Nitrogen in the atmosphere is straight nitrogen, not in from of nitrates or nitrides, or nitrous-oxides.
When plants and animals decay, these compounds are produced. Plants can reabsorb these compounds through their roots, dissolved in water.
Humans get these compounds via chemical reactions in our intestines and through eating a good diet rich in nitrogen-compounds.
Fertilizers for lawns and crops also get nitrogen compounds, added to them.
It's sort of like Sodium and Chloride. Each would kill you, but as a compound, Sodium-Chloride (table salt), it becomes a vital ingredient for good health. You just should not get too much of it, and same goes for most compounds.
