Plant secondary metabolite profiling evidences strain-dependent effect in the Azospirillum-Oryza sativa association

► Azospirillum preferentially increases the growth of its cultivar of origin. ► Azospirillum affects rice secondary metabolism in a strain-dependent way. ► Unlike strain 4B, the endophytic strain B510 triggers systemic responses in rice. ► Flavonoids and hydroxycinnamic derivatives are mostly affected by Azospirillum.