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Well, biogas production is in theory a pretty positive process, because you trap the methane and use it, instead of letting it escape into the atmosphere where it is a significant greenhouse cause. Burning methane does release carbon dioxide, but its greenhouse contribution is much less.

I'd say that the main negative impact of biogas is in its construction, as it can use significant amounts of cement, and/or other materials that need transport.

See this GTZ doc, the lest 3 pages are about environmental conditions and effects.