This study investigates the dynamic root microbiome of soybean under unbalanced fertilization conditions, revealing how microbial communities respond to nitrogen (N), phosphorus (P), and potassium (K) deficiencies and their role in sustaining plant growth. Using quantitative microbiome profiling (QMP), the researchers analyzed the temporal dynamics of root-associated bacteria across soybean development and their response to unbalanced fertilization treatments. They found that root-associated bacteria exhibit strong succession during plant development, with bacterial loads increasing significantly at later stages, particularly for Bacteroidetes. Unbalanced fertilization significantly affects the assembly of soybean rhizosphere bacteria, with the absence of N fertilizer causing the bacterial community to diverge from that of fertilized plants, while P deficiency impairs bacterial load and turnover. A SynCom derived from the low-nitrogen-enriched cluster was shown to stimulate plant growth, corresponding with stabilized soybean productivity in the absence of N fertilizer. The root-associated microbiome, often referred to as the "second genome" of plants, plays a crucial role in plant growth, development, and health. Root-associated compartments, including the rhizosphere and endosphere, provide unique habitats for microbial colonization, resulting in substantial taxonomic and functional differences compared to surrounding bulk soils. Root-associated microbiomes are highly dynamic and strongly affected by plant development, primarily through the impact of root exudates on microbial growth. This dynamic nature may have important implications for plant nutrient acquisition, as evidenced by the temporal complementarity of nitrogen use efficiency between roots and microbes in wheat. Relative microbiome profiling (RMP) has been widely used to detect variation in the relative abundance of taxa in complex microbial communities, but RMP fails to provide information on the absolute abundance of microbes and is not useful for comparing microbial loads among samples. Quantitative microbiome profiling (QMP) provides information on the absolute abundance of microbes and is more sensitive to environmental disturbance. However, due to technical challenges, there remains a lack of detailed high-resolution information on the quantitative dynamics of root-associated microbiomes. Thus, data from QMP is urgently needed to advance our understanding of the relationship between root-associated microbiome assembly and plant development. The assembly of root-associated microbiome is also affected by environmental factors, such as drought, which reduces diversity and disrupts the temporal dynamics of root microbiomes. In agriculture, the use of chemical fertilizers has contributed greatly to yield increases, but intensified agriculture has caused severe environmental pollution and inactivated positive plant-microbial interactions. N amendment is associated with reduced soil microbial biomass, and fertilization was found to significantly decrease the microbial temporal succession rate in soil. However, quantitative studies assessing how soil nutrient conditions affect the temporal dynamics of the root-associated microbiome, particularly by the QMP method, are lacking. Understanding how root microbial dynamics respond to different fertilization regimes and affect crop productivity is essential for the development of sustainable agriculture. Plants are thought to subtly manipulate their root-associated microbiome underThis study investigates the dynamic root microbiome of soybean under unbalanced fertilization conditions, revealing how microbial communities respond to nitrogen (N), phosphorus (P), and potassium (K) deficiencies and their role in sustaining plant growth. Using quantitative microbiome profiling (QMP), the researchers analyzed the temporal dynamics of root-associated bacteria across soybean development and their response to unbalanced fertilization treatments. They found that root-associated bacteria exhibit strong succession during plant development, with bacterial loads increasing significantly at later stages, particularly for Bacteroidetes. Unbalanced fertilization significantly affects the assembly of soybean rhizosphere bacteria, with the absence of N fertilizer causing the bacterial community to diverge from that of fertilized plants, while P deficiency impairs bacterial load and turnover. A SynCom derived from the low-nitrogen-enriched cluster was shown to stimulate plant growth, corresponding with stabilized soybean productivity in the absence of N fertilizer. The root-associated microbiome, often referred to as the "second genome" of plants, plays a crucial role in plant growth, development, and health. Root-associated compartments, including the rhizosphere and endosphere, provide unique habitats for microbial colonization, resulting in substantial taxonomic and functional differences compared to surrounding bulk soils. Root-associated microbiomes are highly dynamic and strongly affected by plant development, primarily through the impact of root exudates on microbial growth. This dynamic nature may have important implications for plant nutrient acquisition, as evidenced by the temporal complementarity of nitrogen use efficiency between roots and microbes in wheat. Relative microbiome profiling (RMP) has been widely used to detect variation in the relative abundance of taxa in complex microbial communities, but RMP fails to provide information on the absolute abundance of microbes and is not useful for comparing microbial loads among samples. Quantitative microbiome profiling (QMP) provides information on the absolute abundance of microbes and is more sensitive to environmental disturbance. However, due to technical challenges, there remains a lack of detailed high-resolution information on the quantitative dynamics of root-associated microbiomes. Thus, data from QMP is urgently needed to advance our understanding of the relationship between root-associated microbiome assembly and plant development. The assembly of root-associated microbiome is also affected by environmental factors, such as drought, which reduces diversity and disrupts the temporal dynamics of root microbiomes. In agriculture, the use of chemical fertilizers has contributed greatly to yield increases, but intensified agriculture has caused severe environmental pollution and inactivated positive plant-microbial interactions. N amendment is associated with reduced soil microbial biomass, and fertilization was found to significantly decrease the microbial temporal succession rate in soil. However, quantitative studies assessing how soil nutrient conditions affect the temporal dynamics of the root-associated microbiome, particularly by the QMP method, are lacking. Understanding how root microbial dynamics respond to different fertilization regimes and affect crop productivity is essential for the development of sustainable agriculture. Plants are thought to subtly manipulate their root-associated microbiome under