Microbiome-Mediated Mechanisms Regulating Adaptability to Iron Deficiency in the Intercropping System of Soybean and Maize

Iron (Fe) deficiency is a pervasive agricultural concern on a global scale. Intercropping plays a pivotal role in activating soil nutrient cycling and crop nutrient uptake and utilization. This study integrates plant physiology, soil physicochemical determination, high-throughput sequencing, and metabolomics techniques to conduct pot experiments using field-collected soils with soybean and maize plants. This study aims to investigate the mechanisms through which microorganisms in a soybean–maize intercropping system regulate Fe deficiency adaptation. The results revealed that intercropping enhances the resilience of soybean and maize in Fe-deficient environments, facilitates nutrient absorption by plants, and enriches soil nutrient content. Moreover, intercropping fostered more intricate microbial interactions in comparison to monocropping. The dominant microorganisms in the rhizosphere of intercropped soybean and maize included genera <i>Microbacterium</i>, <i>Sphingomonas</i>, <i>Shinella,</i> and <i>Rhizobium</i>. <i>Microbacterium</i>, <i>Sphingomonas</i>, <i>Shinella,</i> and <i>Rhizobium</i> have the potential to produce Fe chelators or enhance plant Fe absorption. Additionally, intercropping notably modified the composition of root exudates derived from soybean and maize. The soybean and maize rhizosphere exhibited significant enrichment with oleamide, coumestrol, glycitein, and daidzein. Coumestrol may have an effect of promoting Fe absorption, and it is significantly positively correlated with the genus <i>Nakamurella</i> in the maize rhizosphere and the genus <i>Pirellula</i> in the soybean rhizosphere. Consequently, these findings suggested that the rhizosphere of intercropped soybean and maize significantly enriches specific microbial communities and root exudates, thereby enhancing microecosystem stability and improving plant tolerance to Fe deficiency.