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

The low proportion of extensively applied nitrogen (N) fertilizers recovered as grain by crops contributes to significant economic and environmental impacts worldwide. Therefore, reducing N inputs in agriculture is needed. The optimization of resource-efficient root phenotypes and beneficial microbiomes already identified in maize (Zea mays L.) is a promising approach to improve plant N uptake. However, little is known about the interplay between root phenotypes and microbiomes and how this affects plant performance. In this study, 16 maize inbred lines (IBM, B73 x Mo17) grown under N deficiency in the field were characterized for yield, root architecture and anatomy, and rhizosphere prokaryotic and fungal community structures. N deficiency significantly affected plant performance and rhizosphere microbiomes, but no genotype effect was observed. Root phenotype-microbe correlations were more abundant under control conditions. A higher number of correlations involving prokaryotes (n=20) and fungi (n=10) were observed under N deficiency for low N stress-tolerant genotypes compared to the high-tolerant ones, with living root cortex area, angle and number of metaxylem vessels being the most important phenotypes. This study provides new insights about the root phenotype-microbiome interactions. Future studies need to evaluate the mechanisms and the potential behind these interactions by using manipulation experiment and genetically distant crop lines.