Final answer:
Bacillus megaterium appears blue in an acid fast stain because it is not an acid-fast organism and does not retain the primary red stain, but is counterstained with methylene blue.
Step-by-step explanation:
The color of Bacillus megaterium in an acid fast stain is not red; rather, it is blue because Bacillus megaterium is not acid-fast. The acid fast staining technique is designed to differentiate acid-fast bacteria, like Mycobacterium tuberculosis, which retain the primary stain carbol fuchsin and are not decolorized by acid-alcohol, thus appearing red. Non acid-fast bacteria, such as Bacillus megaterium, do not have this waxy cell wall component and are decolourized, taking up the methylene blue counterstain.