(a) (b) Col-NI Col-I nrt2.5x2.6 NI Col-NICol-I nrt2.5x2.6 NI nrt2.5x2.6 I Fig. S1 DAB staining of Arabidopsis thaliana Col-0 wild-type or nrt2.5xnrt2.6 mutant plantlets inoculated (I) or not (NI) with Phyllobacterium brassicacearum STM196. The seeds were germinated and grown on a mineral medium containing 2 mM NO 3 - as the unique N source in vertically oriented Petri dishes for 7 days. Five to 6 homogeneous plantlets were subsequently transferred into new media inoculated or not with cfu.ml -1 STM196. Eight days after the transfer, 40 ml of 5 mM DAB (3,3’-Diaminobenzidine, D8001 SIGMA) solution were poured on the Petri dishes. The plantlets were incubated in this DAB solution for 12 h. (a) Images of Petri dishes taken with a flatbed scanner (EPSON Perfection V200 photo). The scale bars represent 5 mm. (b) Close-up image of primary root tip taken with a digital camera (DFC420c, Leica) mounted to a macroscope (Z16APO, Leica). The scale bars represent 280 µm.

(a) Col-0 nrt2.1 nrt2.1xnrt2.5 nrt2.1xnrt2.6 a b e cd c cc de (b) Col-0 nrt2.1 nrt2.1xnrt2.5 nrt2.1xnrt2.6 b b a d ab c c (c) Col-0 nrt2.1 nrt2.1xnrt2.5 nrt2.1xnrt2.6 b a d d cd c Fig. S2 The effect of the nrt2.1 mutation on root architecture under control and treated conditions is epistatic to the nrt2.5 and nrt2.6 mutations. The Arabidopsis thaliana Col-0 wild type or mutant plantlets were grown and transferred as described in Figure 1. Eight days after transfer, the primary root length (a), density of lateral root (b), and total lateral root length (c) from non-inoculated (grey) and STM196-inoculated (black) plants were measured. Error bars indicate SE (n = 20-25). Different letters represent significant difference of the means using Fisher’s LSD test at P =

Fig. S3 The nr2 mutation did not significantly affect the accumulation of NRT2 family transcripts. The Arabidopsis thaliana Col-0 wild type or mutant plantlets were grown and transferred as described in Figure 1. Eight days after transfer, the shoots (a) and roots (c) of uninoculated plants or the shoots (b) and roots (d) of STM196-inoculated plants were harvested separately, and total RNA was extracted. The grey bars represent relative transcript levels of NRT2.1, NRT2.2, NRT2.3, NRT2.4, NRT2.5, NRT2.6 and NRT2.7 in the shoots and roots of Col-0 plantlets, while the black bars represent those of the G5 mutant. The transcript levels were normalised against Actin2 (AT3G18780) and Ubiquitine genes (AT4G05320). Each bar represents the mean of at least three biological repetitions. Error bars indicate SE.