Genetic variation in host plant phenology affects microbial assemblages at longitudinal niches of the seedling root after a short residence time

The root tip of a plant is highly sensitive to environmental cues and exerts sensory, chemical and movement responses and has even been likened to an animal’s brain. Yet, the assemblage of microbes at the root tip, the controls governing their diversity, the nature of their recruitment to that particular niche, and their roles in plant phenotypic function, remain poorly understood. This study investigated longitudinal niche differentiation of the root-associated microbiome in chickpeas ( Cicer arietinum L.) and its interactions with both diverse soil types and host plants with genetic variation in phenology, from the exterior to the interior of the root. Compared with late flowering (LF) genotypes, endophyte microbiomes at the apical zone of the early flowering (EF) host were characterised by greater diversity, higher compositional similarity to the basal zone, and closely inhabiting Rhizobacter and Methylotenera across soils. Additionally, EF genotype secreted a specific composition of metabolites from the apical zone, with more carboxylates (benzoic acid) and amino acids (propionic acid) than the LF plant. Our findings demonstrate that longitudinal differentiation within a seedling root is an essential feature shaping the root microbiome and indicative of genetic variation in phenology of host plants.