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This experiment prepared magnetic composite siderophores (DMPs) with strong magnetism, excellent adsorption capacity, and high specific surface area. Exploring the synergistic effect of magnetic nanoparticles and siderophores on Microcystis aeruginosa growth under iron-deficient condition, by utilizing the characteristics of the three-layer core-shell structure of DMPs. This study elucidated the potential mechanism by which DMPs promote the cyanobacterial growth through physiological indicators and transcriptome analysis. On the experiment's final day, cell density in DMPs treatment group at 2, 4, and 8 mg/L were 1.10, 1.14 and 1.16 times higher than those in the control group (Ct), respectively. Similarly, chlorophyll and photosynthetic efficiency results showed improved algae growth with increasing DMPs dosage. The microcystin content in DMPs experimental groups at low, medium, and high concentration were 0.91, 0.86, and 0.83 times that of Ct, indicating alleviation of iron deficiency stress. Additionally, based on extracellular polymers, intracellular and extracellular siderophores, and visualization techniques, DMPs nanoparticles captured free iron sources in the environment, promoting algae growth by entering algal cells and facilitating the uptake and utilization of free iron ions from the solution. During the experiment, the iron uptake and transport genes (feoA and feoB) were significantly upregulated, whereas the algal siderophore synthesis gene (pchF) and the TonB-dependent transport system gene (TonB_C) were significantly downregulated, suggesting heightened activity in intracellular iron uptake and transport. This indicates an abundance of intracellular iron, eliminating the need for secrete siderophores to overcome iron deficiency. Microcystis aeruginosa increased iron bioavailability by using iron transported through DMPs in the environment while internalizing these DMPs. This study explored the mechanism of this synergistic effect to boost algal growth, and provided new ideas for elucidating the mechanism of cyanobacterial bloom outbreaks as well as the innovative application of biotechnology. [Display omitted] • Deepening the interaction with M. aeruginosa through modifying siderophores. • The mechanism of DMPs promoting algal growth via transcriptomics. • DMPs facilitated algae to acquire free iron and were internalized by algae. • High-dose DMPs boosted photosynthesis, glycolysis and protein synthesis in algae. [ABSTRACT FROM AUTHOR]