This study investigates the dynamic root-associated microbiome of soybeans in response to unbalanced fertilizer treatments (lacking either nitrogen, phosphorus, or potassium) and its role in sustaining plant growth over four decades. Using quantitative microbiome profiling (QMP), the researchers found that the root-associated bacteria exhibit strong succession during plant development, with bacterial loads increasing significantly, particularly for Bacteroidetes. Unbalanced fertilization significantly affects the assembly of the soybean rhizosphere bacteria, with the absence of nitrogen fertilizer leading to a divergent bacterial community compared to fertilized plants, and the lack of phosphorus fertilizer impeding the total load and turnover of rhizosphere bacteria. Importantly, a synthetic community (SynCom) derived from the low-nitrogen-enriched cluster was capable of stimulating plant growth, corresponding to stabilized soybean productivity in the absence of nitrogen fertilizer. These findings provide new insights into the quantitative dynamics of the root-associated microbiome and highlight the potential of specific microbial ecological clusters for sustainable agricultural management.This study investigates the dynamic root-associated microbiome of soybeans in response to unbalanced fertilizer treatments (lacking either nitrogen, phosphorus, or potassium) and its role in sustaining plant growth over four decades. Using quantitative microbiome profiling (QMP), the researchers found that the root-associated bacteria exhibit strong succession during plant development, with bacterial loads increasing significantly, particularly for Bacteroidetes. Unbalanced fertilization significantly affects the assembly of the soybean rhizosphere bacteria, with the absence of nitrogen fertilizer leading to a divergent bacterial community compared to fertilized plants, and the lack of phosphorus fertilizer impeding the total load and turnover of rhizosphere bacteria. Importantly, a synthetic community (SynCom) derived from the low-nitrogen-enriched cluster was capable of stimulating plant growth, corresponding to stabilized soybean productivity in the absence of nitrogen fertilizer. These findings provide new insights into the quantitative dynamics of the root-associated microbiome and highlight the potential of specific microbial ecological clusters for sustainable agricultural management.