Starting Seeds Indoors - What Went Wrong?

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Lettuce seedlings

Watch our video for an easy method to successfully start seeds indoors and transplant them as they get larger, or read the article below for advice concerning common problems and how to avoid them.

Last night I dug through the recycling bin to find empty cans I could use to raise my little seed trays of cabbage and kale seedlings closer to the fluorescent light fixture meant to mimic the sun. Ideally, there should be no more than 2 inches (5 cm) between the bulbs and the newly emerged sprouts, and because my light would go no lower, I elevated the seedlings with a pedestal made from dog food cans.

This simple strategy was unknown to me as a beginning seed starter, and I saw my fair share of failures. Many of my seedlings fell over and died, while others suffered from crowding because I lacked the courage to thin them. Some malfunctions were not my fault, though it became my responsibility to set things right. In many ways, starting seeds indoors is like running a day care center. You do what you're supposed to do to take care of the little darlings, and then you must be ready to intervene when troubles arise.

Onion seedlings under grow lights

Stretched Out Seedlings

Vegetable seedlings started indoors hardly ever get as much light as they would like, even when grown beneath pairs of bright fluorescent bulbs. I monitor this situation closely and raise up seedlings or lower lights to keep seedlings from stretching toward the light, but they do it anyway. Beyond doing your best to satisfy your seedlings' hunger for light, you should anticipate seeing a short section of exposed basal stem on seedlings started indoors, as shown in the red chard seedlings at right. As long as the basal stem is never bruised or bent, slightly stretched seedlings will grow just fine if the stem is covered with soil when the seedlings are transplanted.

With my early efforts, the seedlings were so stretched out that they often fell over. This is not a terminal event unless the stem suffers a darkened bruise at the soil line. When the tender tissues on the basal stem are injured, the bruise often becomes a point of entry for fungi that cause the seedling to rot. The easiest way to change this outcome is to sprinkle dry seed starting mix around the base of the tilting seedling to help hold it aloft, perhaps propped up with a toothpick or two. Never touch the basal stem with your fingers; instead use the little seedling leaves as handles. If one breaks off it's no big deal, because plants have little use for their seedling leaves once the true leaves begin to appear.

Leggy chard seedlings

Too Many Seedlings

To a new gardener, every germinated seed is a miracle, and the thought of killing any of them feels wrong. But crowded seedlings rarely grow into healthy, full size plants, so they must be thinned or separated and transplanted – an operation often called pricking out. In my experience, it is better to use a small pair of scissors to snip out excess seedlings of lettuce, celery and most leafy greens when starting seeds indoors, because separating the fibrous roots leads to serious setbacks in the plants' growth. In comparison, onions and tomatoes seem to enjoy the pricking out process, and show new growth immediately after being moved to roomier quarters.

Stuck Seedcoats

The seedcoats of many seeds contain substances that become sticky when wet – a characteristic that helps seeds find firm anchor among soil particles. When sown outdoors in gritty soil, the seedcoat is scraped away as the seedling emerges, but sometimes the mechanics don't work perfectly when starting seeds indoors in seed starting mixes. Instead you see seedlings with the tips of their seedling leaves clamped together with a seedcoat that won't let go. Sometimes you can get the stuck seedcoat to soften by misting it with water, or you may resort to rescuing the chick by removing it with tweezers or your fingers. Just be careful not to pull on the seedling, which can do more harm than good.

Pricking out tomato seedlings

Bad Soil and Good Water

When you think you've done everything right and your seedlings just sit there, refusing to grow and looking sick and spindly, they may be suffering from substandard soil. Although it has not happened often, several times I have purchased bags of compost that would not grow anything and had to be discarded. When a whole tray of seedlings fails to grow properly, I transplant them into fresh compost as quickly as possible, and usually see a happy response within a day.

Watering can be a challenge when starting seeds indoors, and I think the best way to judge how much moisture is in a seed tray or container is to lift it up to check its weight. Those that feel light are in need of water, while saturated containers feel heavy. Most tap water is fine for seedlings, though switching to bottled spring may be helpful if you have a household water-softening system. The best seedling-growing setups include a waterproof tray so seedlings can be watered from the top and from the bottom. Alternating top and bottom watering gives the soil at the surface a chance to dry out, which limits opportunities for the worst diseases of seedlings started indoors.

By Barbara Pleasant

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Show Comments


"This is so interesting since I am about to start my seeds again. I've had mixed success, so these tips will help so much. Thank you!"
Connie on Monday 3 March 2014
" Thank you for the tips.. this will help alot..Jacqueline 3/3/2014 "
Jacqueline Johnson on Monday 3 March 2014
"Thank you for sharing such useful tips."
Murshidah Mustafa on Monday 3 March 2014
"Thanks for the comments, fellow greenies. We all have to start somewhere!"
Barbara Pleasant on Tuesday 4 March 2014
"Do you think I'll have any luck starting healthy seedlings with an LED fixture? I'm trying to reuse a fixture that we purchased for a fish tank and it's meant to help grow algae, so I thought it might. So far, germination has been successful, though the bulbs themselves don't generate any heat..."
Suzanne on Friday 7 March 2014
"Suzanne, as long as the LED aquarium fixture is a "daylight" type, meant to grow green plants, it is worth a try. Others described as blue emit a much narrower spectrum of light and would not satisfy the needs of most plants. "
Barbara Pleasant on Monday 10 March 2014
"I am having difficulty with my tomato seeds shooting and stretching. I mist three to four times a day, and everything looks great except the tomatoes and dukat dill. What am I doing wrong? Any ideas would be greatly appreciated. "
Heather on Friday 11 April 2014
"Misting can do more harm than good, because the leaves don't feel as compelled to do their job. Water only the roots for now, and make sure the seedlings are very close to supplemental light. Good luck!"
Barbara Pleasant on Monday 14 April 2014
"Thank you am excited to wake up and start planting seeds again! You're so right I seem to have experienced these things you're saying...and yes am one of those who find it so hard to uproot a seedling thinking am hurting them! Thank you!"
chit Villegas on Thursday 19 March 2015
"I'd love to go and buy an expensive, ready-to-go growlight fixture, but my budget means I'm trying to rig up a DIY version. However the more I look into this, the more confused I'm getting! Exactly what sort of lightbulbs should I be looking for, please? I have read several conflicting pieces of advice - some say use 'daylight' bulbs some say 'blue', some expressly say NOT'blue' as it might be the wrong sort of blue..... Aaargggh! Is there something measurable such as a particular spectrum range or kelvin I should look for? Also where (in UK) is a good (cheap) place to find them please? "
Tina Staples on Sunday 22 March 2015
"Tina, the least expensive thing to use is 2-bulb florescent fixture. Many "shop lights" come with hanging hardware, which can be attached to the underside of a shelf. You can upgrade to more intense lights, including new LEDs, but people have been growing seedlings under cheapo florescent lights for decades."
Barbara Pleasant on Monday 23 March 2015
"Strongly recommend putting a gentle breeze, even just a half hour a couple times a day. Turn on a ceiling fan or an oscillating fan set several feet away. They dry out a little faster but also helps to prevent damping off and discourages stretching. As they get bigger, increase the duration. Also, don't keep too warm. It's better to have slower growth that's tougher. "
karenj on Friday 29 January 2016
"Nice article! I have started several 288 plug trays and all is up and going. When is the appropriate time to transplant these? When they get their second set of leaves? I just want to make sure I don't do it too early or wait too long and they die off. "
Lisa on Wednesday 16 March 2016
"Lisa, transplant time will vary with veggie, but generally that size plug is good for about 3 weeks after germination. After that, the roots will need more room. Good luck! "
Barbara Pleasant on Thursday 17 March 2016
"I planted two different types of tomatoes 2 years in a row now and one is a Roma type tomato and one a salad type. The Roma type in both years came up and just stayed little with the second set of leaves and just sat there never getting any bigger. Is it the seeds or what? I planted the other ones and beautiful plants growing like weeds. I planted both kinds the same way. What went wrong? Been planting for years and no problems untill the last two years. "
Kim on Saturday 15 April 2017
"Kim, I also have had tomato seeds I had saved go wonky for unknown reasons. Once a variety I had saved for years came up kinked and curled, except for a few plants. My theory is that sometimes things go wrong while the seeds are growing, and seeds from individual fruits can be flawed. Start over with a fresh seed supply of that variety to be sure of good genetics. Hope you have a great season. "
Barbara Pleasant on Sunday 16 April 2017
"Thanks for the tips. In addition to the issues you described, I see a leaf curl on eggplants, lower leaf wilting on tomatoes, and yellowing on the leaves of peppers. I see very teeny gnats too.Thoughts? thanks"
Sasha on Friday 16 February 2018

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