Bacterial endophytic communities during phytoplasmas infection highlight taxa associated with plant health

Disease affects the plant as a whole and may cause deep changes in the associated microbial communities. To prove that these shifts occur, and to provide insights on their extent and on the taxa whose ecology is affected we studied the structure of bacterial communities associated with grapevine leaves during the Flavescence dorée-associated phytoplasmas (FDp) infection process and in recovered plants, and compared them to those in healthy plants. Our results indicate that disease-driven changes in endophytic bacterial communities occur during summer, as disease symptoms become evident. On the other hand, in spring the endophytic community composition was comparable in all samples analysed. Divergence in community composition between healthy and diseased plants was associated with an increase in alpha diversity. Interestingly, plants that had recovered from disease for several years showed endophytic communities similar to those associated with diseased plants, indicating that the disease-driven shift in bacterial endophytes persisted long after the pathogen had disappeared. Sequences assigned to Burkholderia and Acinetobacter were found to be associated with healthy plants, while those assigned to Methylocystaceae and Oxalobacteraceae were more frequent in diseased plants. One Methylobacterium was found most frequently on recovered plants (26,9%), but was detected also on diseased plants (18.9%). Overall, Burkholderia and Acinetobacter are well represented in the grapevine foliar microbiome and their relative abundance is strongly anticorrelated with the Flavescence dorée condition. For these reasons, we suggest that these taxa may harbour candidate biocontrol agents against FD disease.