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Common Seed Starting Issues - And How To Avoid Them!

We’ve all been there – a plant you’re particularly looking forward to seeing spring up just hasn’t, well, sprung. As with most worthwhile endeavors, planting seeds has the potential for heartbreak and this is especially true for indoor seed-starting. This artificial environment can cause stresses and problems rarely seen in the outdoor garden.

Now that many of your seeds may have sprouted already, here are four common indoor seed-starting diseases (and pests!) to watch out for, and what to do about them.

Before jumping in, it may be worth a quick recap of conditions needed for seeds to emerge and thrive in 7 Easy Step to Starting Seeds Indoors.

1. DAMPING OFF.   Damping off is by far the most common disease issue in an indoor seed-starting setup. Caused by a fungus, its hallmark symptom is a narrowing of the plant at the base—until it looks like floss—followed within about twelve hours by the collapse and death of the seedling.

Its main cause? Poor air circulation.

In our experience, it is possible to experience damping off at nearly any temperature between 55 and 85 degrees—so the problem can't be solved simply by heating up or cooling down the environment. The key to avoiding the disease is providing adequate airflow: leave indoor seedlings open to the larger room rather than enclosing them in any way, and if using a cold frame, provide adequate ventilation as temperatures permit.

Avoid overwatering at all costs! Once your seeds have germinated, their water needs decrease dramatically. While a nice, soaking wet flat can look attractive with its bright green sprouts against the dark soil, it is also a perfect environment for damping off. Of course, we are imperfect gardeners and we make mistakes, so if you find that you've accidentally soaked a flat, immediately set up a small fan to dry out the top half-inch of potting soil. If the surface is dry, damping off is very unlikely. (Watering from beneath is one way to achieve this, too. Also: note that seedlings grown in a well-ventilated cold frame are much less prone to damping off than seedlings grown in a room with basically still air, so it's worth experimenting with a cold frame if you never have before.)



2. LEGGINESS. Often those seedlings most prone to damping off (above) are seedlings that we'd also call "leggy"—stretched-out, pale, easily toppled seedlings that often open their cotyledons waaaay higher than they should. Legginess is the top problem of gardeners who start their seedlings on their windowsills. It is rare that a windowsill, even south-facing, can provide enough intense, direct sunlight to make for healthy seedlings. The result is young plants that stretch window-ward in search of more intense rays. The solution is either to provide artificial light for your indoor seedlings or to move your seed-starting setup to a protected location outdoors, either a cold frame or greenhouse. Providing light is usually the easiest solution, but just know that when we say provide light, we mean PROVIDE LIGHT. Drop that shop light fixture to within 1-2 inches of the soil at first, and then gradually elevate it so that it is never more than 1-2 inches from the top of the tallest leaves.

Already have leggy seedlings? Immediately do whatever you can to provide them with stronger light without exposing them to unprotected outdoor conditions. Leggy seedlings can sometimes be rescued but will be knocked down and likely killed if moved outside without some serious hardening off. If your seedlings are still young, it's usually wiser just to pull them and resow in a stronger-light environment.

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3. FAILURE TO THRIVE.   If your seeds pop alright and your seedlings avoid damping off without turning leggy, you're nearly home-free! Alas, sometimes a tray can come this far and then fail to thrive—or more specifically sometimes a portion of a tray, or a couple trays out of the five you are starting. Often these seedlings are discolored and very slow growing. This is an indication that your soil is not fertile enough. Often this problem appears in regions of your seedlings due to inconsistent mixing of your compost and fertilizer into your potting medium. Or, if it's affecting all of your seedlings, it's an indication that your seed-starting medium is too low in nutrition. It is of vital importance to add compost and/or fertilizers to any potting medium you buy at the store, especially if you buy something labeled as a "sterile" potting mix. Sterile mixes have been created to assuage gardeners' fears about damping off, but in reality, many gardeners fail to amend these mixes, resulting in poor-quality, nutrient-starved seedlings. It's a much better plan to make a live mix with compost and give plenty of air circulation; healthy seedlings in this type of environment stand a much better chance of staving off damping off.

4. APHIDS.   Last but not least, an uncommon but occasional pest of the indoor seed-starting set-up is the aphid. Aphids are pests of houseplants and often make their way into the home on green materials bought at commercial greenhouses in winter. They are easy to deal with—a spray of soapy water is usually all it takes to dispense with them—but if they reach your seedlings at a very young age they can make waste of them quite quickly. The good news is that if you have not had an aphid problem with your houseplants, you almost definitely will not see aphids on your seedlings.

Good luck, gardeners! And, should death or disease or weakness visit your young plants, chin up: even the most ardent and experienced gardeners lose seedlings every year. Learn from the experience: commit to oversowing, re-sow what you've lost, and re-think your setup. Soon you will anticipate and avoid the challenges that can so painfully pierce your garden dreams so early in the season.

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10 thoughts on “Common Seed Starting Issues - And How To Avoid Them!”

  • Tom Thies

    Dear Friends,
    I have been working with a community garden in NYC (WestSIdeCommunity Garden.org) for the past 40 years-- from the very beginning. We were lucky to be able to access a greenhouse that had been built as demonstration for roof top food growing at St. John the Divine. After a couple of rebuilding efforts, the diocese decided to build an apartment on the site (also containing a playground, a rose garden and another garden. The proceeds lasted less than a year, but we were given an alternative greenhouse (Growtek twinwall and aluminum 24' x 12') that has been pretty productive, especially this year. In spite of being re-orientated to blinding direct sun light, without any interference by surrounding buildings.
    I have had a problem with the tomatoes getting leggy (actually not my job) as they grew on past transplanting. As I understand it, night temps and crowding can also encourage legginess. I do not have this problem in my Columbia Cty. greenhouse, being able to manage temps better. Any thoughts?

  • susan

    great newsletter....good information!!

  • Schmidt Mary Ann
    Schmidt Mary Ann 04/29/2018 at 7:01 am

    Thanks for the information. So far so good. I’m starting tomatoes and peppers this year. I worry about my seedlings more than my kid! Your information in valuable.

  • Barbara

    So if we think we are experiencing "failure to thrive" and did not supplement the soil before planting, is it a good idea to use some type of
    fertilizer while trying to encourage the seedlings to grow?

    • Isabel Vinton
      Isabel Vinton 04/30/2018 at 5:43 am

      Hi Barbara, great question. Yes, we'd recommend either transplanting the young plants into good, well-composted soil quickly or providing a liquid organic fertilizer until it's time to transplant outside.

  • Julia

    Great article! Due to all of the problems above, this year I invested in a cold frame and have about 80% success. I prop the lid open on those warmer days. Things are not growing as quickly as I would like but I’m guessing it’s the long winter / early spring we’ve had. Things could go haywire when we reach 90 next week in Philadelphia. Today it was 50. :-)

    • Isabel Vinton
      Isabel Vinton 04/30/2018 at 5:51 am

      Thanks Julia, and congrats on your cold frame! This spring has definitely been a bit of a roller coaster ride - these recent cold nights won't have helped but as you say, the gap will start to close very quickly with the high temps coming this week. Even upstate we're expecting 88!

  • John Shearer
    John Shearer 05/03/2018 at 8:09 pm

    Great Article and Great Seeds.

    What is the best recipe for DIY seed starting mix. This the question that has bothered me for years.

    Have a Great Day Everyone



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