High-Throughput Sequencing Reveals Fungal Microbiome of Apricots Grown Under Organic and Integrated Pest Management Systems

Apricots are affected by many abiotic and biotic factors that could negatively impact their vitality and yield, leading to branch and tree dieback. Knowledge of the microbiome composition is key to choosing the optimal measurement strategy. The effect of the two different growing systems, i.e., organic (ORG) and integrated pest management (IPM), on the apricot fungal microbiome was studied. The inner bark was used to isolate DNA, and the present fungi were analyzed using a metagenomics high-throughput sequencing (HTS) profiling approach of the data obtained based on the Illumina sequencing of the ITS1-ITS2 amplicons of the 18S rRNA gene. Of the 20 analyzed samples, Ascomycota was the dominant phylum, and Dothiomycetes was the most abundant. Basidiomycota was the less frequent, with Tremellomycetes being the predominant within this phylum. PCA analysis showed the complete separation of the samples obtained from the orchards grown under the ORG and IPM systems. Cladosporia, Alternaria, Aureobasidium, and Visniacozyma were detected in all samples, but they dominated the IPM samples. Filobasiadiales were recognized as an indicator species for ORG management, while Caliciales, Lecanorales, Lichinales, Mycosphaerellales, Myriangiales, Phacidiales, Teloschistales, and Thelebolales were identified as indicator species for IPM management. Based on the order and genus levels, a significantly higher fungal microbiome richness was detected in the ORG samples. This could be connected to the environmentally beneficial growing system applied in the orchard, but it is impossible to assess the risk of trunk disease development or premature apricot tree decline.