A field-based study of phyllosphere mycobiomes in apple orchards under varying agricultural management strategies

Microbial communities in the phyllosphere are key players in plant health and disease resistance, yet their response to agricultural management strategies remains poorly understood under field conditions. Here, we compare fungal community composition and diversity across conventional and organic apple orchards using ITS amplicon sequencing. Leaf samples were collected from six sites at three distinct time points during the 2023 growing season (in May, July, and August) corresponding approximately to monthly intervals throughout the summer. Flower samples were collected from the same trees in May. Our analyses reveal that agricultural management strategies are significantly associated with fungal community structure, with effects intensifying from May to July. Both types of management strategies showed enrichment for different genera known to include common apple tree pathogens: Alternaria and Podosphaera were associated with conventional sites, while Didymella and Ramularia were associated with organic sites. Although fungal alpha diversity was higher in May at conventional orchards compared to organic orchards, it declined over time at conventional sites while it remained stable at organic sites. Together, these patterns indicate that distinct management interventions impose contrasting selective pressures on the apple tree phyllosphere mycobiome, thus shaping both broad fungal community composition and the dominance dynamics of key fungal taxa. Our findings underscore the ecological relevance and inherent challenges of field-based microbiome research, and provide insights to inform the development of sustainable orchard management strategies grounded in fungal community dynamics.