Root metabolite profiles support a chemical-trophic filtering hypothesis for genotype- and stage-specific rhizosphere assembly in chicory

The rhizosphere is a dynamic interface where plant- and soil-derived factors jointly influence microbial community assembly. In chicory ( Cichorium intybus L.), the respective roles of genotype, developmental stage, and root metabolites in structuring rhizosphere communities remain insufficiently understood. This study aimed to characterize patterns of microbial assembly and to assess their associations with root metabolite profiles. Rhizosphere and bulk soil from three chicory genotypes were sampled at two developmental stages and analyzed using bacterial and fungal metabarcoding. Diversity metrics, differential abundance analyses, and literature-based functional annotation were integrated with root metabolite profiling to explore associations between microbial taxa and metabolite profiles. Rhizosphere microbial communities associated with chicory differed from bulk soil and were structured by plant genotype and developmental stage. Lower α-diversity at early stages may reflect the selective enrichment of specific taxa, suggesting non-random assembly. Community variation was associated with root metabolite profiles, including primary metabolites and sesquiterpene lactones (STLs). Across development, the microbiome shifted from taxa linked to nutrient transformation and microbial interactions including Nitratireductor , Sphingomonas , and Serratia , toward communities dominated by saprotrophic and organic matter-degrading taxa such as Streptomyces , Pseudarthrobacter , and Lecanicillium . Genotype-dependent differences further suggested that plant genetic background contributed to rhizosphere assembly patterns. However, these relationships are correlative, and the underlying mechanisms require validation through targeted experimental approaches. The observed correlations led us to propose a hypothesis of temporally structured chemical-trophic filtering, meaning that plant metabolites and soil nutrient conditions jointly contribute to shaping microbial communities in a genotype-dependent manner.