Cause The fungus Phoma eupyrena is associated with three different diseases called upper stem canker, lower stem canker, and Phoma blight. The fungus can survive in soil by forming chlamydospores and machinery or blowing soil can transport spores to uninfected areas. Upper stem canker infection occurs when spores land in bark fissures caused by rapid seedling growth. Infection for the other two diseases occurs below the soil collar, which builds up from rain or irrigation-splashed soil.