Fig. 1

Composition and diversity of NatComs exposed to wheat roots and the inoculation of Pseudomonas protegens. A Relative abundance per replicate of the top 100 taxa at the bacterial class level in the growing or stable soil NatCom and of P. protegens CHA0 ASV (green bars, left) across sampling times (dpi, days post inoculation). B Differences in the CSS-normalized relative abundance of the three main classes Alphaproteobacteria, Bacilli and Gammaproteobacteria (see Supplementary Fig. 1 for all classes) or C P. protegens CHA0 ASV across samples. Samples taken at different sampling times are merged. For Gammaproteobacteria, P. protegens ASV was removed to avoid an artificial inflation of the class relative abundance. Significance based on Kruskal-Wallis rank-sum test with LSD post hoc analysis and p-value corrected by fdr. Different letters indicate significant differences between groups at p-value < 0.05. D Comparison of Shannon diversity in samples from different community states (growing or stable), environments (bulk soil or wheat rhizosphere (Riz.)) or inoculated with P. protegens CHA0 (represented by green dots) or not inoculated (empty dots). Significance based on Wilcoxon rank-sum test. Not significant (n.s.): p-value > 0.05. E Spearman correlation between the Shannon diversity index and sampling time in growing (green) or stable (yellow) community states. Correlation coefficient (R) and p-value (p) are indicated with the colour according to the growing state. Curves represent the general additive model (GAM) fit (average, line) and the 95% confidence interval (shadow)