Functional and taxonomic characterization of soil microbial communities associated with tolerance to Xylella fastidiosa in olive trees

Xylella fastidiosa (Xf) represents one of the most severe threats to olive cultivation in the Mediterranean basin, causing extensive tree decline and major economic and ecological losses. Although olive cultivars showing tolerance or resistance to Xf have been identified, the biological mechanisms underlying these traits remain poorly understood. In this context, the Italian Ministry of Agriculture, Food Sovereignty and Forests (MASAF) funded, among other initiatives, the NOVIXGEN project, aimed at developing a coordinated strategy to combat Xf through a multidisciplinary approach. One of the main objectives of the project is the monitoring, selection, and characterization of olive genetic material with potential resistance or tolerance traits to Xf, together with the investigation of host–pathogen interaction mechanisms in infected areas of the Apulia region. In addition, plants, like other organisms, are now regarded as one with their associated microbiota, forming holobionts rather than isolated genomic entities. Accordingly, the study of soil microbiota may shed light on the mechanisms underlying the acquisition of resistance or tolerance traits to Xf in olive trees. This study aimed to characterize the functional activity and taxonomic composition of soil microbial communities associated with tolerant and non-tolerant olive cultivars.

Soil samples were collected from the root zones of tolerant and non-tolerant olive trees belonging to different cultivars (i.e. Leccino, Frantoio, Cellina di Nardò, Ogliarola, Pendolino, Nociara, and Cima di Melfi) across infected areas of the Apulia region. The activity of soil microbiota was assessed by community-level physiological profiling (CLPP) using ECOPLATE (BIOLOG), while the community diversity and composition was assessed using a targeted metagenomic sequencing for the bacteria (V3-V4 of 16S) and fungi (ITS2) communities using MiSeq sequencing (ILLUMINA).

By combining functional and taxonomic aspects of soil microbial communities, we aim to identify microbial features potentially associated with olive tolerance to Xylella fastidiosa, providing a framework for future investigations on plant–microbiome interactions in Xf-infected agroecosystems.