Discussion
Our results highlight that niche differentiation along the longitudinal axis of a root system played a determinant role in structuring root-associated microbiota under the interactions with the factors of soil type, plant genotype, and rhizocompartment. The root microbiome of young seedlings with only 16 days growth reflects the genetic variation in flowering phenology of host genotypes. We describe a mechanism through which early flowering chickpea genotypes responded by establishing an endophyte community in the root tip with a greater diversity and higher compositional similarity to endophyte microbiome at the root basal zone. The host-niche selectivity of endophytes was associated with root exudation activities. While the recruitment of rhizosphere microbiome across different soils was more conserved at the basal zone than root tip, the microbiome diversity in the basal rhizosphere was related to pore architecture of the rhizosphere soil, rather than plant root exudation.