Fig. 1. Evolution of bacterial mutualism in the rhizosphere of Arabidopsis thaliana.

Panel a shows the initially antagonistic effect of Pseudomonas protegens CHA0 on A. thaliana after one plant growth cycle in the sterile sand study system (n = 5; aboveground biomass ***P = 0.0001). Panels b–f compare the effects of ancestral and evolved Pseudomonas protegens CHA0 phenotypes on plant performance-related traits in a separate plant growth assays performed on agar plates at the end of the selection experiment (n = 3 for control and n = 5 for each evolved phenotype, see Table S2). Different panels show the shoot biomass in grams (b), root biomass in grams (c), number of lateral roots (d), root length in cm (e), and the amount of plant ‘greenness’ in terms of green-to-white pixel ratio (f) after 14 days of bacterial inoculation (Supplementary Data 2; blue dashed horizontal lines show the non-inoculated control plants). Bacterial phenotype groups are displayed in different colours (black: ancestor; dark grey: ancestral-like; light grey: transient; orange: stress-sensitive, light green: mutualist 1 and dark green: mutualist 2) and were classified and named based on K-means clustering (Fig. S1) using 14 phenotypic traits linked to growth, stress tolerance, production of bioactive compounds and antimicrobial activity (Table S1). All boxplots show median (centre line), interquartile range (25–75%) and whiskers that extend 1.5 times the interquartile range overlaid with a scatter plot showing independent replicates. Statistical testing in all panels was carried out using one-way ANOVA, and asterisks above plots indicate significant differences between control and bacteria-treated plants (*P = 0.05, **P = 0.01, ***P = 0.001; n.s. = non-significant). Data for all panels are provided in the Source Data file.