Extended Data Fig. 2: Microbial alpha diversity and enrichment signatures in plant roots.

a, Microbial alpha diversity measured across all 17 sites in soil, rhizosphere (RS), rhizoplane (RP), and root samples based on the Shannon index. All samples from a given site were taken into account and the datasets were rarefied to 1,000 reads. Individual data points within each box correspond to samples from the 17 natural sites (Kruskal-Wallis with Dunn’s post hoc test: P < 0.05). b, same as a, but the alpha diversity metric observed OTUs is shown instead of the Shannon index. c, Comparison of taxa RA between soil (dark red) and root (dark green) samples for bacteria (left), fungi (middle), and oomycetes (right). RA measured in soil and root samples across the 17 A. thaliana populations were aggregated at the class (bacteria and fungi) and order (oomycetes) levels. Significant differences are marked with an asterisk (Wilcoxon rank sum test, FDR < 0.05). d, Comparison of taxa RA between Swedish soils (SW1-4, blue) and the other European soils (grey) for bacteria (left), fungi (middle), and oomycetes (right). RA is aggregated at the class (bacteria and fungi) and order (oomycetes) levels and significant differences are marked with an asterisk (Wilcoxon rank sum test: FDR < 0.05).