From my perspective the pre-treatment of waste prior to it entering the digester can indeed affect biogas production. If for example you have inadequate pre-treatment and therefore too much inert materials are finding their way into the digester, you are effectively taking up space with materials that cannot produce biogas. In the dairy environment we see this with sand which is used for bedding. Too much sand in the digester can result in sediment build up, which reduces the amount of digester capacity you have, and thereby reduces biogas production. Similar parallels exist in with packaged food waste. I have completed a number of projects in a past life on sewage sludge. Here, pre-treatment is often the explosion of the cells via steam which greatly increases methane potential. Thermal hydrolysis is another example where biogas production can be significantly increased. For each application the tradeoffs would need to be considered.
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