Achieving Healthy Seedlings: 4 Problems To Avoid

by Doug Muller

IMG_2894Like all good work, in seed-starting lies the potential for heartbreak. This is especially true for early-season indoor seed starting—a highly artificial environment that can cause stresses and problems rarely seen in the outdoor garden.

Here are four indoor seed-starting diseases (and pests!) to watch out for, and what to do about them.


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 my 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 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.)

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 in the dark days of February and March 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 I say provide light, I 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.

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.

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.