Maize age and genotype shape the rhizosphere microbiome in the field

Plants shift a large proportion of fixed C into soil, providing substrates that shape the rhizosphere microbiome (RM), which in turn influences plant health. Plant-genotype responsive beneficial microbes are potential targets for plant breeders but remain to be identified for agronomically important crops. Here, we conducted a field study of 27 maize lines to dissect the influences of plant genotype, age, field and weather on RM diversity. Analysis of 4866 samples demonstrated that plant age was the main driver of RM membership and structure, while field influenced mostly membership, and genotype interacted with both. We identified ~150 plant-genotype responsive taxa, many with putative beneficial functions. Additionally, pangenome analysis of RM-dominant Pseudomonas revealed differential distribution of metabolic pathways according to maize genotype. These results can inform breeding aimed at enhancing select rhizosphere taxa or functions.