Contrasting Seed Protein Phenotypes Are Associated with Nodulation and Rhizosphere Microbiome Assembly in Soybean

Soybean seed protein content varies with genotype, nitrogen acquisition, and environmental conditions. Associations between belowground microbiota and seed protein content remain insufficiently characterized. We compared three high-protein cultivars (KD91, SN148, and KD80) and three low-protein cultivars (KD122, KD96, and BD40) to examine relationships among seed composition, nodulation, and root-associated microbial communities. High-protein cultivars produced more nodules, while nodule bacterial diversity and community composition showed no significant between-group differences and were dominated by Bradyrhizobium. In contrast, rhizosphere bacterial and fungal communities differed between protein groups. Dyadobacter, Pseudoxanthomonas, and Chitinophaga had higher relative abundance in the high-protein rhizosphere. Seed protein content was positively associated with Dyadobacter (R2 = 0.234, p = 0.017) and Pseudoxanthomonas (R2 = 0.432, p < 0.001), but not with Chitinophaga. This study compared distinct cultivars grown in a single batch of peat-based greenhouse substrate; the observed microbial patterns are associated with cultivar group and cannot be attributed to seed protein phenotype alone. Dyadobacter and Pseudoxanthomonas are candidates for future functional validation.