Aquaponic Gardening

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I was watching an aquaponics video, featuring a system by Purdue University, that the western regional aquaculture extension agent sent our teacher. In the video they had a water clarifier that also acts as a place for the fish waste to break down anaerobically. It seems like the hydrogen sulfide gas that is dissolved in the water would act as an fertilizer, aeration in ap system would keep it in check so it doesn't harm the fish or plants, and the decomposition of the waste would allow for other nutrients to be released.

So in an AP system is it a problem to just have an inline waste collection system that is just allowed to sit? The follow up is, is there any special considerations for such a system?

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I seem to remember years ago there was an aquarium filtration system that as an adjunct to the normal super-aerobic biofiltration had a protein skimmer type thing that fed an anaerobic chamber, very slowly. The products from this would slowly be fed back into the aerobic filtration.  Theory was good and it seemed to work for an aquarium, even a salt water which was very sensitive to changes. I'm not sure if any of it would apply to an AP system though.

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