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An integrated nano-optoelectronic biological sensor system is developed to obtain insights of the biochemical and physical processes of Geobacter sulfurreducens-based biofilm growth inside a miniaturized microbial fuel cell (MFC) reactor. Gallium nitride (GaN), which was used as a novel electrode material, has been investigated in terms of its biocompatibility and performance to transport the electrons delivered by the microorganisms. Moreover, in order to enhance the produced current density, vertical 3D GaN nanoarchitectures (i.e., arrays of nanowires and nanofins) with larger surface-to-volume ratios were fabricated using a top-down nanomachining method involving nanolithography and hybrid etching technique.