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Our knowledge on the dissolution and passivation mechanisms of chalcopyrite during bioleaching at low temperature has been limited to date. In this study, an <i>Acidithiobacillus ferrivorans</i> strain with high tolerance to heavy metals and UV radiation was used for chalcopyrite bioleaching. At 6 &#176;C, no apparent precipitate was detected on the mineral surface after bioleaching using a scanning electron microscope (SEM). X-ray diffraction (XRD) revealed that the ore residue contained only chalcopyrite and quartz. X-ray photoelectron spectroscopy (XPS) analysis revealed that the content of S⁰ on the mineral surface remained low and the ratio of SO₄^2&#8722; decreased from 46.7% to 20.9%, but the amount of S_n^2&#8722; increased from 10.4% to 21.4% after bioleaching. Expression of five critical iron- and sulfur-oxidation genes during bioleaching was analyzed using quantitative real-time PCR. The gene <i>rusA</i> had higher expression in the mid-log phase than in the stationary phase but <i>hdrA</i> and <i>cyoC1</i> showed an opposite trend. All genes had higher expression at 6 &#176;C than at 28 &#176;C, so as to compensate for the decline in the enzyme activities. The study revealed that polysulfide was the most plausible passivating substance at 6 &#176;C, and the strain can maintain the iron- and sulfur-oxidation activities during low-temperature bioleaching.