spudlydoo as you possibly imply in your post this can be thought of in other ways. For example another side to this issue is the use of soil microbes for increased soil fertility and productivity. Couple that with the use of bio-chars and you start getting a whole new way of growing, developing and managing natural food production. Both increased microbial and biochar usage have shown a reduction in nutrient leaching and an increase in available amounts of many plant nutrients. Of added interest is that these same systems also have good records as both processors and stabilisers of contaminates in soils.
What is deeply disturbing is the dearth of soils research world wide. Of any system known on earth the one that we know least about and is recognised to be the most complex of all is soils. It is commonly agreed that we have identified and know about 2% of all the soil microbes. Simple and well known systems run without any real understanding of what is actually happening. Stand alone septic systems a case in point.
The limitations to our knowledge here could well be more costly that all the environmental damage caused by our abusive practices. For example many of the large fertilizer inputs in agriculture are required because of the death of much soil microbial life due to herbicide regimes. One bad regime driving another and only because of cheap energy inputs. The last doubling of food production came through a seven fold increase in nitrogen usage. That is not sustainable on any criteria.