Microbial diversity in avocado trees: exploring compartmental and phenological shifts in response to fungal diseases

Abstract

Plants host microbial communities in distinct compartments, including the phyllosphere (aerial surfaces), rhizosphere (soil surrounding the roots), and endosphere (internal tissues). These microbial communities can play critical roles in plant health and in the response to fungal diseases. In this study, we characterized the microbial biodiversity associated with avocado trees affected by fungal diseases, specifically white root rot caused by Rosellinia necatrix and branch dieback induced by members of the Botryosphaeriaceae family. We also assessed the variation in these communities across the three compartments and two phenological stages (fruit set and fully mature fruit). To this end, we employed a comprehensive metabarcoding approach targeting the 16S rRNA and ITS regions to profile bacterial and fungal communities, respectively. Comparative analyses revealed significant shifts in microbial diversity and community composition across compartments, phenological stages, and tree health status, and identified specific microbial taxa associated with each fungal disease. We also established a bacterial culture collection comprising 300 isolates derived from the three avocado tree compartments. Through in vitro and in vivo antagonism assays, we identified several bacterial strains exhibiting strong antagonistic activity against Botryosphaeria spp. and Rosellinia necatrix, highlighting their potential as biological control agents. Our findings identified disease-specific taxa in each compartment and demonstrated pronounced shifts in microbial community composition across phenological stages. These results underscore the dynamic nature of avocado–microbiota interactions and provide key insights for the development of sustainable agricultural practices.