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The inactivation mechanism of pathogenic microorganisms in water needs to be comprehensively explored in order to better guide the development of an effective and green disinfection method for drinking water safety. Here, metal-free modified g-C3N4 was prepared and used to inactivate two typical bacteria (namely, Gram-positive E. coli and Gram-negative S. aureus) in water under visible light from a comparative perspective. These two bacteria could be inactivated in the presence of modified g-C3N4 within 6 h of visible light, but their in