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As discussed previously, methane fermentation treatment namely permits the elimination of carbon pollution. The nitrogen and phosphorous eliminated are solely linked to the synthesis of the biomass, but the methanisation treatment is often insufficient to obtain the required values in terms of BOD, COD and a fortiori for NH4 or even total N; to achieve this, an aerobic finishing treatment is necessary.

Depending on its residual concentration, any of the aerobic processes described in anaerobic bacterial cultures and biological processes can be used. It should be noted that anaerobic sludge entering an activated sludge system can be partially mineralized and will behave like inert sludge, forming biological floc without making any major oxygen demand.

In the case of a sulphate rich effluent, water produced by the methane fermentation unit at equilibrium with the gas will also be rich in HS which should generally be eliminated before carrying out any subsequent treatment. This elimination can be achieved either by catalytic oxidation or by a biological treatment using attached growth, permitting, in this case, sulphides to be oxidized and converted into S2- and the sulphur to be settled in wash water.