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What do you recommend for a 1000L IBC tank?
5 oysters.
6, there be overage
You can offset that by changing the feeding schedule. Just replenish the tank with gray water every other day instead of daily and you should be fine with only four.
You might find it hard in a closed system to maintain the alkalinity needed for them to thrive long-term! Source: I study bivalves
Would a little agricultural runoff help?
Hard to say without knowing its composition. If rich in ammonium, the nitrification (oxidation to nitrate) might lead to lower alkalinity. If rich in nitrate, it might help alkalinity, but only if there's some lower oxygen area of the tank like a bank of sediment, where denitrification can happen
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