Final answer:
The deep indents in the tonsils' epithelial lining that capture bacteria are called crypts.
Step-by-step explanation:
The deep indents that trap bacteria in the epithelium lining the tonsils are known as crypts. Tonsils are lymphoid nodules located along the inner surface of the pharynx and are crucial for developing immunity against oral pathogens. Unlike other structures in the lymphatic system, the tonsils lack a complete capsule and have an epithelial layer that deeply invaginates to form tonsillar crypts. These crypts are adept at accumulating various materials from eating and breathing, encouraging pathogens to penetrate deep into the tissue where they are eliminated by the immune response of lymphoid follicles.