Endospore (Spore) Staining An endospore is a special resistant, dormant structure formed within a cell that protects a bacterium from adverse environmental conditions. Although endospores are relatively uncommon in bacterial cells, they can be formed by a few genera of bacteria. Endospores cannot be stained by ordinary methods, such as simple staining and Gram staining, because the dyes don’t penetrate the endospore’s wall. The most commonly used endospore stain is the SchaefferFulton endospore stain (Figure 3.15b). Malachite green, the primary stain, is applied to a heat-fixed smear and heated to steaming for about 5 minutes. The heat helps the stain penetrate the endospore wall. Then the preparation is washed for about 30 seconds with water to remove the malachite green from all of the cells’ parts except the endospores. Next, safranin, a counterstain, is applied to the smear to stain portions of the cell other than endospores. In a properly prepared smear, the endospores appear green within red or pink cells. Because endospores are highly refractive, they can be detected under the light microscope when unstained, but without a special stain they cannot be differentiated from inclusions of stored material.