Why Are My Microgreens Collapsing at the Stem Base?

You check your microgreens tray and find clusters of seedlings lying flat — stems collapsed at or just above the medium surface, the tops of the plants still green and apparently healthy. This is damping off, a condition caused by fungal pathogens (most often species of Pythium, Fusarium or Rhizoctonia) that attack the stem at or near the medium level, rotting the tissue until the plant can no longer support itself and collapses. It can devastate a tray overnight and spread to adjacent seedlings within hours in warm, moist conditions.

What Causes Damping Off

The fungi that cause damping off are naturally present in most soil, growing media and growing environments. They become a problem when conditions favour their growth: persistent moisture at the medium surface, poor airflow, overly dense sowing and reused contaminated trays are the primary enablers. Pythium species, which are technically water moulds rather than true fungi, are particularly common in microgreens and thrive when water sits at the medium surface for extended periods.

Damping off most commonly strikes in the first 3 to 5 days after germination, when the stem is thin and tender and most vulnerable to pathogen attack. Young seedlings of basil, coriander, amaranth and beet are more susceptible than thicker-stemmed brassicas or large-seeded crops.

Prevention — The Most Important Approach

Since damping off is nearly impossible to reverse once it begins in a tray, prevention is the only effective strategy. The core principles mirror mould prevention: switch to bottom-watering only once seeds have germinated; ensure the growing space has passive airflow; sow at the correct density; and sterilise trays between crops with a dilute hydrogen peroxide solution (3%) or a bleach solution (1 tablespoon bleach per litre of water), rinsing thoroughly afterward.

Using a sterile, pathogen-free growing medium is also important. Fresh coco coir from a sealed bag or a sterile seed-starting mix is far less likely to carry damping-off pathogens than reused medium or garden soil. Never reuse growing medium from a previous tray that suffered damping off — it will inoculate the next tray.

What Happens to the Affected Tray

Unfortunately, a tray with active damping off cannot be saved. The collapsed seedlings are dead and the fungal mycelium is already present in the medium. Damping off spreads by contact and through the water in the medium, so affected patches will enlarge over the following 24 to 48 hours. If only a small corner of the tray is affected and the rest appears healthy, harvest the rest immediately and discard the affected area. If damping off is widespread, discard the entire tray, sanitise it, and start fresh with sterilised medium and clean seeds.

Dilute Hydrogen Peroxide as a Preventive Mist

Some microgreens growers use a single mist of very dilute hydrogen peroxide (1 to 3% solution — standard pharmacy concentration diluted 50:50 with water) at the point of sowing or during the blackout phase to reduce pathogen load at the medium surface. This is an optional preventive step, not a treatment. It is most useful for susceptible varieties or in setups that have experienced repeated damping off problems despite correct watering and airflow.