Abstract: The community composition and diversity of endophytes in Sclerotinia sclerotiorum-infected and healthy mulberry fruits were analyzed using Illumina MiSeq high-throughput sequencing. The results showed that at a 97% sequence similarity level, 281 and 259 bacterial and fungal operational taxonomic units (OTUs) were identified. The endophytic bacterial community mainly included Cyanobacteria, Proteobacteria, Firmicutes and Bacteroidetes, and Cyanobacteria_norank and Mitochondria_norank showed a significant downward trend in the infected fruit with high sensitivity; the endogenous fungal community mainly included Ascomycota, Fungi_unclassified and Basidiomycota. Fungi_unclassified and Basidiomycota were significantly affected by the pathogen. Fungi_unclassified was hardly found in the infected group and the abundance of Basidiomycota decreased by 99.07%. The diversity of endophytic fungi could clearly discriminate between the infected and healthy fruits, being much higher in the former than the latter. Linear discriminant analysis effect size (LEfSe) showed that Pantoea was the major bacterial group in the infected fruit. Ascomycota and its branches (Ciboria, Sclerotiniaceae, Helotiales, Leotiomycetes), Sordariomycetes, Dothideomycetes, Xylariales, and its branches (Xylariales_f_Xylariales_Incertae_sedis, Monographella) were the significantly differential biomarkers between the healthy and infected fruits.

Key words: mulberry fruit; endophytic bacteria; endophytic fungi; microbial community structure; diversity