Diversity in endophyte populations reveals functional and taxonomic diversity between wild and domesticated grapevines

Endophytes hold a great potential for the implementation of a more sustainable, bio-based agriculture. Here we investigated the differences between endophytic bacterial populations isolated from wild and domesticated grapevine to improve our understanding of how the agriculture and the agro-environment affect endophytic communities. Bacterial isolates from a total of 88 wild and domesticated grapevines that shared the same climate for at least four years were identified and a representative set of 155 strains was characterised for 30 features, encompassing quorum sensing-related (QS), enzyme production (ENZ), antibiotic resistance (AR), plant growth promotion (PGP) and biocontrol (BiCo) traits. We found microbial diversity to be higher in wild grapevine plants (twenty-five genera), as compared to domesticated grapevines (six genera). Molecular fingerprinting by automated ribosomal intergenic spacer analysis (ARISA) also indicated a greater diversity in wild grapevines. Multivariate analysis of phenotypic traits indicated that strains isolated from wild and cultivated plants often formed distinct clusters, even when belonging to the same genus. Interestingly, endophytes from domesticated grapevines were more likely to perform well in PGP and BiCo tests when compared to endophytes from wild grapevines, suggesting that the decrease in taxonomic diversity in domesticated grapevine microbiota did not correspond to a loss of agriculturally relevant traits.