Terroir is a key driver of seed-associated fungal assemblages

Seeds have evolved in association with diverse microbial assemblages that may influence plant growth and health. However, little is known about the composition of seed-associated microbial assemblages and the ecological processes shaping their structures. In this work, we monitored the relative influence of the host genotypes and terroir on the structure of the seed microbiota through metabarcoding analysis of different microbial assemblages associated to 5 different bean cultivars harvested in two experimental sites. Overall, few bacterial and fungal operational taxonomic units (OTUs) were conserved across all seed samples. The lack of shared OTU between samples is explained by a significant effect of the experimental site on the structure of fungal assemblage. A total of 54 and 46 fungal OTUs were significantly enriched in Luxembourg and Brittany sites, respectively. These OTUs were affiliated to the genera Rhizoctonia and Fusarium in Luxembourg and Cryptococcus in Brittany. On the contrary variance in bacterial assemblage structure was neither explained by host genotype nor experimental site. Altogether these results suggest that seed-associated fungal assemblage is determined by niche-based processes and that the terroir is a key driver of these selective forces. On the other hand neutral processes probably shaped seed-associated bacterial assemblage.