Crown, Stem, and Root Rot are fungal diseases caused by humid warm conditions, wet leaves, soggy soil, and poor air circulation. Infected plant develops mushy stems, brown or black spots indicating dead plant tissue, and unhealthy black roots. The plant finally wilts and dies even though the soil is damp. To treat Crown, Stem, or Root Rot, cut off the diseased areas, and spray with a commercial FungicideLearn what fungicides are and how they are used to treat fungal and bacterial plant infections.. If you are adverse to chemicals, try this homemade remedy. Put a tablespoon or two of baking soda in a spray bottle of water and add a teaspoon or two of mineral oil. Shake well and spray every part of the plant.