Under that assumption, JiK, farmers should get a depletion allowance for certain crops and pay taxes on fertilized fields: if I grow corn it depletes the soil (depletion allowance), but if I fertilize the field (even with the manure from my cows) I make it possible to keep the field in production longer and so I should pay on it.

And how do I determine the depletion allowance for my cattle manure? It's a salable product....

Actually, I don't think that ANY tax system is fair to everyone. It can't be. We can only do our best.