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Background Optimizing the ability of exoelectrogens is a key factor in boosting the overall efficiency of bioelectrochemical systems. In this study, we construct magnetic microbial fuel cells (MFCs) with magnets with different static magnetic field (SMF) intensities for use as anodes. It is proposed as an in situ study of the effects of magnetic fields on the performance and exoelectrogenic biofilm of bioelectrochemical system. Results The magnetic MFCs obtain a 71.0–105% increase in voltage production and a 42.9–104% increase in power density compared with non-magnetic MFCs. MFCs with a MF intensity of 80 mT obtain the best performances. SMF decreases the internal resistance of MFCs, especially its diffusion resistance. The relative abundance of Geobacter in magnetic MFCs is up to 32.5% higher than that of non-magnetic MFC. SMFs also lead to the shifts in microbial community structure of methanogens. Conclusion The constructed magnetic MFCs obtained better performance compared with the non-magnetic MFC, in terms of voltage production, power density, and coulombic efficiency. The relative abundance of Geobacter spp. (one kind of exoelectrogen) was much higher in the magnetic MFCs. The optimal static magnetic field intensity for enriching exoelectrogens is around 80 mT. It is likely that the decrease of internal resistance, enrichment in exoelectrogens, and the syntrophic interactions between exoelectrogens and methanogens result in the enhanced performance of magnetic MFCs. This study provides a magnetic method for the enrichment of exoelectrogens, which can be extensively applied in bioelectrochemical systems.

Understanding how the community structure of anode biofilms is shaped is important for enhancing the performance of microbial fuel cells (MFCs).