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 interlinked, with deficiencies in both adversely affecting soybean growth. However, the strategies employed by soybean to tolerate such conditions remain poorly understood. This study elucidates the interactions of physiological adjustments, host factors, and microbial associations in soybean using multi-omics approaches in Clark (tolerant) and Arisoy (sensitive) genotypes exposed to Fe deficiency and drought. Clark demonstrated stress resilience by maintaining osmotic balance, nutritional status, and photosynthetic efficiency, whereas these were severely affected in Arisoy. Furthermore, Fe retention in Clark, accompanied by the upregulation of ferritin-like proteins, may mitigate oxidative stress by reducing Fenton reactions. Interestingly, the elevated jasmonic acid and salicylic acid in the roots of Clark, compared to the lower levels in Arisoy, may contribute to differential physiological adjustments for stress adaptations. RNA-seq analysis revealed 818 and 500 upregulated, along with 931 and 361 downregulated genes, in roots of Clark and Arisoy, respectively, under stress. We observed the upregulation of symbiotic genes, such as Chalcone-flavonone isomerase 1 and SWEET10 , accompanied by increased rhizosphere siderophore and root flavonoid in Clark. This indicates a significant microbial role in driving differential stress tolerance. Amplicon sequencing revealed distinct root and nodule microbiome dynamics, with Clark recruiting beneficial microbes such as Variovorax and Paecilomyces , known for promoting plant growth, whereas Arisoy displayed an opposite pattern. In addition, Clark maintained Bradyrhizobium and tissue nitrogen status, supported by ammonium retention and induction of Ammonium transporter 1 in the roots. Furthermore, in vitro compatibility between V. paradoxus and P . lilacinus suggests a synergistic interaction, with their localized signals benefiting Clark. Remarkably, enriched microbiomes significantly improved growth parameters, accompanied by elevated rhizosphere siderophore in sensitive genotypes under stress. This study is the first to uncover mechanisms of dual stress tolerance in soybean that may advance breeding and biofertilizer strategies for climate resilience.