Populations of genetically identical Sinorhizobium fredii NGR234 cells differ significantly in their expression profiles of autoinducer (AI)-dependent and AI-independent genes. Promoter fusions of the NGR234 AI synthase genes traI and ngrI showed high levels of phenotypic heterogeneity during growth in TY medium on a single cell level. However, adding very high concentrations of N-(3-oxooctanoyl-)-L-homoserine lactone resulted in a more homogeneous expression profile. Similarly, the lack of internally synthesized AIs in the background of the NGR234-ΔtraI or the NGR234-ΔngrI mutant resulted in a highly homogenous expression of the corresponding promoter fusions in the population. Expression studies with reporter fusions of the promoter regions of the quorum quenching genes dlhR, qsdR1 and the pNGR234b encoded type IV pilus gene cluster suggested that other factors than AI molecules may affect NGR234 phenotypic heterogeneity. Further studies with root exudates and developing Arabidopsis thaliana seedlings provide first evidence that plant root exudates have strong impact on the heterogeneity of AI synthase and quorum quenching genes in NGR234. Thereby, plant-released octopine appears to play a key role in modulation of heterogeneous gene expression.