Detailed statistics for all tests are found in Tables 1 and 2. Sample sizes are N=306 for leaves and N=310 for roots. (a) Within-sample diversity declines with age in roots (ANOVA, F2,57=6.08; P=0.0081) but not in leaves (F2,64=1.11; P=0.67). Least-squares mean diversity estimates are plotted to show the effect of age after controlling for other sources of variation. Bars depict 1 s.e.m. (b) PCoA of weighted UniFrac distances between samples reveals that root bacterial community composition shifts over the lifetime of the plant. In roots, communities of experimental plants become more similar to those of endogenous plants, suggesting a role of succession after transplant (see Supplementary Note 2 for a detailed treatment of this hypothesis). Detailed statistics for the top three PCoA axes are found in Table 2. (c) Least-squares mean estimates of Chao1 richness are plotted for each age group in each site, illustrating how the distinct plant-associated bacterial communities in these habitats respond differently to host age. Leaves: F4,63=1.48; P=0.36. Roots: F4,56=7.85; P=8.6e−5. Error bars depict 1 s.e.m. (d) In leaves, the effect of plant age on the abundance of several phyla differs among sites (Likelihood ratio test, P<0.05 after Benjamini–Hochberg correction for multiple comparisons). Estimated mean abundances from NBMs are plotted for each age group at each site. ‘Actino.’=Actinobacteria; ‘Armatim.’=Armatimonadetes; ‘Verruco.’=Verrucomicrobia.