Background: Root-microbiome interactions are of central importance for plant performance and yield. A distinctive feature of legumes in this context is that they engage in symbiosis with rhizobia, which are abundant in soils and include both symbiotic and non-symbiotic bacterial strains. If and how the capacity of rhizobia to form symbiosis modulates root-associated microbiomes are not well understood. Results: We address this question by inoculating soybean (Glycine max) plants with wild type

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... WT) or a noeI mutant of Bradyrhizobium diazoefficiens. The noeI mutant produces a defective Nod factor and is thus compromised in its ability to establish functional symbiosis. Compared to soybean plants inoculated with WT rhizobia, plants inoculated with the noeI mutant showed a significant decrease in nodulation and root-flavonoid exudation, and exhibited strong changes in microbiome assembly in the rhizosphere and the rhizoplane. NoeI mutant-inoculated roots exhibited reduced diversity, co-occurrence interactions and a substantial depletion of beneficial microbes on the roots. The effects of the noeI mutation were absent in soils without plants, demonstrating that they are plant dependent. Complementation experiments showed that flavonoid supplementation is sufficient to restore recruitment of beneficial microbes. Conclusion: The results illustrate that the capacity of a rhizobium to form microbial symbiosis dramatically alters root-associated microbiomes, most likely by changing root exudation patterns. The results of this study have important implications for our understanding of the evolution of plant-microbiome interactions in the context of plant-bacterial symbioses.