The BMFC utilizes the natural potential difference between water and sediment. By tapping microbial metabolic processes power is produced. The anode is buried in the anoxic sediment, and the cathode is immersed in the oxygenated water. There is no need for a proton-permeable membrane as in common fuel cells, because protons are exchanged over the oxic-anoxic interface at the water-sediment boundary. The natural potential difference of 0.7 V between the water and the sediment allows electrical current flow.

The electrons needed for the current flow are provided by metabolic processes of microorganisms populating the anode. These are mainly ferric iron or sulphate reducers that are able to use the electrode surface as electron acceptor. The electrodes originate from the degradation of organic material. But also abiotic processes can occur at the electrode surface: for instance sulfide can be oxidized to elemental sulfur.

The supply with bioavailable organic matter to the bacterial community in the periphery of the electrode is critical for the metabolic activity of the microorganisms. The sinking and settling of marine snow in coastal waters and shelf seas provides organic input to the sea floor. For this reason BMFC find their application primarily at sites with a constant supply of organic matter.

The power produced by microbial metabolic processes is low, but it increases with increasing electrode surface. The power can be stored and discharged in pulses. Hence, typical employments of BMFC are long term measurements with intermittent data acquisition with low energy demanding sensors.

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