They are made up of anode and cathode sections with a membrane in-between that can pass cations. The anode compartment contains microbes that oxidize the fuel (in anaerobic conditions they use water for this instead of oxygen) and generate protons and electrons (and carbon dioxide) in the process. The membrane lets protons pass through resulting in positive charge on the cathode and negative on the anode. When plugged into an electric circuit, the electrons will travel through it to the cathode to combine with the protons (which is same as hydrogen ions) and oxygen to form water. Most bacteria require mediators, special chemicals that enter cells, take electrons, exit the cell, and release electrons outside. Some microbes, however, can transport electrons outside the cell by themselves, using special structures called pili.
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