Objective The diversity and flora structure of endophytic fungi in needles of Pinus sibirica with different lesion grades were studied to provide a theoretical basis for the microecological control of Siberian red pine diseases.

Method The fungi in needles of P. sibirica were sequenced by high-throughput sequencing method, α and β diversity were analyzed by Spearman correlation coefficient, and fungal trophic groups were predicted by FUNGuild database.

Result (1) α and β diversity analysis showed that the endophytic fungal diversity in asymptomatic needle leaves was higher, and the diversity of endophytic fungi was significantly different from infected needles. There was no significant difference in needle leaf diversity among different lesion grades, and the diversity of endophytic fungal communities of needle leaves was more similar in later stages of disease. (2) Fungal community LEfSe analyses showed the highest number of significant biomarkers (19) in the sample group of asymptomatic needle leaves. (3) Community structure analysis showed that, compared with the endophytic fungal community structure of infected needle leaves, the endophytic fungal community structure of asymptomatic needle leaves was more complex, in which Fusarium spp. was dominated; there were also differences in the fungal community structure of P. sibirica needle leaves with different lesion grades, in which 43.94% of dominant endophytic fungi in mildly infected needles was Penicillium spp., and as lesion grades deepened, the dominant endophytic fungus was Dothistroma spp. (4) The endophytic fungal trophic classification of diseased needle leaves changed significantly compared with asymptomatic needles. The relative abundance of endophytic fungal trophic classification in asymptomatic needle leaves was relatively uniform, and as the level of lesion increased, the endophytic fungal trophic classification in needle leaves shifted from pathological fungi to saprophytic fungi, and a large number of unknown functional fungal groups existed.

Conclusion The diversity and community structure of endophytic fungi are significantly different (P < 0.05) in the needles of Pinus sibirica with different lesion grades. In healthy needles, endophytic bacteria have the highest diversity index and most indicator groups. However, with the increase of lesion grade, the nutrient type of endophytic fungi community changes from pathological type to saprophytic type.