Moderate organic-inorganic fertilization optimizes soybean productivity by reshaping rhizosphere...

Soybean, a key oilseed and fodder crop, is pivotal for national food security in China. And sustainable soybean production requires fertilization strategies that enhance yield while restoring rhizosphere ecological function. Balancing chemical and organic fertilization is crucial for sustainable soybean production, yet the underlying rhizosphere mechanisms driving crop performance remain underexplored. We conducted a nutrient-equalized gradient substitution experiment comparing chemical fertilizer (CF) with 30%, 70%, and 100% organic fertilizer replacement (OF30, OF70, OF100), investigating the effects on soybean growth, rhizosphere soil properties, bacterial and fungal microbiomes, and metabolomes, while maintaining equivalent nutrient inputs. Moderate organic-inorganic fertilization (30/70% organic substitution, designated as OF30 and OF70) significantly enhanced plant height, root length, biomass, nodulation, nitrogenase activity, photosynthetic capacity, and yield compared to full chemical fertilization (CF, 0% organic) and full organic fertilization (OF100%, 100% organic), the application of 30% organic and 70% inorganic fertilization in combination identified as the optimal strategy. These gains suggest that rhizosphere soil exhibited improved pH, organic carbon, and nutrient availability (K and P), alongside balanced nitrogen. Bacterial communities showed conserved core structure but increased α-diversity and turnover toward metabolically versatile genera (e.g., Flavobacterium, Geobacter, Luteibacter) under organic-inorganic fertilization. Fungal assemblages preserved a stable core while enriching saprotrophic and beneficial guilds (e.g., Serendipita, Chaetomium, Arthrobotrys). Metabolomics revealed conserved profiles with targeted enrichment of carbon-related classes (e.g., glycerophospholipids, flavonoids like delphinidin), supporting microbial activity and plant-microbe signaling. Integrated analyzes indicated that moderate organic substitution (30/70%) reshapes the rhizosphere toward balanced nutrient cycling, enhanced microbiome diversity, and functional metabolite pools, fostering symbiotic interactions and improving nutrient availability. These findings highlight moderate organic-inorganic blending as an optimal strategy for improving soybean productivity and soil health, with implications for sustainable cropping systems.