Endophytic microbiota diversity in the phyllosphere of Sicilian olive trees across growth phases and farming systems

This study investigates the diversity and interactions of endophytic microbial communities in the phyllosphere of Sicilian olive trees, focusing on both cultivated varieties (cultivars) and wild accessions. The research aims to explore the influence of anthropogenic factors, phenological stages, and farming practices on endophytic diversity. Samples were collected from three Sicilian olive cultivars subjected to two different olive cultivation management (organic and conventional) and six wild olive accessions (natural environments), across four key phenological phases. Using culture-independent methods, bacterial and fungal communities have been characterized through high-throughput sequencing. The results indicate that phenological stages and agricultural practices significantly affect microbial communities, while the type of olive host mainly affects the fungal diversity. Winter season emerged as a key period for microbial diversity, especially for bacteria, whereas fungal diversity varied less across growth phases. Organic farming management reduced bacterial diversity compared to conventional management and wild habitats. Furthermore, interactions between bacterial and fungal communities revealed positive correlations, highlighting potential synergy among endophytes. These findings underscore the dynamic nature of olive tree microbiota and suggest that both plant–microbe and microbe–microbe interactions play vital roles in structuring endophytic communities. This study is innovative as it compares, for the first time, the complete phenological cycle of local olive cultivars and wild accessions. It also analyzes the endophytic microbial community and its relationship with organic and conventional management. • Diversity and composition of olive tree phyllosphere bacterial endophyte communities were influenced by growth phases and orchard managements, but not by host type. • Olive host, winter season and agriculture practices had a structuring effect on olive mycobiota composition. • The correlations mostly positive and negative are present between bacterial and fungal communities in olive tree phyllosphere. • Guilds recovered were mostly saprotroph followed by pathotroph and symbiotroph in NGS method.