The peculiar smell of soil when plants are uprooted and removed can be attributed to -
Henle's loop and Mitochondria
The truth is that roots not only absorb, they also sometimes secrete. ‘Brugaman’ a botanist proved from his experiments that the roots not only absorb fluid from the soil but returns a portion of their peculiar secretions back into it. It is for this reason when plants especially potted plants are uprooted and removed, they leave their characteristic smell in the soil.