Metabolitic and transcriptional network in seeds germination of Ephedra sinica by inoculating with endophytic Fusarium citricola of mutualistic symbiosis

The poor germination of seeds from the renowned medicinal plant Ephedra sinica poses a significant challenge in production. An endophytic fungus was isolated from the roots of E. sinica , named Fusarium citricola (EBS-22), which exhibits seed germination-promoting activity. However, the physiological mechanisms underlying F. citricola ’s effect on E. sinica seed germination remain unclear. Through fungus-seedling interaction studies, it was found that a total of 897 differential abundant metabolites were identified ( P < 0.05; Parts Per Million (ppm): [-5, 5]) were identified in the seeds inoculated with F. citricola , among which 107 metabolites exhibited significant differences ( P < 0.05; Variable Importance in Projection (VIP) > 1). Additionally, 1771 significantly or extremely significantly differentially expressed genes (DEGs) were detected (q-Value ≤ 0.05; |Fold change| ≥ 2). This study revealed that fatty acids and lipids represented the predominant class of F. citricola responsive metabolites, comprising 16.82% of the total 107 differentially abundant metabolites. Concurrently, while the majority of fatty acid species (72.22%) exhibited decreased accumulation, the expression of corresponding DEGs and key enzyme-encoding genes within lipid metabolic pathways was uniformly upregulated, implying that F. citricola inoculant stimulates the catabolic utilization of stored lipids as an energy source for germination. These metabolites and DEGs primarily participated in energy metabolism essential for seed germination, including oxidative phosphorylation, pyruvate metabolism, the TCA cycle, and the pentose phosphate pathway. The second most influential metabolites were amino acids, involving 18 common amino acids, which directly influenced the metabolism of downstream secondary metabolites. The study also found that some pathways related to signal transduction were activated, for instance the calcium signaling pathway and the plant MAPK signaling pathway. These findings collectively reveal that the mechanism by which F. citricola regulates E. sinica seed germination involves a complex metabolic network centered on energy and amino acid metabolism.