Plant health and performance are highly dependent on the root microbiome. The impact of agricultural management on the soil microbiome has been studied extensively. However, a comprehensive understanding of how soil types and fertilization regimes affect both soil and root microbiome is still lacking, such as how fertilization regimes affect the root microbiome’s stability, and whether it follows the same patterns as the soil microbiome. In this study, we carried out a long-term experiment to see how different soil types, plant varieties, and fertilizer regimens affected the soil and root bacterial communities. Our results revealed higher stability of microbial networks under combined organic-inorganic fertilization than those relied solely on inorganic or organic fertilization. The root microbiome variation was predominantly caused by total nitrogen, while the soil microbiome variation was primarily caused by pH and soil organic matter. Bacteroidetes and Firmicutes were major drivers when the soil was amended with organic fertilizer, but Actinobacteria was found to be enriched in the soil when the soil was treated with inorganic fertilizer. Our findings demonstrate how the soil and root microbiome respond to diverse fertilizing regimes, and hence contribute to a better understanding of smart fertilizer as a strategy for sustainable agriculture.

Optimizing manure use and reducing chemical fertilizers are crucial for achieving the Sustainable Development Goals. However, optimal manure redistribution for cropland yield, nitrogen emissions, and greenhouse gas benefit remains unclear at large spatial scales. Here, we employed genetic algorithms and meta-analysis to obtain an optimal substitution rate for major crops in China. This could reduce synthetic nitrogen use and reactive nitrogen pollution by 13.3 and 2.0 Tg, cut ammonia and nitrous oxide emissions by 15.6% and 16.2%, and lower nitrogen runoff and leaching by 32.9%. The yield of eight major upland crops could be increased by 2.0-19.5%. The strategy involves relocating about 255 million pig equivalents, with 32.3% moved across provinces, mainly from central to northern and northeastern China. An estimated US$6.1 billion investment in livestock relocation could yield US$25.9 billion in benefits.