Germinating Seeds

Understanding Damping-off When Starting Seeds Indoors

Primrose Creations | Damping-Off

You’ve got your seeds set and now comes one of many stressful points involving growing flowers and vegetables. You truly never know how things will turn out until the plants are transplanted into the ground and you get to the harvest stage. Before a plant can make it into the ground, it first needs to be germinated and cared for until it is strong enough to withstand the elements. In areas where the growing season is shorter, starting seeds indoors is the only way to have a harvest-able plant at the end of the season.

Having the proper amount of seed germination is essential for a profitable growing season. Especially when certain plants have a short window of time to work with. The best-case scenario is you start more than you need, they all germinate, and you have extra starts to sell! The worst-case scenario? Losing most if not all of the newly germinated seedlings to damping off.

What is damping off?

Symptoms of damping-off include thin and thread-like stems, failure of seedlings to emerge from the growing medium, and absent or stunted root growth.

Evidence of damping off

What are the signs of damping off?

An indication of a fungi attack is a radial occurrence of damping off. In some instances, this is not the case if contamination has occurred due to splashing irrigation water. Rhizoctonia solani infections are marked by reddish-brown to black lesions on the stems and roots causing soft stems. These seedlings also often fall over due to weak stems.

What causes damping off?

The fungi, Rhizoctonia spp. and Fusarium spp., along with the water mold Pythiumspp. are the most common pathogens responsible for damping off1.

fungus on seedling
Fungus attacking a germinating seed

The pathogens can be introduced into the seedling tray in several ways and are not limited to:

  • Use of contaminated garden soil when starting seeds inside in a warm and wet environment
  • Use of tools, growing medium, and containers from the previous season without proper sterilization
  • Using shared irrigation water with contaminated growing medium
  • Transfer of spores can be blown in or carried by insects such as fungus gnats

The development of diseases that are responsible for damping-off can occur when seeds are planted in a growing medium that is too cool for optimal germination. Pathogens thrive in cool and wet conditions. Cool temperatures also slow plant growth which allows these pathogens to attack a seedling in its weakest state.

Fungus on seedlings
Damping-off due to over-watering

Damping-off in cool and wet growing mediums is primarily due to the emergence of PythiumSclerotinia, and Phytophthora while Rhizoctonia, Fusarium and Sclerotium rolfsii are more likely to cause damping-off in warm and dry growing mediums2. The latter typically attack at the soil line and while the others attack below the surface.

While Rhizoctonia solani does not produce spores, it does thrive on dead organic matter. As the attacked seedling begins to die, Rhizoctonia solani can continue to live on its dead organic matter3.

If a seed germinates while environmental conditions are optimal for pathogen growth, the species Pythium is able to react and expel mold spores that attach roots within minutes3. This specific species is also known to produce asexual spores that leave the mold present regardless of temperature or moisture content making the use of unsterilized growing medium less of an option.

Thielaviopsis is another producer of asexual spores. Unlike Pythium, Thielaviopsis can survive in growing mediums for several years3. Regardless of how long these spores have been dormant, they will continue to germinate when optimal temperature and moisture levels are maintained.

Why seedlings?

Seedlings infected by organisms that cause damping-off rarely survive and often effects a large section of seedlings in trays.

The young leaves, roots, and stems of newly germinated seeds are the most susceptible to disease when emerging under environmental conditions that promote pathogen growth and attack.

How to prevent damping off

Damping-off is difficult to prevent or treat due to the responsible pathogens’ ability to survive for extended periods of time in soil and other debris.

Prevention of damping-off can be achieved by sterilizing all used pots, trays, and tools by placing them in a solution of 1 part bleach to 9 parts water for 10 minutes. Be sure to rinse your materials before storing them. If possible, use new potting mix when starting seeds. Sterilization of garden soils and compost is also possible if the medium is placed in an oven at 160*F for a minimum of 30 minutes. Optimal soil temperatures can be achieved by using heat mats under seed trays when beginning seeds indoors.

The only known method for reducing the spread of a pathogen attack is to allow the soil to dry out completely between waterings. To expedite this process, increase the temperature in the room or greenhouse, turn on a fan, and provide better drainage for the seed trays.

Sterilization and sanitation of all work surfaces, tools, and growing containers are important to prevent an attack by damping-off causing pathogens. These fungi and other organisms can survive in dust, contaminated growing medium, and growing medium particles left are used trays and pots. Removal of diseased plants also reduces the chance of a damping-off issue.

Sanitation is important because spores of the organisms that cause damping-off can survive in dust, planting medium, or soil particles in flats and pots. To reduce the survival of the pathogens, remove and discard diseased plants and sterilize containers.

Vermiculite on top of a growing medium keeps the medium moist for germination while preventing mold and algae growth by providing aeration above the soil line.

Can damping-off be a sign of other seedling growth issues?

Leggy Stems

Having long, skinny stems while starting seeds is an indication that light and temperature needs are not being met. Cool nights accompanied by warm days will often result in seedlings stretching and producing leggy stems. Reducing seedling stretching can be achieved by maximizing light absorption by lowering grow lights to 6-8 inches above the growing medium. The same can be said about water and temperature. The more consistent the temperature and moisture in the growing medium will reduce the occurrence of stretched seedlings. If leggy stems do occur, transplanting the seeding to a larger pot or directly into the ground will allow the root system to expand, supporting the stems and leaves.

Leggy seedling stems
Leggy seedling stems
Pest Infestation

The most prevalent pest to manage when starting seeds is the fungus gnat. The larvae prefer moist soils and feed on plant roots before becoming adults. Although the adults don’t fly or feed on plants, they do lay eggs in the growing medium which can cause an infestation if not managed properly. Maintaining proper moisture levels will cause larvae to dry out causing death and reducing damage.

To be successful this growing season and beyond, creating optimal germination conditions is essential. A heat mat provides warmth that the soil and seeds need, bottom watering ensures uniform water uptake while covering seed trays or pots with a plastic lid or sheet can increase the humidity that is important for some species. Seed depth is also of importance as some seeds require darkness for germination while others require direct sunlight and due best when placed on top of or just below the growing medium surface.

For more information about what seeds to start and when, click the button below for a downloadable chart.

seed starting chart
1, Grabowski, M. (2018). How to prevent seedling damping off. Retrieved from
2. Meadows, I., Sharpe, S., & Henson, M. (2017, December 6). Damping-off in Flower and Vegetable Seedlings. Retrieved from
3. Olsen, M. W. (2011, January). Retrieved from
Starting seeds indoors can make or break a growing season. Understanding damping-off could make the difference in your success this growing season!

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