Drought is the most significant abiotic stress that impedes agroforestry development. In nature, drought tolerance also depends on the ability to compensate after water restoration. Dark septate endophytes (DSEs) are believed to enhance plant tolerance in drought environments. However, the compensatory mechanisms of DSEs for rehydration after drought stress have not been reported. To assess the drought tolerance and compensatory capacity of DSEs, the following DSEs were investigated in this study using solid–liquid screening and potting tests under different drought gradients, rehydration conditions, and field water-holding capacities: Stagonosporopsis lupini, Microsphaeropsis cytisi, Macrophomina pseudophaseolina, Paraphoma radicina, Alternaria alstroemeriae, Alternaria tellustris, and Papulaspora equi. The results showed that M. pseudophaseolina reached the maximum diameter for plate growth in only 4 d. In a liquid shaker, the biomass of S. lupini peaked after rehydration. The Mantel heatmap indicated that lipid metabolites were significantly expressed in M. pseudophaseolina and S. lupini under drought stress. Correlations between drought tolerance indexes and amino acid metabolites increased dramatically in both DSEs after rehydration. Moreover, in rehydration after drought, the treatments inoculated with M. pseudophaseolina and S. lupini showed significant increases in root weight of 20.36% and 23.82%, respectively, compared with the uninoculated treatment.

Salvia miltiorrhiza is a traditional herbal remedy for cardiovascular diseases and is in high demand in the market. Excessive chemical fertilizer application, resulting from unscientific fertilization practices, reduced the tanshinone content in S. miltiorrhiza roots. This study investigated how different fertilization types alter the endophytic microbial community composition of S. miltiorrhiza through field experiments, aiming to understand how fertilization affects its medicinal quality. The results showed that root fertilizers (F1) significantly increased root biomass and tanshinone I content, whereas foliar fertilizers (F2) increased tanshinone IIA content. High-throughput sequencing further revealed that F2 treatment significantly decreased the Shannon index of endophytic bacteria while significantly increasing the Shannon index of endophytic fungi. Co-occurrence network analysis revealed that fertilization significantly altered fungal community complexity and modularity, with F1 increasing network nodes and edges. Variance partitioning analysis indicated fungal diversity more strongly influenced medicinal compound levels under F2 and a combination of both (F3) than bacterial diversity. Septoria and Gibberella were positively correlated with tanshinone I and cryptotanshinone content under F2 treatment, respectively. Notably, the unique strains were isolated from different fertilization treatments for subsequent bacterial fertilizer development. These findings elucidate microbial responses to fertilization, guiding optimized cultivation for improved S. miltiorrhiza quality.