Nitrogen from atmosphere is converted to ammonium ion through the action of nitrogenase enzyme. This ammonium ion is taken up and utilized by plants to produce among, other things, amino acid.
Ammonium ion can also be oxidized to nitrite ions through action of nitrifying (AOB -ammonia oxidizing bacteria). It is mainly involves two enzymes: ammonia monooxygenase and nitrite oxidoreductase.
Nitrite ions can further be oxidized into nitrate ions through the action of nitrite oxidoreductase.
Nitrate ions are taken and reduced to nitrite and ammonia successively. The latter (along with the ammonium ions taken up directly from the soil) can then be incorporated into amino acids via the glutamine synthetase-glutamate synthase pathway. Read nitrogen assimilation
Nitrate ions can also be used as terminal electron acceptor in oxygen poor regions inside soil. In this process ( denitrification ), nitrate is reduced to nitrogen and released back into the atmosphere
More detail here:https://en.wikipedia.org/wiki/Nitrifying_bacteria
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