Your article is primarily about nitrogen fertilizers, which is usually made by processing fossil fuels.

Air, actually! (Well, nitrogen from air, and hydrogen. Which might come from fossil fuels, but that's a relatively minor consideration)

It's just a really energy intensive process, so fuel is the main input in cost terms.

Also, fun fact about phosphorus: it's expected deposits will be depleted in a few decades. Efforts are already underway to start recovering it from sewage, instead.