BackgroundSince the dawn of agriculture, human selection on plants has progressively differentiated input-demanding productive crops from their wild progenitors thriving in marginal areas. Barley (Hordeum vulgare), the fourth most cultivated cereal globally, is a prime example of this process. We previously demonstrated that wild and domesticated barley genotypes host distinct microbial communities in their rhizosphere. Here we tested the hypothesis that microbiota diversification is modulated by, and in response to, nitrogen (N) application in soil and we assessed the impact of microbiota composition on plant growth.MethodsWe grew two wild (H. vulgaressp.spontaneum) and a modern domesticated (H. vulgaressp.vulgare) barley genotypes in an agricultural soil amended with and without nitrogen (N) inputs. By using a two-pronged 16S rRNA gene survey and a shotgun metagenomics approach, we determined the impact of N application on the taxonomic composition of the barley microbiota as well as the functional diversification of microbial communities exposed to limiting nitrogen supplies. In parallel, we used metagenomics reads to reconstruct genomes of individual bacterial members of the microbiota. Finally, we implemented a plant-soil feedback experiment to assess the microbiota’s contribution to plant growth.ResultsRhizosphere profiles were distinct from unplanted soil controls and displayed a significant, plant-mediated, N application-dependent taxonomic diversification which is maximised under N-limiting conditions. Strikingly, this diversification mirrors a metabolic specialisation of the barley microbiota, with functions implicated in nitrogen and sulphur metabolism enriched in a wild genotype as opposed to the RNA and cell capsule metabolisms enriched in a modern genotype. We reconstruct 28 high-quality individual bacterial genomes with a bias for Bacteroidetes and Proteobacteria, which are among the taxa differentially recruited between wild and modern genotypes. A plant-soil feedback experiment revealed that modern plants exposed to heat-sterilised soils grew less compared to plants maintained in untreated soils, although this difference was significant only for plants exposed to the wild barley microbiota.ConclusionsOur results point at nitrogen availability as a modulator of the structural and functional configuration of the rhizosphere bacterial communities and suggest a limited, but significant, contribution of the wild barley microbiota to plant growth. This knowledge will contribute to devise strategies to enhance sustainable crop production.