Response of rice yield to organic amendments was regulated by soil chemical properties, microbial functional genes and bacterial community rather than fungal community

Integrated fertilization using mineral fertilizer and organic amendments is common practices for sustainable crop production. However, the impacts of different organic amendments on soil chemical properties, function genes, and microbial community, as well as their contribution to rice yield have not been well illustrated. In this study, soil chemical properties, microbial diversity, community structure and stability, and functional genes were evaluated after 10 years of fertilization. Compared with the mineral fertilizer regime, the integrated addition of mineral fertilizer and organic amendments improved soil fertility and increased the grain yield by 0.32 %–11.45 %, in terms of five-year average yield. Bacterial diversity and microbial community stability were significantly improved by organic amendments (p < 0.05). Additionally, organic amendments significantly reshaped the microbial community and increased the relative abundance of beneficial bacteria and fungi, as well as suppressed the growth of plant pathogenic fungi (p < 0.05). Besides, multiple functional genes were upregulated by organic amendments, and had significant relationships with grain yield. Soil chemical properties explained most of the variation in grain yield. PLS-PM result further revealed that functional genes and bacterial community (diversity, composition, and stability), rather than fungal community, which were positively affected by fertilization and soil chemical properties, had a strong influence on grain yield. Overall, organic amendments strongly improved soil chemical properties and function and regulated bacterial community, thus enhancing rice yield.