Combined application of organic and microbial amendments reshapes soil microbiome diversity and improves soybean growth performance.

Agricultural practices, including organic amendments and microbial inoculants, strongly influence soil microbial communities, which play a crucial role in maintaining soil function and structure. To identify an effective strategy for improving soil microbiome diversity and crop production, we assessed and compared the soil microbial community in fields treated with cattle manure amendment (MA), microbial inoculant (MI), and a mixture of cattle manure and microbial inoculant (MM), while an untreated field served as the control. We then evaluated treatment effects on soybean production. Microbial diversity analyses showed that MM treatment was associated with increased bacterial diversity in bulk soil, whereas a pronounced enhancement of fungal diversity was observed in the rhizosphere. Community composition analyses indicated the elevation of relative abundances of Acidobacteriota and Chloroflexi in bulk soil upon either treatment. Notably, the Proteobacteria, including the rhizobial genus Ensifer, was significantly enriched in the rhizosphere upon MM treatment, while the relative abundance of Ascomycota was increased in both bulk and rhizospheric soil upon MA treatment. To co-relate with these soil microbiome features, the MM treatment was shown to have the most significant effect on the soybean growth promotion, including the notably higher aboveground and underground fresh weight, plant height, accompanied with markedly more root nodules, than either MI or MA treatment. Collectively, our results suggest that the combined application of organic and microbial amendments effectively reshapes the soil microbiome by enhancing microbial diversity and enriching nitrogen-fixing bacteria in the rhizosphere, thereby promoting the nitrogen-fixing potential and productivity of soybean.