Microorganisms are an important component of global biodiversity and play an important role in plant growth and development and the protection of host plants from various biotic and abiotic stresses. However, little is known about the identities and communities of endophytic fungi inhabiting cultivated medicinal plants in the farmland ecosystem. The diversity and community composition of the endophytic fungi of cultivated medicinal plants in different hosts, tissue niches, and seasonal effects in the farmland of Northern China were examined using the next-generation sequencing technique. In addition, the ecological functions of the endophytic fungal communities were investigated by combining the sequence classification information and fungal taxonomic function annotation. A total of 1025 operational taxonomic units (OTUs) of endophytic fungi were obtained at a 97% sequence similarity level; they were dominated by Dothideomycetes and Pleosporales. Host factors (species identities and tissue niches) and season had significant effects on the community composition of endophytic fungi, and endophytic fungi assembly was shaped more strongly by host than by season. In summer, endophytic fungal diversity was higher in the root than in the leaf, whereas opposite trends were observed in winter. Network analysis showed that network connectivity was more complex in the leaf than in the root, and the interspecific relationship between endophytic fungal OTUs in the network structure was mainly positive rather than negative. The functional predications of fungi revealed that the pathotrophic types of endophytic fungi decreased and the saprotrophic types increased from summer to winter in the root, while both pathotrophic and saprotrophic types of endophytic fungi increased in the leaf. This study improves our understanding of the community composition and ecological distribution of endophytic fungi inhabiting scattered niches in the farmland ecosystem. In addition, the study provides insight into the biodiversity assessment and management of cultivated medicinal plants.

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.