Troubleshooting seedling issues

Author: Natalie Hoidal, University of Minnesota Extension Educator, Local Foods and Vegetable Production, with input from members of the Great Lakes Vegetable Working Group

Originally published 2021, updated 2025.

While we hope your seedlings are healthy and vigorous, some of you are likely seeing some common problems such as seedling collapse, or tall, spindly plants. This guide is meant to help you troubleshoot issues. 

Poor germination

If your seedlings simply are not germinating, the most likely cause is salts. Some potting mixes contain very high concentrations of salts, which inhibit germination. If you're making your own potting mix, applying high rates of potassium, blood meal, or other fertilizers can lead to high salt concentrations. To confirm that this is the problem, or to test a new potting mix before planting, you can always submit a potting soil sample to the UMN soil lab (click on Testing Services --> Greenhouse, Florist, & Nursery Tests, and select a soil/media test).

Seedlings collapsing from the top & experiencing leaf wilting

The seedlings in the photo below are tipping over from the top; a condition known as epinasty. Epinasty occurs due to the generation of ethylene gas, which happens when the root zone becomes hypoxic (oxygen-limited) due to overwatering. This condition can be a bit misleading, because it can look like wilt, which may cause you to want to water even more! Many people think they need to water seedlings daily, but that’s often more water than your plants need. Especially when plants are small, their root systems are not yet developed, and they will not take up very much water. Keep your soil moist, but try to avoid soaking it. As your plants’ root systems develop, they will take up more water each day.

If the leaves are wilting, they may also be wilting due to a lack of water - monitor your soil to ensure that it is moist at all times, but not water-logged.

Overwatering can happen even to experienced growers. Your potting mixture will determine how well water drains from your system, so every time you try a new potting mixture (or sometimes companies change their mixtures without notifying customers!), you’ll need to adapt your watering regime.

Photo: Chris Barth, epinasty and stretched seedlings

In rare cases, epinasty can occur due to gaseous ethylene injury. If you heat your germination chamber, high tunnel, greenhouse, or basement (wherever you start your seeds) with propane or natural gas and you start to notice epinasty, check to make sure that the heat exchanger in your heater is working properly. If your heater is releasing unburned gas, your seedlings may react. Consider your plants the canary in the coalmine; unburned gas is potentially lethal to people too. 

Damping off

One of the most common problems affecting seedlings is damping off. This problem is caused by a number of pathogens including Rhizoctonia spp., Fusarium spp., and Pythium spp. This condition typically results in seedlings collapsing at the base of the stem, and you can often see fungus growing where the stem meets the soil. Seedlings infected by damping off rarely survive. To avoid damping off, clean all of your potting media (trays, pots, any tools) thoroughly with soap and water. Follow with a sanitizer. Only work in your seeding area with clean hands and tools, and use sterile potting media. More info about damping off.

Photos: Michelle Grabowski, damping off

Tall, spindly seedlings

Are your seedlings looking leggy? “Legginess” in seedlings is caused by low light, as plants stretch to reach a light source. Eventually this will result in weak stems, and the plant will struggle to support itself. If you’re not already using supplemental lighting, consider adding some. If you have artificial lights already, try moving them closer to the plants or adding more / stronger bulbs.

Light stress can also occur in the germination chamber. Many farms do not provide light in their germination chambers because it’s not necessary for germination. However, the window for certain crops between germinating and needing light can be slim; take care to move emerged seedlings into a lighted area quickly following germination.

If plants become stretched due to insufficient light, they can collapse with even a little bit of over or under watering. Stretched seedlings are also more susceptible to damping off. 

Insect damage

If you’re seeing small dots on your plants such as those in the photo below, check for the presence of small insects like fungus gnats. These insects typically show up when you have wet, exposed soil. Adapting your watering routine to avoid over-saturating your soil should help to minimize insect problems. Adding a fan to promote good ventilation should also help.

Photos: Chris Barth, fungus gnat damage

 

Slow growth, yellow leaves

If your seedlings have been very slow to grow and you're noticing yellow leaves, you likely have a nitrogen deficiency. Onions and Brassicas tend to be quick to show nitrogen deficiencies, so look to these crops as indicators. While many potting soils have the opposite problem (too many nutrients & high salts), we occasionally see potting soil that just doesn't have enough nutrients to keep plants going, especially in years like this one where growers may be holding transplants in the greenhouse a little longer due to cold temperatures outside. 

Image: Rodrigo Cala, nitrogen stressed onions

Are you having any other problems with your seedlings? Feel free to post comments and ask more questions in the chat below! You're also welcome to reach out directly with questions: hoida016@umn.edu