Kaempferol drives genotype-specific microbiota Bacillaceae to enhance nitrogen acquisition in rapeseed.

introductionHost genotype is a key driver in shaping plant microbiome in response to dynamic changes in soil nitrogen (N) availability. However, the effects of rapeseed (Brassica napus) genotypes with different N use efficiency characteristics on microbiome assembly, as well as the underlying plant-microbe interaction mechanisms, remain poorly understood.

objectivesThis study aims to: (1) assess microbial assembly differences between N-use efficient and inefficient genotypes; (2) identify specific microbiota associated with plant N acquisition; and (3) reveal the molecular mechanisms driving plant-microbe interactions.

methodsWe conducted comparative microbiome profiling of N-use efficient and inefficient genotypes, followed by functional validation of microbial roles in plant N uptake. Multi-omics approaches, including RNA-seq and metabolomics, were used to uncover the regulatory interactions between the host and rhizosphere microbiota.

resultsThe N-use efficient genotype constructed more diverse root-associated microbes than the inefficient genotype, with Bacillaceae emerging as the most enriched taxon. A representative isolate, Bacillus sp. 41S2 from the N-use efficient genotype, markedly enhanced root biomass and N uptake in the N-use inefficient genotype, as confirmed by

conclusionsOur findings reveal a novel, microbe-dependent N acquisition pathway in N-use efficient rapeseed genotypes, driven by kaempferol-mediated recruitment of Bacillaceae. This work highlights the potential of host genotype and metabolite signaling to shape beneficial microbiota for improved nutrient efficiency and sustainable crop production.