Root stoichiometry explains wheat endophytes and their link with crop production after four decades of fertilization

Fertilization can impact root endophytic microbiomes and food production. However, the impacts of decades of continued fertilization on root microbiomes, and their link with ongoing crop production, remain poorly understood. Here, we used a four decade-long fertilization experiment, including contrasting types of organic and inorganic fertilization, to investigate the effects of long-term fertilization on multi-kingdom root endophytic microbiomes, including keystone species (modules within microbial networks), and their indirect associations with the production of wheat, which is one of the most important crops worldwide. We found that long-term inorganic (nitrogen, phosphorus, potassium (NPK)) and organic (NPK with straw (NPKS) and NPK with cow manure (NPKM)) fertilization had significant impacts on the community composition of endophytic arbuscular mycorrhizal fungi (AMF), bacteria, and non-mycorrhizal fungi. In addition, compared with NPK fertilization, NPKS and NPKM amendments significantly decreased the microbial network complexity, which was associated with changes in the root iron content. Finally, we identified an important subset of keystone root endophyte species within the microbial network (Module #2), which was positively correlated with wheat yield, and affected by changes in root carbon to phosphorus ratio. This study provides evidence that long-term fertilization can affect keystone root endophytic species in the root microbiome, with implications for food security in an over-fertilized world.