The nitrogen from the ground was taken at some point from the air by bacteria using a protein called nitrogenase. However, plants cannot use this protein themselves because it is a very sensitive protein and damages really easily. Plants sometimes cooperate with these bacteria to get nitrogen while the plants give them other nutrients. Nitrogenase is also the source of the natural nitrogen deposits in many geological formations and the ground.
This protein, which is older than photosynthesis, is very interesting to scientists though and would constitute an environmentally friendly way to make fertilizer for plants. However, the protein is very hard to handle. So similar to plants, humans have a hard time controlling nitrogenase too.
Source: Getting my PhD in a field related to nitrogenase
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