To simulate seed-borne virus transmission, a noninvasive protocol was designed to infect the radicle of germinating seeds, with 100% effectiveness. Preinfection of 24-h-old black bean (Phaseolus vulgaris L.) radicles by Southern bean mosaic virus (SBMV) followed by Rhizobium inoculation 48h later caused a drastic reduction in root nodulation. Results were attributed to active virus replication within the elongating zone of the radicle at least 32h before Rhizobium inoculation, which elicited severe anatomical malformations; an abnormal accumulation of apoplastic reactive oxygen species in the rhizodermis, cortex, inner cortical and endodermic root cells; the formation of atypical root hair tips and the collapse of 94% of the root hairs in the SBMV-preinfected radicles. Adult SBMV-preinfected plants showed exacerbated virus symptoms and 80% growth reduction ascribed to major virus-induced ultrastructural alterations in the nodules. The accumulation of ureides, α-amino acids and total reducing sugars in the leaves and nodules of SBMV-preinfected plants are indicators of the hindering effects of SBMV infection on N2 fixation and ureide catabolism, causing N starvation. The exogenous addition of 1 or 4μM naringenin, genistein or daidzein did not counteract the deleterious effects of SBMV preinfection on nodulation.