A Field-Based Study of Phyllosphere Mycobiomes in Apple Orchards Under Varying Agricultural Practices

Microbial communities in the phyllosphere are key players in plant health and disease resistance, yet their response to agricultural practices 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: once in May, July, and August, corresponding approximately to monthly intervals throughout the summer, while flower samples were collected from the same trees in May. Our analyses reveal that agricultural practices are significantly associated with fungal community structure, with effects intensifying from May to July. While conventional practices are associated with increased absolute abundance of commensal and potentially beneficial taxa, higher abundance of several genera which include known pathogens is also observed at organic sites. Alpha diversity declined over time at conventional orchards but remained stable at organic sites. These patterns suggest that shared interventions and distinct inputs impose contrasting selective pressures on the phyllosphere mycobiome, thus affecting not only community composition but also diversity. Our findings underscore the ecological relevance of field-based microbiome research and offer insights to support the development of sustainable orchard management strategies informed by fungal community dynamics.