Final answer:
Dead zones in the Chesapeake Bay, resulting from fertilizer runoff leading to oxygen depletion, cause the loss of energy in the food chain affecting bottom-dwellers.
Step-by-step explanation:
The issue that causes a loss of energy in the food chain due to the lack of growth of bottom-dwellers like worms and clams in the Chesapeake Bay is related to the creation of dead zones. These areas emerge largely due to excess nutrients from fertilizer runoff, which lead to oxygen depletion. The hypoxic or anoxic conditions in these zones make it impossible for many species that dwell at the bottom of the bay, such as worms and clams, to survive, disrupting the food chain and affecting the overall health of the ecosystem.