Beyond bradyrhizobium: Host genotype and organic vs. conventional farming drive the dominance of non-rhizobial endophytes in soybean nodules

Although Bradyrhizobium species are recognized as the primary nitrogen-fixing symbionts in soybean nodules, the assembly rules and functional roles of diverse nonrhizobial endophytes (NREs) are poorly understood. This study examined the root nodule bacteriome and predicted functional potential across six commercial soybean cultivars (JS 2098, JS9560, NRC37, NRC136, NRC142, and RVS1135) from Central India using 16S rRNA gene amplicon sequencing and PICRUSt2 predictive functional inference. Proteobacteria, particularly Pseudomonas, were predominant across all cultivars, challenging the traditional notion of exclusive dominance of Bradyrhizobium. A conserved core microbiome comprising Acinetobacter, Arthrobacter, Bacillus, Enterobacter, and Streptomyces plays essential roles in this symbiotic environment. Cultivar-specific variation was pronounced: JS2098 supported the highest richness (Chao1 805.97 ± 42.42) but an uneven, Pseudomonas-dominated community, NRC37 the most even assemblage (Shannon 3.16 ± 0.16), and JS9560 and NRC136 the least even (Shannon 1.87 and 2.00), indicating strong genotype-driven host filtering. A comparison of organic versus inorganic management in the cultivar NRC142 revealed that farming methods significantly reshaped the nodule bacteriome; organic management produced a community dominated by the phosphorus-mobilising genera Arthrobacter and Acinetobacter, whereas conventional management supported a more evenly apportioned, stress-tolerant assemblage with higher observed richness and Shannon diversity. Canonical Correspondence Analysis showed no significant effect of the measured soil physicochemical properties on community structure (p = 0.701), pointing instead to host genetics and management history. PICRUSt2 profiling, which infers genomic potential rather than measuring it, indicated a conserved core metabolic repertoire characterized by functional redundancy in essential nutrient cycling, coupled with significant cultivar- and management-specific enrichments in pathways associated with stress response, secondary metabolite synthesis, and plant–microbe signalling. These findings underscore the dynamic nature of nodule microecosystems, suggesting that next-generation biofertilizer strategies must integrate plant genetics, agricultural history and microbial metabolic potential to enhance sustainable crop production.