Beneficial microbes (rhizobium and AMF), offer a sustainable solution for improving nutrient uptake in crops. Root nodules (rhizobium) are external organs formed through the symbiotic relationship between legume plants and the bacterial group rhizobium. Once formed, these nodules convert atmospheric nitrogen into a usable form for the plant, essentially replacing the need for nitrogen fertilizer application. However, the complexity of development, N-fixation, and nutrient uptake at the ‘sub-cellular level’ is elusive and not investigated in soybean or many other legumes. This project aims to understand these critical processes and provide solutions to improve nutrient uptake and N/P use efficiency in soybeans. We integrated X-ray fluorescence, wet chemistry, single-cell transcriptomics, and gene-editing technologies to provide new knowledge and germplasm to the U.S. soy industry. In the first year of this project we (1) developed and published a method to isolate nuclei from soybean nodules and roots and, perform snRNAseq analysis; (2) screened diverse germplasm for tripartite interaction between roots, rhizobium, and AMF; (3) Identified novel QTLs for mineral nutrient uptake; (4) identified novel cell types involved in Si uptake and (5) identified signaling metabolites that are differentially expressed under rhizobium and AMF inoculation through untargeted metabolomics study.