Insect pathogenic fungi can be found throughout the fungal kingdom (Humber, 2008), all being capable of invading their hosts and overcoming their immune systems. Two fungal genera (Ascosphaera and Aspergillus) are known to infect honey bee brood, causing chalkbrood and stonebrood diseases. Both are ascomycetes within the order Eurotiales. The fungus causing chalkbrood in honey bees has a narrow host range and a unique infection route, it relies solely on sexual reproduction and has many host-specific adaptations. Therefore many methods known from common insect pathogenic fungi are not easily adopted to study chalkbrood.

In contrast, the fungi causing stonebrood are facultative pathogens with a broad host range, they produce asexual conidia and their infection biology resemble many well-known insect pathogenic fungi, like Beauveria and Metarhizium; so several standard insect pathological methods can be directly transferred to this system. In the current chapter, we compile, discuss and provide detailed protocols for various methods to assist beekeepers and bee scientists entering this area of research.

In addition to fungal pathogens causing chalkbrood and stonebrood, two species of microsporidia, Nosema apis and Nosema ceranae, are known to infect adult honey bees. Although recently suggested to be fungi at the very base of the fungal tree (James et al., 2006), these intracellular pathogens have a very different biology and are considered in a separate paper in the BEEBOOK  (Fries et al., 2013).