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Good Seeds Gone Bad

It can be so frustrating to put in the effort to start seeds, only to encounter lack of germination or death of a seedling soon after. Here are 5 common problems and insights.

Problem #1: Seeds do not germinate or sprout

First, make sure you are patient enough to wait the expected number of days to germination. Some seeds can take up to 14 days to germinate.

If that time frame has passed, assess these important factors:

  • Depth of seed: did you plant the seed at the appropriate depth? Seeds planted too deep can expend their stored energy trying to reach the surface to sprout.

  • Water: Were the seeds kept moist the entire time? If seedlings begin to germinate, but then dry out, they can die.

  • Temperature: was the soil kept at the minimum required temperature to germinate? I really suggest using a soil thermometer to monitor soil temperatures and adjust them as needed.

  • Age and germination rate: if you met all these factors, but your seed still did not germinate, the age of the seed or germination rate could be the problem. In which case I would suggest buying new seeds from a quality source or keep trying. Strive for progress not perfection.

Problem #2: Seedlings emerge, then quickly die

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If a seedling emerges and then falls over at the base and dies, it is likely due to a fungal disease called dampening off. This disease thrives in overly moist conditions with poor air circulation. Unfortunately their is nothing you can do to resuscitate the dead seedlings, but here are some solutions to prevent this from occurring again:


  • If you are reusing pots or trays, sanitize them with a 10% bleach solution before planting.

  • Use a sterile, peat-based seed starting mix. Peat-based mixes have a natural fungicidal property that reduces the chance of this pathogen.

  • Provide good air circulation. This may mean setting up a fan near your seedlings.

Problem #3: Seedlings get long, leggy stems

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Thin, weak stems with large gaps in between leaves is a sign of inefficient light.


  • If your seedlings are in a windowsill and appear this way, it is time to invest in an artificial light source (T8 shoplights or LED Lights)

  • If your seedlings are under grow lights and appear this way, you need to adjust the height. Grow light should be adjusted to 4 inches above seedlings.

Problem #4: Soil develops algae or mold

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If mold or algae is growing on the surface of the soil, but doesn’t seem to be affecting the plants, the likely cause is overwatering or not enough air circulation.


  • Wait until top of soil appears to be drying out before watering again and set up a fan near your seedlings to improve air circulation.

  • A sprinkle of cinnamon on the soil surface can also help inhibit growth of the fungus.

If the leaves of your plants become slimy or fall off, it is likely botrytis and you’ll need to toss the tray and start again.

Problem #5: Seedlings become discolored

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Discolored leaves can mean they are nutrient deficient.

Pale yellow: nitrogen deficient

Bronze edges: potassium deficient

Purple underside: phosphorus deficient

Solution: Use a mild fertilizer on your seedlings once they have their second set of leaves. A small amount of fish emulsion and liquid seaweed should do the trick. Each brand is different so follow the instructions on the label for best results. Careful of the backsplash, this stuff STINKS!!

Last year my snapdragon leaves were yellow with green veins indicating they were iron deficient. The iron was bound up due to the high pH of the soil. So I had to supplement with iron chelate.

Seed-starting isn't fool proof. Don’t be discouraged if you encounter these problems. I have dealt with my fair share of them and because of it, I learn and improve each gardening year. I'm here to encourage you, to celebrate the lessons learned, and strive for progress, not perfection.

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