Indigenous Olive Orchard Bacteria as Biocontrol Agents: An Integrated Culture-Dependent and Soil Microbiome Approach

Olive orchard soils are a source of microorganisms capable of inhibiting major olive pathogens. In this study, rhizobacteria were isolated and characterized based on plant growth-promoting traits, and soil 16 rRNA gene sequencing analysis was performed to analyze microbial communities at two key olive phenological stages (flowering and fruit formation). Using a culture-dependent approach, a total of 90 bacterial isolates representing distinct colony morphotypes were recovered from olive soils, with 35 during the flowering stage and 55 during the fruit formation stage, indicating a higher cultivable diversity during the latter period. We identified some bacterial strains with antagonistic activity and observed phenology-related shifts in the soil microbiome. Using differential abundance analysis, we identified bacterial taxa that were significantly enriched or depleted during olive fruit formation. Overall, this study demonstrates that olive-associated bacteria harbor antagonistic potential against olive pathogens. The use of bacteria adapted to olive agroecosystems represents a promising strategy for sustainable disease management.