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This paper shows that Saccharomyces cerevisiae efficiently interact with magnetite-based ionic magnetic fluid, leading to the formation of magnetically labeled cells which could be easily separated from the system using an appropriated field-gradient-based magnetic separator. Scanning and transmission electron microscopies were used to investigate the interaction of Saccharomyces cerevisiae cells with magnetite nanoparticles. The high-resolution microscopy data suggested that particle incorporation occurs via an active process. Further, the microscopy data shows that the particles did not reach the cell cytoplasm, staying in the periplasmatic space.