Nitrogen (N), phosphorus (P), and potassium (K) are three macronutrients that are crucial in plant growth and development. Deficiency or excess of any or all directly decreases crop yield and quality. There is increasing awareness of the importance of rhizosphere microorganisms in plant growth, nutrient transportation, and nutrient uptake. Little is known about the influence of N, P, and K as nutrients for the optimal production of
Chrysanthemum morifolium. In this study, a field experiment was performed to investigate the effects of N, P, and K on the growth, nutrient use efficiency, microbial diversity, and composition of
C. morifolium. Significant relationships were evident between N application rates,
C. morifolium nutrient use, and plant growth. The N distribution in plant locations decreased in the order of leaf > stem > root; the distributions were closely related to rates of N application. Total P fluctuated slightly during growth. No significant differences were found between total P in the roots, stems, and leaves of
C. morifolium vegetative organs. Principle component analysis revealed that combinations of N, P, and K influenced soil nutrient properties through their indirect impact on operational taxonomic units, Shannon index, and abundance of predominant bacterial taxa. Treatment with N, P, and K (600, 120, and 80 mg·plant
−1, respectively) significantly improved plant growth and quality and contributed to the bacterial richness and diversity more than other concentrations of N, P, and K. At the flowering time, the plant height, leaf fresh weight, root dry weight, stem and leaf dry weight were increased 10.6%, 19.0%, 40.4%, 27% and 34.0%, respectively, when compared to the CK. The optimal concentrations of N, P, and K had a positive indirect influence on the available soil nutrient content and efficiency of nutrient use by plants by increasing the abundance of Proteobacteria, decreasing the abundance of Actinobacteria, and enhancing the potential functions of nitrogen metabolism pathways. N, P, and K fertilization concentrations of 600, 120, and 80 mg·plant
−1 were optimal for
C. morifolium cultivation, which could change environmental niches and drive the evolution of the soil microbial community and diversity. Shifts in the composition of soil microbes and functional metabolism pathways, such as ABC transporters, nitrogen metabolism, porphyrin, and the metabolism of chlorophyll II, glyoxylate, and dicarboxylate, greatly affected soil nutrient cycling, with potential feedback on
C. morifolium nutrient use efficiency and growth. These results provide new insights into the efficient cultivation and management of
C. morifolium.
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