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Here's some numbers on nutrient export from a system composed of a ball python in an enclosure, using nitrogen as an example. I had fun running these numbers, as I had not done so before.
Feeder rats have a protein content of about 60% of dry weight, and are about 70% water, so are about 20% protein by live weight (data taken from Mader's Reptile Medicine, p. 218). Thus, a 100g feeder rat (the smaller ones in the medium bag) has about 20g protein.
Protein is 16% nitrogen (source). Thus, a 100g feeder rat contains 3.2g N.
Looks like the highest N content in plants is about 3% of dry weight (source).
So, when a rat is fed to a snake, two things can happen to the N in the rat. One is that the N can be taken up into the snake's tissues as protein. This happens a lot when the snake is young (as it is building tissue), and less as it slows its growth. The second thing that can happen is the N (either that which was ingested, or that which is the product of cellular breakdown as tissues get repaired with new protein) gets excreted in feces and urates. At any rate, all the N in the rat stays in the system (snake + enclosure) until it is removed.
The microfauna take up a little N in their diet, but (a) there's not more than a couple ounces of microfauna in the system so their contribution to N uptake is negligible, and (b) the same factors regarding excretion of N apply to the microfauna as do to the snake -- so once their population stops increasing, they are not a factor in sequestering N.
Each time a 100g rat is fed (I assume about weekly), 3.2 g of N enter the system. At the point the snake stops growing, basically all this N will be excreted by the snake. In order to export it from the system only through uptake by the plants, approximately 100g of plants (dry weight) would have to be removed from the system. Various sources state that plants in general are about 80-90% water (example); lets shoot low so to be very conservative and say a plant is 70% water. Thus, 233g (8 ounces; 1/2 pound) of fresh plant mass would have to be removed from the system per week -- about 25 pounds per year -- to take up the nitrogen in our example system.
I think that shows that nutrient export by plants alone from this sort of "bioactive" system is implausible, and by extension I think it is safe to say that such systems do not effectively process the waste of the animals housed in them, but rather build up waste products in a way that the keeper cannot see. We could figure out how much footprint would be needed to grow 25 pounds of plants per year and use that to appropriately size "bioactive" enclosures, though this would still not take into account the pathogen accumulation concern.
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