Shovelomics meets microbiomics: root phenotype-microbiome associations and links with maize yield under nitrogen limitation

Improving crop nitrogen (N) uptake is essential for a more sustainable agriculture. Deploying resource-efficient root phenotypes, beneficial soil microbiomes and their interplay is a promising approach. To test the hypothesis that adaptive root phenotypes under N limitation associate to specific microbial taxa, we characterized 11 architectural and 13 anatomical root phenotypes, and associated rhizosphere prokaryotic and fungal communities across 16 field-grown maize ( Zea mays L.) inbred lines under optimal and low N availability. While maize genotypes were not significant to the rhizosphere microbial diversity, the number of crown roots significantly affected fungal β-diversity under N limitation. Moreover, the relative abundance of 98 rhizosphere microbial taxa significantly correlated with individual root architectural or anatomical phenotypes in a N- and plant yield-specific way. Interestingly, a greater number of correlations was found under optimal than under low N availability. Our results suggest the importance of investigating root phenotypes as predictors of rhizosphere microbial communities in maize inbred lines. Moreover, maize root architecture and anatomy may associate with microbes more frequently under optimal than under suboptimal N conditions. The relative contribution of root phenotypes and specific microbial taxa to plant performance under N limitation deserves more attention in future research. • Nitrogen limitation but not maize genotype influenced rhizosphere microbiomes. • Number of crown roots affected fungal β-diversity under nitrogen limitation. • Individual rhizosphere microbial taxa correlated with root architecture and anatomy. • These correlations were more numerous under optimal nitrogen conditions. • Root phenotypes as predictors of rhizosphere microbiomes require further attention.