If nearly 79% of the atmosphere is made of nitrogen, how could there be a shortage of nitrogen in the soil.

could

We represent the dinitrogen molecule as $N\equiv N$...because (i) the filled bonding orbitals are so stable it is difficult to oxidize, and since the unoccupied molecular orbitals are high in energy, is (ii) difficult to reduce.

There are a few micro-organisms that can fix atmospheric nitrogen, i.e. bacteria that live in the roots of legumes, i.e. peas and beans....and only very recently have convincing model systems been developed that model dinitrogen fixation and reduction...

At any rate, the upshot of all this is when we grow plants and veggies we usually add nitrogenous fertilizer, i.e. nitrates, and ammonium salts, that contain nitrogen in a soluble and usable form.