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Stunted seedlings: just the cold weather, or is there something more going on?

Authors: Natalie Hoidal & Marissa Schuh, UMN Extension horticulture educators

A cold, cloudy April is bad news for seedlings, and slow growth under these conditions is to be expected. However, there may be more going on if your seedlings are looking yellow and stunted. It can be hard to pinpoint the cause of stunted seedlings, so in this article we'll cover some issues we're seeing this season and how to identify them. 

Potting soil issues

Potting soil can have a major impact on the health of your seedlings. The physical make-up of it (e.g. the ratios of peat to bark to compost to perlite, etc.) impacts water holding capacity, and even minor shifts in composition can mean that growers need to change their watering routines to avoid drying out or over watering. The chemical properties of your potting soil are also critical. Potting soils vary widely in their pH, electrical conductivity, and nutrient availability. Potting soil with very high electrical conductivity can negatively affect germination, a pH outside of the 6-7 range can make nutrients less available, and potting soil without enough fertilizer can lead to stunted plants. The UMN Soil lab offers potting media tests, which provide you with an overview of the pH, soluble salts, and levels of nitrate, ammonia, phosphorus, potassium, calcium, magnesium, sodium, iron, manganese, zinc, copper, molybdenum, and boron in your potting soil for $25. The lab also provides a guide to what is considered sufficient for growing seedlings so that you can identify deficiencies and correct them with supplemental fertilizer before planting. Private soil testing labs offer this service as well. 

If your potting soil supplier cannot provide you with a test or some verification of their product, it's a good idea to test your potting soil every year, especially if you are growing a large volume of seedlings. The same product can vary from year to year, and it's better to be informed up-front than to find out a month into the season that your soil is deficient in a key nutrient.

I have heard from dozens of growers this fall that their seedlings seem stunted beyond what would be considered reasonable for a cold spring; many of these growers have also had yellow leaves on their seedlings. A few have tested their potting soil and found insufficient nitrogen.

Onions are often the first plants to show symptoms since they are planted so early. Yellow leaves and dying tips are a sign of nitrogen deficiency. 

Photo: Rodrigo Cala

Cabbage and other Brassicas are also quick to show nitrogen deficiencies. The photo below is not a seedling, but it displays chlorosis (lack of green pigment) and stunting. The purplish color of the leaves could either be the variety, or a phosphorus deficiency, which is common in cold spring soils and not necessarily indicative of insufficient soil P.

Photo: Rasbak, Wikimedia Commons

What can you do about it? 

Our colleagues at Purdue have been studying how growing media affects transplant health for a few years. One of their primary takeaways has been to confirm that adding fertilizer to potting soil can have a significant effect on plant health, especially when the potting soil is low in nutrients to begin with. 

Some options for adding fertility to your potting soil include: 
  • Incorporating a solid fertilizer like composted manure prior to filling flats
  • Top dressing at emergence
  • Using a liquid product like fish emulsion (or, our Purdue colleagues used EnviroKure, a liquid emulsion of chicken manure, sodium nitrate, bone meal, and sulfate of Potash) after emergence

Keep in mind that fertilizer often increases the electrical conductivity of your soil, and it is absolutely possible to over-fertilize your seedlings. Given that seedling trays contain a very low volume of soil, a little bit of fertilizer goes a long way. Over-fertilization can result in lower emergence, "burned" seedlings, and in some cases, higher disease pressure. A media test will help you to make an informed decision about how much fertilizer to add. 

To read more about the work our Purdue colleagues are doing, check out: 


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. Especially in cold, cloudy weather, seedlings don't use much water on a daily basis.

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.

Seedling diseases

The cold April has also created ideal conditions for many of the pathogens that attack seedlings. Plants are growing slowly, which can prolong the period during which they are exposed to diseases in the transplant house. If you are seeing yellow, unhappy seedlings, here are some things to think about.

Plants melting down? Look into damping off

There are a couple of pathogens that cause plants to damp off. When plants are growing slowly in cold, damp conditions, there can be a large window where plants are vulnerable to pathogens. If supply shortages led to the re-use of pots and trays, damping off is something to really consider. 

Damping off is causing brown, wilting stems and leaves in this tray of melon transplants. Photo: Gerald Holmes, Strawberry Center, Cal Poly San Luis Obispo,
Damping off might be the cause of transplant issues when the problem seems to start at the soil line. Seedlings with damping off often flop over or are described as “melting down.” Check out the roots of impacted seedlings to see if they are firm and bright (healthy) or mushy and brown (diseased). Stems may also appear thin and wiry.

For more information on damping off, see the UMN page on preventing seedling damping off.

Seedlings discolored and distorted? Look into viruses

If what you are seeing is going beyond leaf yellowing, especially if you are seeing crinkled leaves or distorted growth, consider plant viruses. There are many vegetable viruses, which in the greenhouse can be moved around by aphids or thrips. For more information on viruses in transplants, see “Virus issues? Take a look at transplant production.”

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