Genistein Exudation Drives Spatial Root Allocation and Heterogeneous Microbial Communities to Enhance Phosphorus Acquisition in Soybean‐Maize Intercropping

Soybean-maize intercropping improves phosphate (Pi) acquisition in phosphorus (P) deficient soils through flavonoid-mediated plant-microbe interactions. Yet, the molecular mechanisms driving spatially heterogeneous root-microbe interactions mediated by secreted flavonoids remain unexplored. Using GmHAD1-2 suppression line (Ri) and wild-type (WT), we demonstrated that root-secreted flavonoids, particularly genistein, drive spatial differentiation of root allocation and rhizosphere microbial communities in intercropped soybean with maize, specifically under low-P conditions. Compared to WT, Ri reduced genistein secretion and restricted root allocation to the root non-interaction zone, thereby diminishing the intercropping advantage by less shoot biomass and P uptake. In all cropping systems, WT in intercropping recruited Bacillus in root non-interaction zones, while Pseudomonas in root interaction zones. Furthermore, inoculation experiments demonstrated their synergistic roles. Bacillus stimulated root elongation and enhanced transcription of auxin-responsive genes (i.e., GmPIN2b and GmYUC2a), whereas Pseudomonas elevated Pi availability in rhizosphere soils and upregulated Pi transporters (i.e., GmPHF1 and GmPT4). Taken together, spatial root allocation and heterogeneous microbial communities across root zones play a critical role in determining intercropping advantages, which is regulated by genistein exudation in soybean roots. Our study provides novel insights into root exudate-driven microbial zonation as a strategic adaptation to nutrient stress, with implications for optimising sustainable intercropping systems.