The food chain depends on a delicate balance of nature, when one organism is removed that delicate balance can be affected in a number of ways. The prey/predator relationships change. Removal of a predator causes overpopulation of prey. In areas where bobcats and wolves neared extinction, the deer population increased exponentially. This put stress on vegetation that the deer feed on.
If the loss of an organism is caused by environmental factors, the balance again can be tipped. When sharks move north along the East Coast due to the warming of ocean waters, the seal population is decreased as the sharks move into their territory, feeding on them faster than they can reproduce. In addition, the opposite can occur.The loss of an organism can cause a change in the environment in a geographic area due to over or undergrowth of the native vegetation that served as a food source for that species. This phenomenon is evident in the layers of the rainforest.
The removal of an animal of a specific species can reduce the biodiversity of the whole species once again reducing the food chain for those who depend on that species for food. When biological changes occur in a species, the animals who feed on that species have to adapt their eating habits or perish.