How to Keep Seedlings From Dying: 10 Mistakes to Avoid


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Starting seeds is not as easy as putting seeds in the ground. Seeds are like small miracles – they contain within them the power to transform and grow into a beautiful plant if we give them the right conditions. Most gardeners will kill a lot of seedlings when first starting out – it’s a process of trial and error. But they soon come to learn there are a number of things to get right.

Seedlings need four essential things to thrive: the right amount of moisture, the right amount of light, the proper size of module trays, and a good starting mix. Besides good watering habits, you need soil that is fluffy, retains enough water, has good drainage, and provides the necessary nutrients.

If you go wrong with even one of these basic necessities, your plants will not have a good start. That could translate into slower growth, becoming more susceptible to pests and disease, or worst-case scenario – even dying.

But once you learn about all these mistakes to avoid, you’ll surely do a great job at keeping your seedlings alive and thriving.

1. Avoid losing your seedlings to damping-off disease.

Damping-off is a fungal disease that affects seedlings in their early stages, and either prevents them from germinating or weakens them right after germination. It’s caused by certain fungi such as Rhizoctonia solani, Fusarium, Phytophthora, and Pythium that contaminate the soil, the seeds, or the tools that are used when starting seeds.

Although fungi are likely present in the growing medium most of the time when we’re starting our seeds, they won’t be causing damping-off disease unless certain conditions are met.

Damping-off occurs when the soil is wet and cold, with improper drainage. It can also happen if the soil is too dense, and the seeds are planted too deep. But mostly, poor air circulation, lack of air within the soil, and high humidity will cause your seedlings to die from this fungal disease.

Seedlings that are damping-off are affected at the base of their stem as if someone pinched them. Regardless of how well they grew previous to damping off, they will suddenly fall over and die. When inspected, the base of the stem will look narrow and wilted, while the seedling’s root will look weak and thin.

Can seedlings suffering from damping off be saved? Unfortunately, once they become affected, they can’t be recovered. You will have to start over. That’s why it’s better to prevent this problem in the first place. Before reaching out for fungicides, make sure you avoid the mistakes that lead to damping off in the first place:

  • Get good soil: a sterile starting mix that is fluffy and light is best;
  • Sow your seeds shallowly on top of moist soil;
  • Don’t overwater – instead, allow the topsoil to dry out a little;
  • Water from below, but don’t overdo it;
  • Place seedlings in a well-ventilated area.

2. Avoid using any type of soil as a starting mix.

Not all soil is created equal. I made many mistakes when first starting seedlings because I wasn’t satisfied with the regular big-box store starting mix. I used regular soil from the garden and aged cow manure with little success because that soil was dense and contaminated.

Starting mixes are different than normal potting soil because they have to provide the perfect conditions for seeds to germinate and thrive in their first weeks of life. For this reason, your starting mix needs to be:

  • sterile
  • fluffy
  • absorb and retain enough moisture
  • but drain the excess moisture
  • nutritious

Let’s start with sterile: you can easily get sterile soil from any packaged starting mix, but you can still make your own by mixing in your own soil and sterilizing it inside an oven. However, I don’t recommend doing that inside the kitchen, as your whole house will smell like dirt for days.

Your starting mix should be fluffy in order to provide roots with enough oxygen, which is essential to their development. For this reason, all starting mixes have a certain amount of peat moss or coco peat. Peat moss and coco peat are inert fibrous materials that help create layers of soil around the seedlings’ roots.

Fibers like peat moss are also great at retaining just the right amount of moisture, while non-organic minerals like perlite and vermiculite ensure good drainage.

Starting mixes don’t necessarily need to be nutritious in the first stage of germinating seedlings, as the seed, just like an egg yolk, has enough nutrition to sustain growth at first. But just as soon as the first true leaves are emerging, the seedlings will need more nutrition.

You can have nutrients readily available in the soil by mixing 3 parts of the starting mix with one part of vermicompost. Or you can skip this step and fertilize your seedlings with various organic options: fish fertilizer, fish & seaweed fertilizer or earthworm tea.

3. Make sure you get the temperature right for germination.

While seedlings can withstand temperature variations – especially the cool-weather crops – seeds are very sensitive when it comes to germination temperatures.

Too hot for cold-loving plants and they won’t germinate, and too cold for heat-loving plants and they will refuse to sprout. Quality seed packages should have a lot of information about caring for the plant, including germination temperature because not all plants need the same conditions.

Most seeds will germinate between 68°F(20°C) to 86°F(30°C), with cold-loving crops such as carrots and cabbage germinating at temperatures as low as 45°F(7°C). The colder the temperature, the longer it will take seeds to germinate.

But what if you’re starting your seeds indoors and you need a lower temperature to germinate certain seeds (like lettuce for example) and higher temperatures for other seeds such as peppers, eggplants, and tomatoes?

You can start these seedlings in the same room, set a lower temperature, and supplement the heat-loving seeds with a heat mat underneath their trays. This way you get the best of both worlds.

4. Don’t start your seedlings on a windowsill, they WILL get leggy.

You’ve probably heard the advice of starting your seedlings on the windowsill of a south-facing window. But for most climates, if you’re starting seeds very early, that’s just not feasible – there isn’t enough sunlight.

The seeds will germinate and grow, but the seedlings will develop very long stems and stretch towards the window. Gradually, they will grow so long that their stems will become very weak and unable to sustain the leaves, causing your leggy seedlings to fall over and die.

You can still save leggy seedlings by delicately pricking them out (using a knitting needle or a chopstick) and planting them deep in another starting cell. But that requires a lot of work, and for a lot of seedlings, it’s just not worth it.

So how do you get your seedlings to grow short, stocky stems from the first try? You could wait until the weather conditions are right and either sow them directly or start them inside trays under the protection of a cold frame or greenhouse.

If you choose to start your seeds indoors, you need to supplement the natural light with grow lights. These can be either fluorescent or LED.

Fluorescent lights have worked well in the past, but they consume too much electricity and give out quite a bit of heat. LED lights are far more efficient, and they supply the plants with the light intensity and spectrum they need.

Not all lights are created equal, though, so do your research before buying. These are the lights that I use and love, their intensity is dimmable – perfect for each stage of seedling growth.

Don’t forget that, even though they require at least 14 hours of light per day in order to thrive, seedlings also need a period of darkness to rest.

5. Moisten your soil but don’t water-log it.

Temperature is not the only thing that seeds need for germination – it’s a combination of heat and moist soil. Your watering habits should adapt according to what stage your seedlings are in. That’s why, when first starting your seeds it’s best to pre-moisten your starting mix.

Keep the top surface of the soil moist by spraying it regularly (about twice a day) until seeds germinate. You can also cover the soil with a plastic lid to prevent evaporation. Some gardeners put plastic wrap on top of their soil until seeds germinate.

After the seeds germinate and the seedlings are starting to grow, you should water the seeds from underneath, by pouring small amounts of water inside the seed tray. It’s best to water seedlings from below to avoid damping off.

Water your seedlings only when the topsoil is starting to dry off a little bit, and don’t let too much water accumulate inside the tray.

Watering your seedlings from above isn’t necessarily a bad practice, but it’s best to save this method for when the seedlings are older and sturdier.

6. Don’t forget to water – seedlings are like babies.

On the opposite side of the spectrum – you could go wrong by not watering your seedlings enough. This usually happens if you go away for a couple of days, or if the environment in which you keep your seedlings (a cold frame, for example), gets too hot and the soil quickly dries out.

At this stage, seedlings are like needy babies. Too much water will drown them just as much as too little water will dry them up.

If you ever have to leave home, even having friends who have no idea what they’re doing water your plants can destroy an entire batch of seedlings. That’s why many gardeners choose to stay home during the essential spring months.

Another reason why soil might dry out too quickly even if you make sure to water your seedlings daily is not having deep enough module trays. This leads us to the next point.

7. Don’t choose module trays that are too small.

You really can’t go wrong with choosing larger module trays – the only downside to them is wasting too much space. But you can definitely go wrong by going too small.

When starting seedlings for the first time, it’s tempting to choose the smallest module trays possible. This way you can maximize space and grow lots of seedlings. That was one of the first classic mistakes I made when first starting seedlings.

Small modules in combination with poor starting mix resulted in soil that was either too dry or soaked in water, and it varied greatly throughout one day. Combine that with a poorly ventilated cold frame that got too moist during cloudy days and too hot during sunny days, and only a third of my seedlings ever survived.

I recommend choosing trays with cells that are at least 1.5″ square and 2″ deep. These 72-cell plug trays are a popular choice. I recommend buying trays that are sturdy and thick to last you many years, instead of going for a cheaper but flimsier option.

8. Avoid keeping your seedlings inside modules for longer than 4 weeks.

Even with a generous-sized module tray, seedlings can grow and become rootbound over time. As the roots grow and no longer have room to expand, the plant’s growth will become stunted.

You can check if this is the case by gently removing the soil from the module and check to see if you’re seeing lots of root growth outside of the soil.

You can prevent stunting your plants’ development by doing one of these two things:

  • Wait a few more weeks before starting your crops, even if you’re tempted to start them now;
  • Start your seeds early, but pot them on as they grow and occupy the soil.

You have lots of options for moving your seedlings to gradually larger pots. This works well if you want to get a head start on plants like tomatoes, peppers, eggplants, or chilies. You can do the same for crops like cabbage, which are easy targets for pests when they’re small, frail seedlings, but as they become larger, they will no longer become affected.

9. Don’t keep too many seedlings inside one module.

You might think that keeping more seedlings in one module will increase the chance of getting at least one sturdy seedling. And that’s not entirely wrong. There is such a thing as multi-sowing, where we grow vegetables in clumps, and certain plants thrive with this method.

But even with multi-sowing, there are limitations – anything more than 4 seedlings for root crops, and 6-8 seedlings for greens is probably not a good idea. For larger plants, two seeds are the maximum I would recommend sowing inside a module.

So what happens if you’ve been generous with your seeds when sowing, and now you have a dense forest of seedlings? Don’t pull them, you don’t want to disturb the remaining seedling. Instead, pinch them at the base or cut them with fine scissors. This will leave you only with the seedlings you need, and you’ll avoid crowding, competing for nutrients, and becoming rootbound.

10. Don’t forget to thoroughly harden off your seedlings before planting.

Your seedlings have now formed their true leaves, they are about 4 weeks old or older, and they’re ready to go in the garden. It’s beautiful and sunny outside, and you’re impatient to transplant everything. Not so fast!

If you’ve started your seedlings indoors, and you transplant them without any kind of preparation, they will all die. They’re not yet used to the wind, the cold, the powerful light from the sun, and the temperature variations.

Here’s what you can do to ensure successful transplanting of your indoor-started seedlings:

  • when growing your seedlings, regularly run your hand through them or set up a fan to get them used to winds and movement;
  • harden them off by taking them outside 7 days in a row: starting with one hour per day, and increasing one hour each day;
  • transplant your seedlings on an overcast day, or in the evening, to give them a better chance to get established in the soil overnight, before the sun starts blazing;
  • if the danger of the frost hasn’t passed, keep all your seedlings covered with at least a layer of fleece until the last frost day.

Takeaways

Hopefully, you got the chance to read this before starting your seeds this year, but if you haven’t, all hope is not lost. Aside from damping off, you can still fix seedlings that are leggy, dried, and lacking nutrients, or have stunted growth.

Just remember to avoid these 10 mistakes:

  1. Avoid losing your seedlings to damping-off disease;
  2. Avoid using any type of soil as a starting mix;
  3. Make sure you get the temperature right for germination;
  4. Don’t start your seedlings on a windowsill, they WILL get leggy;
  5. Moisten your soil but don’t water-log it;
  6. Don’t forget to water – seedlings are like babies;
  7. Don’t choose module trays that are too small;
  8. Avoid keeping your seedlings inside modules for longer than 4 weeks;
  9. Don’t keep too many seedlings inside one module;
  10. Don’t forget to thoroughly harden off your seedlings before planting.

I know this is a lot to keep in mind, but it’s easier than it seems. See it as problem-solving and a learning experience, and most importantly, don’t stress if you lose some of your seedlings. You can always start over.

Check out these must-have gardening products

You don’t need much to start gardening, but some tools and products will make a difference in how comfortable and effective gardening can be for you. Here are my favorites:

  • Garden Trowel. A good garden trowel will last you many years. I love how sturdy this hand trowel from WOLF-Garten is, the metal doesn’t bend and it has a nice grip.
  • Trimming Scissors. I use them for delicate pruning and harvesting all summer long, and they’re super handy. These Teflon Trimming Scissors are extra nice because they don’t rust as easily.
  • Dutch Hoe. Dutch hoes may seem old-fashioned, but there’s nothing like a quick sweep through the topsoil to get rid of small weeds – no bending required. I love WOLF-Garten’s selection: this dutch hoe coupled with their universal handle.
  • Grow Lights. These grow lights from Mars Hydro are super strong, yet dimmable, so they fit every stage of growth. They don’t put out too much heat and are very economical.
  • Seedling Trays. There’s an art to choosing the best size for seedling trays so that it holds the perfect amount of water and gives the roots enough room to grow. These germination plugs are perfect when coupled with 1020 bottom trays
  • Liquid Fertilizer. You’ll need to feed your plants from the seedling stage, all the way to fruiting. This organic fish & seaweed blend is a very versatile option. Use it half-strength for young plants and full-strength for established plants.

Browse our list of tools, fertilizers & pesticides, indoor growing products and seed shop recommendations – we hope you find our selection useful and it saves you some time!

Adriana Sim

Hi, I'm Adriana Sim, owner of Tiny Garden Habit. I practice my green thumb in beautiful Transylvania, Romania, zone 6b. While my garden is not quite tiny, it's definitely compact and super-productive. You can grow a lot of food in a small space, and it's my mission to teach you how!

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