Second Genome: Rhizosphere Microbiome as a Key External Driver of Nitrogen Use Efficiency in Maize

Abstract

Improving nitrogen use efficiency (NUE) in maize is critical for reducing fertilizer inputs and mitigating environmental impacts. The rhizosphere microbiome—the plant’s “second genome”—plays a key role in nitrogen acquisition, assimilation, and signaling. This review synthesizes recent advances from multi-omics studies, functional validation, and field experiments, highlighting how maize roots recruit and coordinate microbial taxa, including diazotrophs, nitrifiers, organic nitrogen mineralizers, and growth-promoting bacteria, to enhance NUE under variable nitrogen availability. We integrate mechanistic insights into transporter-mediated nitrogen uptake, microbial regulation of root development and exudation, and host genetic determinants, such as ZmC2, ZmSBT3, and ZmNLP8, that influence microbiome assembly. Evidence from synthetic communities, isotope tracing, and host–microbiome association studies demonstrates that microbial contributions to plant nitrogen can be substantial and genetically modulated. Finally, we discuss microbiome-based interventions, including functional strain discovery, microbial fertilizers, biostimulants, and microbiome-assisted breeding, assessing their potential and limitations. We conclude by highlighting key challenges and proposing an integrative framework to guide microbiome-informed strategies for sustainable improvement of maize NUE.