Endophyte-induced metabolic divergence in wheat genotypes: implications for plant–soil interactions

This study assessed the metabolic and enzymatic responses of winter wheat (cv. ‘Hondia’, ‘Tytanika’) and winter spelt (cv. ‘Rokosz’) to the endophytic biopreparation InnoEndop with biochar as a carrier. In vitro experiments optimized endophyte viability and growth promotion across biochar variants, identifying 6.67 × 10 4 cells mL⁻ 1 at 15–20 °C as optimal conditions. A 40-day greenhouse pot trial was then conducted using inoculated seeds. Plant responses were monitored through untargeted LC/Q-TOF–MS metabolomics, HPLC–PDA phenolic profiling (every 10 days), and PAL/POX enzymatic assays (every 5 days). Optimal inoculation improved seedling vigor. At Day 0, both cultivars shared exclusive induction of metabolites linked to redox regulation, hormonal signaling, and the phenylpropanoid pathway, including GSSG, L-tryptophan, allantoin, scopoletin, and 12-OPDA. Metabolomic responses differed between genotypes: 'Rokosz' showed a balanced distribution of up- and down-regulated features, whereas 'Hondia' showed greater non-polar feature induction (980 vs. 419 differential features). By Day 40, 'Hondia' exhibited late POX activation (1.5 U·min⁻ 1 ·g⁻ 1 ) and wax ester accumulation (palmityl palmitate 39.7-fold), while 'Rokosz' maintained a sustained PAL peak (11.81 IU·g⁻ 1 FW) and phenylpropanoid accumulation. InnoEndop induces genotype-specific metabolic strategies rather than uniform responses. Modern wheat employs progressive structural and biochemical defenses, whereas ancient spelt activates focused phenylpropanoid-based resistance. These findings highlight the importance of host-specific microbiome interactions for sustainable agriculture and crop resilience.