT1. These findings suggest a putative systemic metabolic mechanism by which P. indica may enhance alkaline tolerance, potentially through rebalancing primary metabolism. This offers molecular insights into fungal-mediated stress adaptation in strawberry and supports its potential as a sustainable bio-inoculant for improving productivity in alkaline soils.