What I made of all of of it: first it's "fixed" by converting nitrogen from air to ammonia (nitrogen fixation), then it's converted to nitrites and then nitrates (nitrification), then faeces and dead bodies shed their organic nitrogen which is converted into ammonium (ammonification) (I'm only interested in how nitrogen becomes bioavailable so I skip the denitrification phase).

The articles say all the three are bioavailable, but Wikipedia says ammonia, at least in its gaseous form, is toxic to plants. So a step of converting ammonia to ammonium was missed, wasn't it? And if ammonia is available enough then what does nitrification have to do with it? I read somewhere (I don't remember where, I closed the tab apparently) that ammonium is good for some plants but generally they, plants, prefer nitrates.

Could you give me an article that confirms and, hopefully, explains it? An intelligible explanatory article from an authoritative source would be helpful