Belowground microbial communities respond to water deficit and are shaped by decades of maize hybrid breeding

Summary Root‐associated microbial communities are important for maintaining agricultural productivity. However, belowground microbial community response to drought in temperate maize agroecosystems, as well as how these responses to water‐stress are shaped by host genotype are poorly understood. Ten maize hybrids (six newer and four older) were grown in a replicated field trial. The endosphere, rhizosphere and soil bacterial and archaeal communities were sampled and analyzed using 16S rRNA gene amplicon sequencing. Sampling was done at two developmental stages in a water‐limited environment with and without supplemental irrigation. Significant shifts in microbial community composition (β‐diversity) were measured between two sampling times during the season, in well‐watered and water‐stressed conditions and in newer and older generation maize hybrids. The microbial community diversity within samples (α‐diversity) was not affected by drought stress or host factors. The phyla Actinobacteria and Firmicutes were more abundant in the rhizosphere of newer hybrids under water stress. These results highlight the importance of temporal variation, environmental stress and plant genetics as influenced by breeding history in shaping the composition of root associated microbial communities. These insights may provide new approaches to the improvement of crop stress tolerance through optimizing microbial communities.