Fig. 1. Siderophore production by rhizosphere bacteria and their growth effects on the plant pathogenic R. solanacearum bacterium.
a, Relative siderophore production of the 2,150 rhizosphere isolates (measured in culture supernatants using the CAS assay) under iron-limited (top) and iron-rich (bottom) conditions. The black dashed vertical lines show the average CAS background values measured in the supernatants of two defined siderophore-deficient mutants (non-producers). We used this cut-off line to distinguish background noise from siderophore production. Measuring CAS background is important because this assay also measures the activity of other organic iron-binding compounds in the supernatant. Furthermore, the cut-off can vary slightly between species and the media from which the supernatants were collected (see also Extended Data Fig. 2). The green vertical lines represent siderophore production of our model pathogen R. solanacearum strain QL-Rs1115 (CAS value = 0.462 in iron-limited medium). b, Siderophore production (measured as CAS activity) across all isolates significantly correlated with rhizosphere bacterial growth (determined as the optical density (OD) at 600 nm, OD600) under iron-limited conditions (top), indicating that siderophores are important for growth. This effect was much weaker under iron-rich conditions (bottom). The black dashed vertical lines show the background CAS assay values of defined siderophore non-producers, the yellow and purple lines and the shaded area depict the best-fit trendlines and the 95% confidence interval of the linear regression, respectively. Regression model for iron-limited condition (top): adjusted R 2 = 0.388, F 1,1248 = 1,362 and two-sided P < 2.2 × 10-16; iron-rich condition (bottom): adjusted R 2 = 0.039, F 1,1248 = 87.7 and two-sided P < 2.2 × 10-16 based on a Student’s t-test; n = 2,150 biologically independent rhizobacterial isolates for both. c, The growth effects were measured in supernatants collected under iron-limited (high siderophore concentration + other secreted metabolites), iron-rich (low siderophore concentration + other secreted metabolites) and iron-limited conditions replenished with iron (siderophore effect removed, while the effect of other metabolites is retained). The net effect caused by siderophores alone (right column) was obtained by subtracting the growth effect of the iron-replenished supernatant from the growth effect of the iron-limited supernatant. The values indicate the percentage fold-change in growth. The box plots encompass the 25–75th percentiles, the whiskers extend to the minimum and maximum points, and the midline indicates the median (n = 2,150 biologically independent rhizobacterial isolates). P < 2.2 × 10-16 (left) and P = 0.882 (right) based on an analysis of variance followed by a paired two-sided Student’s t-test. ***P < 0.001; NS, not significant.