No. Nutrients in an anaerobic digester do not disappear. The reason some people claim that a digester "eats" nutrients is the fact that some of the nutrients settle out in the sludge and stay in the digester until it is mechanically cleaned out. This is especially true in "Plug Flow" digesters. Phosphorus (P) is an excellent example. Often, P settles out in the digester, thus giving a net reduction of P through the digester. In reality, the P is being stored in the solids (sludge) accumulating in the digester. For nitrogen (N), some of the organic N may settle and a very small fraction may be lost with the biogas as ammonia, but essentially the N is not reduced in a digester.
More information can be found in the following fact sheet:
The Fate of Nutrients and Pathogens during
Anaerobic Digestion of Dairy Manure.
Author: Patrick Topper, Pennsylvania State University
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