Hierarchical structural and functional assembly of maize bacteriomes across root anatomical micro-niches

Root-associated microbiomes are commonly described along a radial soil-rhizosphere-endosphere gradient, yet it remains insufficiently resolved whether anatomically adjacent root zones function as discrete structural and functional habitats. Here, we investigated bacterial assembly across bulk soil (S), adjacent rhizosphere compartments (RS1 and RS2), and two developmental root micro-niches, the cap-to-elongation zone (R1) and the root hair-to-mature zone (R2), in two contrasting maize genotypes representing distinct breeding trajectories: a creole landrace (SM) and a modern double-hybrid cultivar (SH). We integrated 16S-rRNA metabarcoding (alpha-, beta-, and gamma-diversity), culture-dependent quantification of heterotrophic and diazotrophic bacteria, enzymatic activity assays (fluorescein diacetate hydrolysis), and community-level physiological profiling (EcoPlate) to test whether root anatomical heterogeneity generates hierarchical ecological filters. Across genotypes, α-diversity declined sharply toward root tissues, with the greatest collapse in richness and intensification of dominance observed in R1. Β-diversity analyses identified that both genotype and compartment are interacting drivers of community differentiation, with genotype modulating the spatial expression of assembly without altering its hierarchical organization. Notably, R1 and R2 consistently formed distinct assemblages, demonstrating axial micro-niche partitioning within the endosphere. Despite strong local filtering, γ-diversity remained high at the system level, driven by substantial compositional turnover among compartments, with the creole landrace (SM) consistently exhibiting greater cumulative richness than the hybrid (SH). Culture-based counts, enzymatic activity, and substrate utilization profiles mirrored these structural gradients, revealing coordinated functional restructuring and increasing specialization toward the root interior. Together, our findings support a two-axis framework in which maize bacteriomes are hierarchically assembled through radial compartment filtering and axial micro-niche differentiation, coupling structural turnover with functional specialization while maintaining system-level diversity through spatial heterogeneity.