Conclusions
Overall, this study improved the resolution of root-associated niches harbouring microorganisms by identifying the importance of different segments along the longitudinal axis within one root system. Modulating the endophyte communities at the root tip by root exudation was associated with the genetic variation in phenology of the host plant. Across different soil types, the rhizosphere soil architecture potentially explained the diversity of microbial consortia at the basal root. Our findings demonstrate that longitudinal niche differentiation within a root architecture is an essential feature influencing the rhizobiome development. The plant root metabolism and microbial functions corresponding to plant growth, nutrients cycling, and plant health will be the objective of the future research.