Genotypic variation in Pinus radiata responses to nitrogen source are related to changes in the root microbiome.
Variation in traits within a plant species contributes to differences in soil physicochemistry and rhizosphere microbial communities. However, how intraspecific variation in plant responses to nitrogen (N) shapes these communities remains unclear. We studied whether plant responses to organic and inorganic N forms vary among genotypes, and if these responses were associated with variation in root-associated communities. We investigated how the root microbiomes of two Pinus radiata D. Don genotypes were altered by two years of N-fertilisation in field conditions. We characterised rhizosphere bacterial and fungal communities, as well as root-associated fungal communities, of trees receiving yearly additions of NH4NO3 or L-arginine, and control trees. We also measured plant traits and rhizosphere soil physicochemical properties. Two main findings emerged: (i) N form and tree genotype affected soil physicochemical properties as well as plant measures, and these responses were associated with variation in microbial communities, and (ii) rhizosphere and root-associated communities differed in their responses to N form and host genotype. Our results suggest that N forms have different influences on N and carbon dynamics at the plant-soil interface by inducing root-mediated responses that are associated with shifts in the root microbiome such that communities more closely associated with roots are more sensitive to genotype-specific responses.