Enrichment of root-associated bacterial communities by root metabolite profiles influences oilseed rape tolerance to nitrogen deprivation

• Both genotype and N availability modulate root metabolites and bacterial communities in the rhizosphere. • Oilseed rape genotypes with contrasting low-N-tolerance recruit distinct rhizosphere bacteria. • Leveraging beneficial plant-microbe interactions enhances N-use efficiency of rapeseed. Harnessing beneficial plant-microbe interactions in the rhizosphere presents a promising strategy for plants to combat unfavorable environment. However, the mechanisms by which rapeseed ( Brassica napus L.) genotypes regulate root-associated microbiota through root metabolites under nitrogen (N) deprivation has not been fully explored. To address this issue, we planted rapeseed genotypes with varying tolerance to N deficiency—G364, which is susceptible, and G294 and ZS11, which exhibit tolerance—under both N-starved (N0) and N-sufficient (N1) conditions in pots. As expected, G364 was the most susceptible to N deficiency, experiencing a 30.8 % reduction in dry biomass when subjected to N deprivation. In contrast, G294 exhibited the greatest tolerance to N-deficiency, with only a 14.1 % decline in biomass due to N deficiency, underscoring its superior N utilization efficiency. The rhizosphere bacterial microbiomes of these genotypes exhibited distinct patterns at the rosette stage. Under N deprivation, the bacterial classes that significantly enriched in the rhizosphere of G294 and ZS11 genotypes were Chloroflexia, Bacilli, TK10, Gammaproteobacteria, and Acidimicrobiia. These microbial enrichments were positively correlated with increased biomass and N uptake in rapeseed. Furthermore, the compositional shifts in the rhizosphere bacterial community were associated with greater intensity of metabolites like flavonoids, amines, terpenoids, steroids, hormones and transmitters etc. Taken together, our study underscores the pivotal role of root metabolites in harnessing the beneficial plant–microbe interactions, thereby potentially improving the N use efficiency of rapeseed. This insight is valuable for manipulating the rhizosphere microbiome for breeding crops aimed at developing varieties with enhanced N efficiency.