Iron retention coupled with trade-offs in localized symbiotic effects confers tolerance to combined iron deficiency and drought in soybean

Iron (Fe) and water availability are closely linked, yet the mechanisms of tolerance to these combined stresses in soybean remain poorly understood. This study elucidates host–microbe interactions in Clark (tolerant) and Arisoy (sensitive) genotypes exposed to Fe deficiency and drought. Clark exhibited resilience to stress through sustained osmotic regulation and nutrient uptake, in contrast to Arisoy. Particularly, Fe retention in Clark, along with up-regulation of ferritin-like proteins, may reduce oxidative stress by limiting Fenton reactions. In RNA-seq analysis, we observed the up-regulation of symbiotic genes, such as Chalcone-flavonone isomerase 1 and SWEET10, accompanied by increased rhizosphere siderophore and root flavonoid in Clark. Interestingly, the combined stress led to distinct root and nodule microbiome dynamics, with Clark recruiting Variovorax and Paecilomyces, whereas Arisoy exhibited the opposite pattern. Clark also maintained nodule Bradyrhizobium and tissue nitrogen status, supported by ammonium retention and induction of Ammonium transporter 1 in roots. Furthermore, in vitro compatibility between Variovorax paradoxus and Paecilomyces lilacinus suggests a synergistic interaction, with their localized signals benefiting Clark. Remarkably, enriched microbiomes enhanced growth and increased rhizosphere siderophore levels in sensitive genotypes under stress. This study reveals key mechanisms of dual stress tolerance in soybean, offering targets for breeding and microbiome-based biofertilizers.