Fertilization is a common agricultural practice used to modify the physicochemical properties of soil, which in turn affects plant growth and the rhizosphere microbial community. However, the mechanisms underlying the variation in the cucumber rhizosphere microecosystem have not been thoroughly investigated. In this study, we conducted three rounds of continuous plant growth experiments in pots to test different fertilizers and reveal the evolutionary features of the rhizosphere microecosystem. Through topological analysis of the microbial co-occurrence networks, we identified putative taxa associated with fertilization disturbances. Structural equation models (SEMs) predict plausible mechanistic links between soil physicochemical properties, plant growth and the rhizosphere microbiome. The results suggest that continuous fertilization with single fertilizers reduces microbial diversity and may disrupt the structure of the microbial network. Furthermore, it was found that the predicted distribution of keystone taxa (Bacteroidetes, Ascomycota, etc.) was significantly sensitive to the application of certain fertilizers. Moreover, it was modeled by the SEMs that the accumulation of NO3− and Na+ in fertilized soil was one of the putative principal causes of rhizosphere microbial network deterioration. This study provides new insights into the dynamic changes in the cucumber rhizosphere microbial community under continuous fertilization and highlights the potential utility of SEMs in analyzing causal relationships in agroecosystem studies before experimental validation.
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