Influence of phytopathogenic micro-organisms on the seed microbiota. metaSEED3

n the present work, we assessed the effect of the plant pathogenic fungus Alternaria brassicicola (Ab) and the plant pathogenic bacteria Xanthomonas campestris pv. campestris (Xcc) on the diversity of microbial assemblages associated to radish seeds. Seed samples were either harvested from plants inoculated with Ab and Xcc or from uninoculated plants. The microbial diversity associated to these different seed samples was assessed through sequencing of two bacterial markers (16S rRNA gene and gyrB) and one fungal marker (ITS1). Sequences analyses revealed that the fungal richness significantly decreased in seed samples inoculated with Ab. In contrast, the bacterial richness remained constant in all treatments. Moreover, β-diversity analyses highlighted that while the plant pathogenic fungus Ab had a significant impact on the fungal community structure, no effect was observed on the bacterial community. In addition, Xcc inoculation did not impact the structure of seed microbiota. Finally, different interactions were detected between fungal aOTUs closely related to the genus Alternaria. Some of these specific aOTUs could potentially be involved in pathogen exclusion and may contribute to plant health.