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 spotHow to identify and treat Black Spot Disease, a houseplant disease caused by a fungal infection.s 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 FungicideFungicides are chemical compounds that are used to kill or inhibit fungi or fungal spores. Fungi can cause serious damage to your houseplants.. 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.