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How to Solve Common Seed-Starting Problems

Renee Valdes
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How to solve common problems when seed-starting ll The Home Depot Garden Club

Seed-starting indoors can be rewarding and fun. It doesn’t take much time and it’s fairly simple once you collect the seed-starting supplies. But what happens when you encounter problems along the way while seed-starting?

Seed expert Robin Ruether with W. Atlee Burpee Seed Co. helps solve common seed-starting problems you may encounter while starting your garden indoors. Read on to see what she suggests about starting seeds.

How to Solve Common Problems when seed-starting


Burpee seed-starting kit makes seed-starting a breeze ll The Home Depot Garden Club

PROBLEM: My seed(s) did not germinate.

SOLUTION: There could be a lot of reasons for why flowervegetable and herb seeds don’t germinate. These are the common solutions.

  • Plant at the right depth. Many seeds don’t need to be planted too deep in the soil. You’ll want to read the seed packet to get the correct depth.
  • Use fresh seeds or test old ones first. It’s true that some seeds can be long-lived, but it’s anyone’s guess if old seeds will germinate. All seeds from Burpee packets come germination-tested and are considered fresh for that year only. However, some people don’t plant the full packet of seeds and save the packets for the following year and beyond. How the seed is stored can affect the germination. For example, maybe you stored the seed packets outside in the shed, where it got hot and damp. Seed should be stored in a cool and dry place for the best viability. Because it can delay your garden if your seeds don’t germinate, try a simple germination test first. Put a sample of seeds in a folded wet paper towel in a plastic bag. Keep in a warm place and monitor it over the course of a week or two. If a high proportion of the seed cracks open, plant the rest of the packet. You can sow more than one seed per pot to ensure you’ll have something growing. However, as a guide, use fresh seeds for better rates of success.
  • Pot seeds with proper soil. When seed-starting, you can’t just go into your yard and dig up dirt. When you start seeds, you need fresh seed-starting mix or a soilless media that drains well and doesn’t carry any fungus and disease. 
  • Balance watering. If your seeds get too much or too little water, it can affect how they grow. When you start your seeds you want the soil to be moist, but not too wet and not too dry. We like the Burpee seed-starting kits because there’s a self-watering mat enclosed. Essentially, you can fill the tray with water and it keeps the potting soil moist but not saturated. The soil wicks up as much water as it needs. Even if you don’t have the self-watering kit, it’s a good idea to keep your pots in a tray and using a watering can or other vessel, add water to it from the bottom. That’s so you don’t disturb the delicate seedlings. Just be mindful not to overwater this way.
  • Consider temperature. Why your seeds may not germinate could be related to soil temperature. Seeds need a warm, even temperature, usually about 70 to 75 degrees Fahrenheit. To help your seeds germinate, you can use heat mats that will keep them warm. Some like to start seeds on top of the refrigerator or in another warm spot. Just be sure to check them frequently.

Seedlings | The Home Depot's Garden Club

PROBLEM: My seedlings are too spindly or leggy.

SOLUTION: Once your seeds sprout and you remove the greenhouse cover from the seed kit, if you’ve used one, several other common problems can happen, including when your seedlings aren’t growing thick stems and they’re too spindly or leggy. Here’s how to solve those problems.

  • Add light. Inadequate light is the most likely cause of leggy seedlings. Try using a grow light. You can set the grow light on a timer so that the seedlings get 16 hours of light a day and take a rest for the night. Place the light close to the plants, just 3 to 4 inches above them, and adjust as the seedlings grow taller. If you don’t have a grow light, place the seedlings in a south facing window and turn them every few days, but realize that the sunlight is weaker in the winter and it can be cold by the glass. Grow lights ensure your plants get the light they need, regardless of the conditions outside. 
  • Thin your seedlings. This is a hard step for many gardeners to do but if you thin your seedlings, they won’t need to fight for water or nutrients. To thin seedlings, simply use micro snip pruners to cut the stems at ground level of all but one plant per cell. Or, if you want more plants wait until they have one to two sets of leaves and gently uproot them, tease them apart and transplant them into their own containers. Tip: For certain plants like chives, it’s okay for several plants to grow together in a cell or tray.
  • Turn on a fan. A lack of air flow can contribute slightly to floppy seedlings. Wind helps make stems strong, so by turning on a fan (set to low setting) or using your hands to occasionally brush the seedlings, you can mimic naturally occurring breezes. For fun, you can talk and play music to them, as studies have shown that the vibrations can help plants grow.

PROBLEM: The seedling leaves don’t look very green.

SOLUTION: As your seedlings are growing, you may notice some leaves aren’t a healthy green, especially on certain types of plants like tomatoes. Your solution for this is plant fertilizer. Choose a well-balanced fertilizer and read the label for instructions. Usually, when seedlings are small you use a light dose of fertilizer once a week. As seedlings get bigger, use a larger dosage.   

Seed-starting problem solvers ll The Home Depot Garden Club

PROBLEM: My seedling grew but the stem tipped over near where it touches the soil and the plant died.

SOLUTION: There is a disease called damping off that can attack a growing seedling, causing the stem to rot and tip over. This can be caused by using the wrong soil or trays that already had the fungus or mold on them. Overwatering and cool temperatures contribute to the disease. If this happens, remove the affected seedlings and throw them away. For those not affected, let the potting soil dry slightly in between waterings and put a fan on to create good air circulation. This can help prevent the fungus from spreading. Use sterile potting soil and trays and follow the above tips on temperature and light to keep future seedlings healthy.

PROBLEM: There’s mold on the soil beneath my seedlings.

SOLUTION: If you see mold or algae growing on top of the soil, it usually is not fatal. You can start by physically removing the mold and letting the soil dry out slightly between waterings. Another solution is to put a fan on near your seedlings for air circulation. The mold will not kill the seedlings, but the excess water and poor air circulation that cause it can.

Harden off seedlings and other season-stretching tips | The Home Depot's Garden Club

PROBLEM: You set your seedlings outdoors but the plants flop over or burn up.

SOLUTION: Check your weather forecast. Your seedlings could be set back by cold temperatures or perhaps they flop over because the stems are not ready for that 10-mile-an-hour wind. Try acclimating seedlings to outdoor temperatures over the course of a week a few hours at a time, gradually building up to overnights. Set them in shade with not much wind. You can also place them in a cold frame or portable greenhouse to protect them from wind and the temperature. After acclimation, seedlings are ready for their final planting place.

Get more tips about starting a vegetable garden indoors.

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