Responses to Agricultural Practices in Apple Orchards: A Field-Based Mycobiome Study of the Phyllosphere

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. Flower and leaf samples were collected from six sites over three time points during the 2023 growing season. 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 containing known pathogens is observed in organic sites. Alpha diversity declined over time in conventional orchards but remained stable at organic sites. These patterns suggest that shared interventions (e.g., biocontrol) and distinct inputs (e.g., synthetic vs. organic treatments) impose contrasting selective pressures on the phyllosphere mycobiome, thus affecting not only community composition but also diversity. Our findings underscore the ecological relevance of on-farm microbiome research and offer insights to support the development of sustainable orchard management strategies informed by fungal community dynamics.