Are environmental factors correlated with the diversity of Phytophthora in organically and conventionally managed citrus orchards in Sicily? Insights from metabarcoding and baiting

Abstract Phytophthora species pose a significant threat to citrus production in the Mediterranean, particularly in Sicily, a major citrus-producing region. This study explores the diversity and distribution of Phytophthora taxa in Sicilian citrus orchards, addressing the urgent need to tackle increasing agricultural challenges, such as climate change. Specifically, it aimed to evaluate how environmental factors, such as the type of management (organic vs. conventional) and geographical area influence the composition of Phytophthora communities in Sicilian citrus orchards, and whether these communities correlate with tree health. An additional objective was to compare the effectiveness of traditional baiting and high-throughput metabarcoding techniques (targeting the ITS1 region and RPS10 gene) in capturing this diversity, as well as to assess potential shifts in community structure resulting from climate change by comparing current data with historical records. Soil samples were collected from ten citrus-producing areas under two distinct agronomic management and tree health conditions. Traditional baiting recovered 556 isolates of three already described Phytophthora species, while ITS1 metabarcoding identified ten additional taxa, demonstrating higher specificity (99.5% of ITS1 reads classified as Phytophthora compared to 82.5% for RPS10 ). Our findings indicate that geographical location is a key driver of community composition. Although statistical analyses did not reveal significant differences in Phytophthora diversity between organic and conventional management systems, these results provide valuable insights into the factors shaping pathogen communities. These insights are crucial for developing targeted disease management strategies and for understanding how environmental stressors, including climate change, impact pathogen dynamics in Mediterranean citrus orchards. Graphical Abstract