Fig. 4

The establishment of Pseudomonas protegens causes discrete changes in growing or stable NatComs. A Differential abundance analyses comparing samples from the growing or stable community states, in the bulk soil or the wheat rhizosphere, inoculated with P. protegens CHA0 with those uninoculated at the initial or final sampling times (dpi, days post inoculation). The wheat rhizosphere (Rhiz.) was not sampled at the initial sampling time (1 dpi) due to limited biomass. Dots represent ASVs, with sizes according to adjusted (adj.) p-value and coloured according to their phylum assignation. The numbers of differentially abundant ASVs are indicated above (left, more abundant in the inoculated condition; centre and grey, not significantly different between conditions; right, more abundant in the uninoculated condition). ASVs with a |log₂FoldChange| > 2.5 and a adj. p-value < 0.01 were considered significant. B Average relative abundance of the top five Pseudomonas ASVs at the initial (1 dpi) or final (9 dpi) sampling time. ASV1148 (green) corresponds to P. protegens CHA0. C CSS-normalized relative abundances of individual Pseudomonas ASVs across community states, environments, and inoculation patterns. Bars (±standard error) represent the average. Coloured dots represent individual replicates. Significance is 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. The type strain closest to the ASV is indicated below the ASV name (% sequence identity)