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.