[salawat]

>We spread manure from farm animals over produce fields

You do not want to stop this. Topsoil is a damn complicated thing, and bacteria and other decomposers are critical to freeing up and breaking down organic material to keep the nutrient cycle going. Try growing a plant in a sterile soil, and you end up having to maintain it on artificial fertilizers instead of being able to let microbiota do their thing.

I've got a hunch part of our degradation in crop nutrition and loss of topsoil quality is probably stemming from overuse of chemical fertilizer, as well as fundamental microbiome depletion from overuse of antibiotics in industrial farming processes. The unfortunate part being there may not be much to be done about it if there is a desire to maintain our current population carry capacity, because replenishing of it would require reversion to less short-term efficient agriculture, but more long term sustainable methods.