The results shown here represent only the constitutive or environment-independent component of genetic variation, that is, genotype differences averaged across all sites. Sample sizes are N=306 for leaves and N=310 for roots. (a) Least-squares mean estimates of within-sample diversity are plotted for each plant genotype, after controlling for other sources of variation using linear mixed effects models. Leaves: F4,265=4.68, P=0.0023; Roots: F4,261=0.344, P=1. Bars depict 1 s.e.m. (b) Each point is an estimated differential abundance of one OTU between a pair of plant genotypes, plotted as a fold change (note log scale on vertical axis). Leaf OTUs are shown in green, root OTUs in grey. Differential abundance estimates and statistical significance were both generated using variance-stabilized NBMs that also controlled for site, year of observation, plant age, genotype-by-site interaction, age-by-site interaction and year-by-site interaction. Only statistically significant contrasts are shown (Wald test, P<0.05 after Benjamini–Hochberg correction for multiple comparisons). (c) Bacterial community composition separates by host plant genotype in weighted UniFrac ordination for leaves, but not roots. Least-squares mean PCoA coordinates are plotted to highlight the influence of host genotype after controlling for other sources of variation using LMMs. Detailed statistics for each PCoA axis are found in Table 2. Bars depict one standard error of the mean.