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

Method The fungi in the 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) Analysis by the α and β diversity analysis showed that the endophytic fungal diversity in the asymptomatic needle leaves was higher, and the diversity of endophytic fungi was significantly different from that of infected needles. There was no significant difference in needle leave diversity among different disease spot grades, and the diversity of the endophytic fungal communities of the needle leaves was more similar in the later stages of the disease. (2) Fungal community LEfSe analyses showed the highest number of significant biomarkers (19) in the PM1 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 PM1 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 disease spot grades, in which 43.94% of the dominant endophytic fungi in mildly infected needles PM2 were Penicillium spp. and as the spot grades deepened, the dominant endophytic fungus in PM3, PM4 and PM5 was Dothistroma spp. One of the most abundant endophytic fungi was Dothistroma spp. (4) The internal 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 diseased spots increased, the internal 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 were significantly different (P < 0.05) in the needles of Siberian red pine with different plaque grades. In healthy needles, Endophytic bacteria had the highest diversity index and most indicator groups. However, with the increase of lesion grade, the nutrient type of endophytic fungi community changed from pathological type to saprophytic type.