Why Are My Seedlings Collapsing at the Base? How to Stop Damping Off

You sow seeds, they germinate beautifully, then within days the stems pinch at soil level and seedlings topple over one by one. This is damping off — a fungal disease that spreads rapidly through overcrowded, wet, poorly ventilated seed trays. It is one of the most demoralising problems in indoor seed starting, but it is almost entirely preventable.

What Causes Damping Off?

Damping off is caused by a group of soil-borne fungi and water moulds — principally Pythium, Rhizoctonia, and Fusarium species. These organisms thrive in exactly the conditions that seed trays often provide: high humidity, warm temperatures, poor airflow, and wet compost. They attack the stem at or just below soil level, rotting through it so the seedling collapses. The disease spreads through water, so once one seedling is affected, the whole tray is at risk.

Immediate Action: Remove Affected Seedlings

As soon as you see collapsed seedlings, remove them immediately and dispose of them — do not compost them. Open any propagator vents fully or remove the lid. Reduce watering immediately and allow the surface of the compost to dry out between waterings. Improve airflow around the tray by moving it to a less enclosed space. A small fan running on low nearby makes a significant difference.

Prevention Step 1: Use Sterile Seed Compost

Branded seed compost is heat-treated to kill fungal spores. Garden soil, reused potting compost, or homemade compost all carry damping-off fungi. Always use fresh, sterile seed compost for indoor sowing — it is the single most effective prevention step.

Prevention Step 2: Don't Overwater

Water from below, allow the surface compost to dry slightly between waterings, and never leave trays sitting in standing water. After germination, remove the propagator lid progressively to reduce humidity.

Prevention Step 3: Don't Sow Too Thickly

Overcrowded seedlings restrict airflow between stems. Thin seedlings as soon as they are large enough to handle, leaving space for air to circulate. Sow in modules rather than flat trays to automatically space seedlings.

Prevention Step 4: Use Copper or Chamomile

A weak chamomile tea solution watered over seedlings has mild antifungal properties and is used by many organic growers. Copper-based products (available at garden centres) also suppress damping-off fungi and are approved for organic use.