Fig. 4

Temporal variation in the root-associated bacterial community of apple trees. A Changes in alpha diversity based on the Shannon index in the two root compartments over time. Error bars indicate the standard error. B Constrained analysis of principle coordinates (based on DEICODE distance matrices and constrained by the variables tree and timepoint) to assess the relevance of time on variation in bacterial community composition in the L-compartment (left) and T-compartment (right). A colour gradient differentiates the twelve sampling timepoints. The stars are the calculated centroids of the samples from each timepoint and are connected with a red line along the timeline. C Statistical evaluation of differences in bacterial alpha and beta diversity in the L- and T-compartment. Effect sizes in beta diversity were assessed by PERMANOVA based on DEICODE distance matrices, while differences in Shannon diversity were analysed based on linear mixed models