Objectives This study investigates the impact of green manure and microbial fertilizer on the soil fungal community in Korla fragrant pear orchards. Specifically, it aims to assess how biofertilizer combined with various green manure species and planting configurations influence soil fungal diversity and to recommend an optimal fertilization strategy to support sustainable pear orchard management.

Methods Field experiments were conducted in 2022 and 2023 a Korla fragrant pear orchard in Bayingolin, Xinjiang, using Pyrus betulifolia as rootstock in age of 7～8 years old. The treatments were: (1) conventional fertilization control (CK); (2) microbial fertilizer (JF); (3) oilseed sunflower planting with a row spacing of 25 cm and a seeding rate of 27 kg/hm² (DK1); (4) oilseed sunflower planting with a row spacing of 20 cm and a seeding rate of 33 kg/hm² (DK2); (5) sweet clover planting with a row spacing of 25 cm and a seeding rate of 21 kg/hm² (CM1); (6) sweet clover planting with a row spacing of 20 cm and a seeding rate of 27 kg/hm² (CM2). Soil samples were collected from the 0–20 cm depth during the fruit setting, fruit enlargement, and maturation stages in 2023. Soil properties were analyzed, and fungal community composition and diversity were assessed using high-throughput ITS gene sequencing. At maturity, fruit yield was recorded.

Results Compared to the CK, JF treatment reduced the relative abundance of Ascomycota by 22.87%, DK2 treatment increased the relative abundance of Plectosphaerella by 729.83%. Both DK2 and CM2 treatments significantly enhanced fungal diversity. LefSe analysis revealed that the CM2 treatment exhibited the highest number of differentiated species during the fruit expansion and ripening stages. Correlation analysis demonstrated that all fungal community diversity indices were significantly correlated with soil organic matter, available P, total N, and microbial biomass carbon and nitrogen. Redundancy analysis indicated that pH, available K, and total N had significant effects on community structure at both the phylum and genus levels; Soil organic matter, available K, available P, alkaline hydrolysis N, total N, and microbial biomass nitrogen all significantly influenced fragrant pear yield. All the JF, CM1, CM2 and DK2 treatments were recorded significantly higher pear yields than CK, and the yield in JF were comparable to that of CM1, CM2, and DK2, but significantly higher than that of DK1.

Conclusions On the basis of conventional chemical fertilizer application, the application of microbial fertilizer and the cultivation of green manure demonstrated considerable yield-increasing effects. However, they differed in their impacts on improving the structure and diversity of soil fungal communities, with notable variations particularly observed during the fruit enlargement stage. During the fruit enlargement period, the application of microbial fertilizer containing Bacillus spp. reduced the relative abundance of Ascomycota in the soil. Cultivating high-density oilseed sunflowers enhanced soil fungal community diversity and increased the relative abundance of Plectosphaerella. Cultivating high-density sweet clover also improved fungal community diversity, as evidenced by the highest number of differential fungal species. Therefore, applying microbial fertilizers and planting high-density green manure crops are effective measures for enhancing the yield of fragrant pears and improving soil fertility in orchards.