its simply that the base of your stem is staying too moist, and not getting enough air passing through. Could be that you are watering too much. I have fans under my canopy as well as above to ensure the stalks and soil and undersides of the leaves get constant fresh air.
Root rot is usually culminated in a fungicide. I always put cinamin in my soil as a preventative measure. But you could use this or a similar product:
For Treatment of Root Diseases:
SM-90 is a root disease inhibitor which controls common anaerobic fungal and bacterial pathogens. Effective treatment for root disease from ascomycetes pathogens including fusarium, pythium, rhizoctonia, phytopthera, sclerotinia, etc. When added in small quantities directly to plant nutrient solutions, root disease infestations are inhibited and new root growth emerges. Treated plants develop greater root area and root runs and exhibit a generally healthier root development.
Application rate: Apply 2-3 ml to each gallon of nutrient solution on a weekly basis or whenever solutions are replaced. Routine use will provide preventative treatment to keep problems from developing during all stages of growth.
For treatment of tissue fungus (stem and leaf):
When applied directly to foliage or stem SM-90 is an effective agent to treat for many molds, mildew and leaf spot, etc. Effective treatment for botrytis, blight, fusarium, leaf mold, rhizoctonia stem rot, sclerotinia stem rot and others. SM-90 is prepared from natural plant oils and is completely non toxic to humans, animals or of course plants. It is totally biodegradable and environmentally friendly.
Application rate: Dilute 1 part SM-90 with 5 parts water to prepare a concentrate spray. Apply directly to affected areas of plant leaves, stems. Treatments may be repeated twice weekly until infestation is eliminated.
For treatment of insect infestation:
When applied directly to foliage or grow mediums SM-90 is an effective agent to discourage and eliminate many common pests including aphids, thrips, spider mite, and whitefly, etc. It is believed to act as a systemic to inhibit insect colonization and to deter reinfestation.
Application rate: Dilute 1 part SM-90 with 5 parts water to prepare a concentrate spray. Apply directly to affected areas of plant leaves, stems, or roots. Treatments may be repeated twice weekly until infestation is eliminated.
Additional Benefits:
Controlled lab and greenhouse tests revealed an unexpected benefit that was observed with the treated subjects. Results indicate that SM-90 dramatically increases the transpiration rate which improves the plants water and nutrient uptake capability. The plants treated consistently used 30% more water and nutrients than the control plants. This would result in an increased metabolism and accelerated growth rate.