So basically, modern farmers don't have one iota of sustainability in their methods. Aren't you just strengthening the premise of the article, even if you disagree on the details?
Exactly which of the above will run out in the next 1000 years? You've made a statement without any evidence. Even peak phosphorus mentioned in other comments seems as dodgy a concept as peak oil.
Or do you mean they are not following the religion of mothernature knows best and using science and technology for sustainability instead.
Phosphorus. http://www.sciencedirect.com/science/article/pii/S0959378008...