Dedomestication of modern soybean is potentially revealed by variation in the root-associated bacterial community along a domestication gradient

Aims The plant root-associated microbial community, which is influenced by plant species and environmental factors, supports host growth by providing nutrients and facilitating stress resistance. However, the effect of modern breeding technology on this community has not been thoroughly investigated. Methods In this study, the root-associated (rhizosphere and root endosphere) bacterial communities of four types (wild, semiwild, landrace, and modern) of soybean varieties distributed along an evolutionary transect were investigated using 16S rRNA gene amplicon sequencing. Results The alpha-diversity indices, composition and ecological assembly process based on null models of the root-associated bacterial community, especially the rhizosphere community, of modern soybean were more similar to those of the wild variety than to those of semiwild and landrace varieties. Patterns of co-occurrence showed that the root-associated bacterial communities of wild and modern soybeans were more complex than those of the other soybeans. The core bacterial taxa among the four types of soybean varieties mainly belonged to order Rhizobiales, which was most abundant in modern soybean. Source tracking analysis further revealed that the root-associated bacterial communities of the semiwild, landrace and modern varieties were mainly derived from those of the wild, semiwild and landrace varieties, respectively. Conclusions The similarity of root-associated bacterial community between modern and wild soybeans during domestication may reveal the dedomestication of modern soybean. The findings of this study expand our understanding of crop root-associated microbial selection under domestication and are highly significant for the advancement of modern breeding and understanding of biological evolution involving plant-microbe symbiosis.