Seedling stem pinched and collapsing at the soil line

Likely causes, most likely first

Ranked for this sign on its own. Your stage, medium and readings change the order, so run the checker for your plant.

1. PossibleDamping-off

   DiseaseAct within a day or twoRead: Damping-off: why seedlings collapse at the soil line

   Fix: A collapsed seedling can't be saved. For the rest: clean containers, fresh mix, warm medium (22-26 °C / 72-79 °F), water lightly, good light and airflow.

   Recovery: No further collapses.

   How to confirm it

   • Lift the pot and check moisture at depth. Lift the pot right after a full watering to learn its wet weight, then lift before each watering. Water when it is clearly lighter (about half the added water gone). Push a finger or a moisture probe 5 cm (2 in) down. Heavy for 3-4+ days with droop: overwatering. Very light with limp papery leaves: thirst.

2. PossibleFungus gnats

   PestLow urgencyRead: Fungus gnats: the watering problem with wings

   Fix: Fix the watering first: let the top 2-3 cm dry. Then Bti drenches (larvicide), Steinernema feltiae nematodes or Stratiolaelaps mites; yellow cards for adults. Larvae chew seedling and clone roots and can open the door to Pythium.

   Recovery: Card catches fall within 2-3 weeks; no larvae under potato slices.

   How to confirm it

   • Sticky cards for 1-2 weeks. Hang yellow cards at canopy height and lay one flat on the medium surface; add blue cards for thrips. Count catches every 3-4 days. Rising counts of small dark flies at the medium mean fungus gnats; slender insects mean thrips; white wedge-shaped fliers mean whiteflies; winged aphids mean a colony nearby.
   • Potato slice test for larvae in the medium. Press 2-3 raw potato slices (1 cm thick) cut side down onto the medium surface. Lift after 2-4 days and look underneath: translucent larvae with shiny black heads are fungus gnat larvae.

3. Less likelyRoot rot (Pythium)

   DiseaseAct nowRead: Root rot and Pythium in cannabis

   Fix: Act now. Fix conditions first: solution at 18-21 °C (65-70 °F), strong aeration (6-8+ mg/L DO), no overwatering. Change the reservoir, trim dead roots with clean scissors, clean and disinfect the system. Then either re-establish beneficial microbes (Bacillus, Trichoderma; house-preferred) or commit fully to a sterile regime (e.g. dosed hypochlorous acid or peroxide). Isolate affected plants on recirculating systems.

   Recovery: New white root tips within 3-7 days and wilting stops; brown roots don't recover.

   How to confirm it

   • Look at the roots. Hydro: lift the net pot and look at the root mass in good white light. Containers: tip the plant out with a hand over the medium and look at the edges and bottom of the root ball. Healthy roots are white to cream with fine fuzzy tips. Brown roots whose outer layer slides off between the fingers leave a bare thread: rot. Firm, evenly tan roots with white tips in coloured solution are staining.
   • Smell test of roots, medium and reservoir. Smell the roots, the bottom of the root ball, the drain water or the reservoir up close. Healthy roots smell earthy or of nothing. A sour, rotten, swampy or sewage smell means anaerobic conditions and rot. In hydro, a slimy feel on the reservoir walls or tubing adds to the case.
   • Measure reservoir and root-zone temperature at the end of the light period. Measure the solution in the reservoir and in the root chamber or bucket, at the warmest time of day. Target 18-22 °C (64-72 °F). Above about 23-24 °C (73-75 °F), dissolved oxygen falls and Pythium risk rises; below 16 °C (61 °F) uptake slows.
   • Dissolved oxygen check. Measure DO with a meter in the root zone, or check the system: air pump running, stones bubbling evenly, return water splashing, no dead spots. Target 6-8+ mg/L. Without a meter: if stones are clogged or the pump is undersized for the volume, assume low DO.
   • Send a sample to a plant diagnostic lab. For rots, wilts, leaf spots and viruses you can't separate by eye, send a fresh sample (whole plant with roots or a wilting branch with healthy and diseased tissue) in a sealed bag to a university or commercial plant diagnostic clinic. Results in days to 2 weeks.

Look for

Thin, dark, water-soaked stem at the soil line on a fallen seedling..