Genomic comparative analysis of Bradyrhizobium elkanii strains: Exploring the diversity of nod factors

Bradyrhizobium elkanii is an important rhizobial species that nodulates a wide range of legumes, including soybean, and is widely used as an inoculant to enhance biological nitrogen fixation. This symbiosis is mediated by chemical signaling between plant flavonoids and bacterial nodulation factors (NFs; lipo-chitooligosaccharides, LCOs), whose structural diversity determines host specificity. In addition, genes related to plant growth–promoting (PGP) traits contribute to efficient root colonization and symbiotic performance. Here, we performed a comparative genomic analysis of five B. elkanii strains from distinct geographic origins within the SEMIA collection (SEMIA 5011, SEMIA 5026, SEMIA 5027, SEMIA 5019, and SEMIA 587), including two elite inoculant strains, focusing on nodulation gene repertoires and NF profiles. A broader comparison including 56 genomes revealed a open pangenome, characterized by a large accessory fraction enriched in mobilome-related functions, while the core genome was dominated by housekeeping genes. PGP gene profiles were largely conserved among strains, encompassing functions associated with phytohormone production, stress mitigation, and plant interaction. Nodulation gene repertoires comprised 25–33 genes organized into four to six clusters. A conserved main nod cluster was identified in all five SEMIA strains and was predicted to be plasmid-associated. NF profiling revealed 37 variants composed of three to five N-acetylglucosamine residues and four major types of chemical modifications. Overall, this study provides new insights into the genomic diversity, nodulation gene architecture, and NF variability of B. elkanii , contributing to a better understanding of the molecular basis underlying symbiotic interactions.