Industrial processes usually do because the cost of proper treatment reduces profits. Unnatural substances accumulate in the environment as pollution because nature is overwhelmed or no energy harvesting organism exists.
In natural processes, nature harvests energy from the waste to support downstream life.
Aquaponics is a good example of copying and simplifying a natural process to produce calories. Although how and where the inputs (fish food) comes from is an important consideration.
RE: Synthetic meat that is