Integrated analysis of changes in soil microbiota and metabolites following long-term fertilization in a subtropical maize-wheat agroecosystem

Although the application of inorganic fertilizer is a widespread agronomic practice used to boost soil productivity and crop yields, the effects on soil microbiome and the metabolic mechanisms involved in the high-yield response of crops to long-term fertilization remain poorly described. In this study, combined metagenomic and metabolomic analyses were used to explore the mechanism of crop yield response to the 20-year application of nitrogen-phosphorus-potassium fertilizers in a subtropical agroecosystem in Southwest China. Soil bacterial and fungal communities were monitored using 16S rRNA (bacteria) and internal transcribed spacer 1 (ITS1) full-length gene (fungi) amplicon sequencing technologies, and metabolites were detected using a liquid chromatograph mass spectrometer. The results revealed that, in addition to providing nutrients, long-term fertilization shaped the compositions of bacteria and fungi to increase crop yields. Long-term fertilization significantly increased the relative abundances of plant growth-promoting rhizobacteria and arbuscular mycorrhizal fungi and promoted the secretion of soil metabolites such as carbohydrates, organic acids, and organic nitrogen compounds, which were primarily enriched in amino acid metabolism pathways. The increases in carbon and nitrogen sources and bioactive substances in soil promoted the increases in plant biomass and thereby maintained soil quality and production capacity. The findings highlighted the importance of soil metabolites in maintaining soil productivity as well as crop yields, and suggested that regulating key metabolites could increase crop yields in agroecosystems.