Keystone phylotypes determine soil functions and nutrient cycling processes in a 33-year field fertilization experiment

Abstract Background: Soil microbiome plays a crucial role in terrestrial ecosystem functions. However, its response to long-term fertilization and contribution to soil functions in agricultural ecosystems are unclear. Here, we investigated soil bacterial and fungal communities along vertical profiles (0 to 100 cm) and explored the importance of soil microbiome in controlling soil functions (soil multifunctionality and functionality of C, N, and P cycling) and nutrient cycling processes (C mineralization, N2O release, and biological N-fixation) in a 33-year field fertilization experiment. Results: We obtained solid evidence that long-term fertilization (with chemical N, cow manure, straw, and green manure) enhanced the soil functions compared with no fertilizer control and that the functionality of N cycling was significantly associated with crop production. Soil functions and nutrient cycling processes were more closely correlated with the relative abundance and diversity of keystone phylotypes within the global network than the entire soil microorganism community. These keystone phylotypes were positively associated with the absolute abundance of functional genes related to C, N, and P cycling, and they also contained many essential functional microbes involved in C mineralization, N2O release, and biological N-fixation. The application of chemical N, green manure, and cow manure showed the highest abundance of amoB, nifH, and GH48 genes and Nitrosomonadaceae, Azospirillaceae, and Sphingomonadaceae within keystone phylotypes, which were significantly and positively correlated with N2O release, biological N-fixation, and C mineralization, respectively. Moreover, our results suggested that organic fertilization improved the effects of network size and keystone phylotypes on subsoil functions by facilitating the migration of soil microorganisms across soil profiles.Conclusions: This study highlights the importance of relative abundance and diversity of keystone phylotypes in controlling soil functions and nutrient cycling processes after long-term fertilization, in addition to providing selectable fertilization strategies for regulating them in agricultural ecosystems.