Diversity in Endophyte Populations Reveals Functional and Taxonomic Diversity between Wild and Domesticated Grapevines

Abstract

Endophytes hold great potential for implementing a more sustainable, bio-based agriculture. Here we investigated the differences among populations of endophytic bacteria isolated from wild and domesticated grapevines to improve our understanding of how agriculture and agro-environment affect endophytic communities. Bacterial isolates from 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 characterized for 30 features, including quorum sensing-related, enzyme production, antibiotic resistance, plant growth promotion (PGP), and biocontrol (BiCo) traits. Microbial diversity was greater in wild grapevines (25 genera) than in domesticated grapevines (six genera). Molecular fingerprinting by automated ribosomal intergenic spacer analysis 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 they belonged to the same genus. Interestingly, endophytes from domesticated grapevines were more likely to perform well in PGP and BiCo tests than endophytes from wild grapevines, suggesting that the decreased taxonomic diversity in domesticated grapevine microbiota did not correspond to a loss of agriculturally relevant traits.