What about the fact that our agriculture system is (mostly) open loop? Every time you harvest food and consume it, where do the waste products end up? I think we need to also work on closing this loop.
It's not just sewage either. Every time you till the earth, you expose it to the air. This oxidises the minerals and often makes them unavailable for the plants. Because the fertiliser we add is very water soluble it drains through the water table and ends up in the rivers and eventually washes out to sea (or just clogs the rivers with algae).
Tilling and pesticides also kill the organisms that are responsible for moving nutrients around under the earth. Additionally, we tend to plant mono-culture crops with short root structures. This stops a variety of plants from breaking down nutrients in the soil and moving them to the top layer of humus. So either we till deeper (exacerbating the problem) or we essentially lock all of the nutrients below the level that the plants can access.
In the end, you basically are slowly extracting all of the bioavailable nutrients out of the soil, and depositing them in the sewage treatment fields. At the same time you are oxidising what's left and washing everything else out to the sea. Any fertility that remains is below the access of the plant roots (and probably not in a form that can be utilised right away).
"Closing the loop" means looking at the places where we are losing fertility and making sure that it is looping back. So, if you take nutrients out in the form of food, we return it in the form of sewage. You avoid tilling and you plant a variety of crop varieties that circulate the nutrients in the soil layer. You avoid adding highly water soluble salts that simply leach out of the soil and into the water table.
It sounds simple-ish, but it's actually quite a bit challenge. We don't really do a lot of research in this area (as far as I can tell). Most agricultural research is geared toward increasing yields and reducing costs as opposed to sustainability.