1. Crop diversity management is widely used to increase agricultural productivity and sustainability. Recent studies have demonstrated that maize root exudates can drive interspecific facilitation to enhance N₂ fixation of bean in intercropping systems. However, the mechanisms of N₂ fixation enhancement stimulated by root exudates in the intercropping systems remain unclear.

2. Four experiments were designed to provide a progressively deeper understanding of how root exudates stimulate microbial-mediated N₂ fixation. First, the effects of faba bean/maize intercropping on yields and soil microbial communities were determined in a field experiment. Second, root-derived interspecific facilitation was evaluated using a root partitioning approach. Third, the key microbial taxa in the faba bean rhizosphere were traced using ¹³C-labeled maize root exudates. Fourth, the codriven mechanism of maize root exudates and microorganisms in the faba bean rhizosphere were explored.

3. Faba bean/maize intercropping with maize residue return increased the yields of faba bean (26%), maize (27%), and broccoli (9.1%) compared to that under monocropping. Nodulin-like 4 (NODL4), chalcone-flavanone isomerase (CFI), and early nodulin-like (ENODL2) gene expression in faba bean roots intercropped with maize increased by 1.5-2.3-fold compared to that observed under monoculture. More than half of the N₂ fixation of faba bean increase under intercropping was due to interactions with microorganisms. Nine key bacterial genera in the faba bean rhizosphere were identified by ¹³C-DNA based stable isotope probing analysis. Among them Agromyces, Arthrobacter, Bacillus, Lysobacter, and Paenibacillus directly fix N₂, while Gemmatimonas, Heliobacillus, Natronocella, and Sorangium increase the N₂ fixation capacity of Azotobacter by providing additional carbon sources. These key bacteria triggered by maize root exudates played an important role in the rhizosphere facilitation of intercropping.

4. Synthesis and applications. We demonstrated a novel root-root facilitation of N₂ fixation and increased crop yields codriven by root exudates and rhizosphere bacteria under faba bean/maize intercropping, and nine key bacteria associated with this process were identified by ¹³C-DNA based stable isotope probing. We recommend the adoption and optimization of intercropping systems with residue return to reduce the shortcomings of continuous cropping and to increase the sustainability of crop production.