Large scale aquaponics would have the same antibiotic problem that farmed fish have.
I'd also be concerned that the produce would lack micro nutrients because the system is artificial.
That said, I think aquaponics will be part of the solution.
I'd also be concerned that the produce would lack micro nutrients because the system is artificial.
That said, I think aquaponics will be part of the solution.
Plant nutrition isn't that complex. Plant nutrition deficiencies are easy to diagnose and easy to treat. It only takes a few drops of say, molybdenum to give an entire field all micro-nutrient it needs.
There is no vital essence to micro-nutrients that are lost in a potted plant or aquaponics. It is simply a formula for nutrition, where a plant needs quantities fulfilled to be healthy.
In fact, it's gotten better. So much better that now obesity is the problem, not malnutrition.
Basically, yeah, artificialness is a liability, and it should be minimized intelligently. Not by imitating a jungle, that is impossible, but by being highly aware of the local microbiomes and gently supporting beneficial negative feedback loops.
Make friends with a biologist.
As for the micro nutrients, this is what the fish and insect side of the system takes care of. If there is a deficiency, try to make it up through fish feed, not by directly feeding the plants. Fish hate concentrated fertilizers. Maintaining a barrel of "compost tea" is also an option, but it should be filtered through lots of grow media before the fish get it.
If you are really really brave, you might choose to experiment with a graywater system, but there is huge potential for problems like parasites and bacterial (i.e. E-coli) explosions.