Problems with Your Seedlings? Here’s What to Do!


Most of the time, if you sow seeds and give them reasonable growing conditions, you’ll end up with quite decent results. On the other hand, when things go wrong, they usually do so very quickly, so always keep a close eye on your seedlings, ready to give them a helping hand at a moment’s notice.

Here are some situations you may encounter with young seedlings along with an explanation of what to do to help them recover.

Poor or no germination.Seeds unviable or of poor quality; poor growing conditions; soil allowed to fully dry outBuy fresh seeds; improve conditions; keep soil evenly moist during whole germination process
Seedlings wilt, soil dryLack of waterWater gently, but deeply; if seedlings recover, keep soil moist in the future; if not, resow
Seedlings wilt, pinched at the baseDamping off (fungal disease)Use fresh seedling mix; avoid soil from garden for indoor sowing; improve ventilation
Indoor seedlings leggy and pale greenLack of lightGive seedlings better light: sunny window or artificial lighting
Indoor seedlings leggy and dark greenToo hotReduce night temperature
Small black flies presentFungus gnatsRarely cause much damage, but can carry diseases. Allowing soil to dry a little longer between waterings will kill larvae
Outdoor seedlings cut off at the baseCutwormsInsert tin can with bottom removed around unaffected seedlings to serve as a barrier; harvest cutworm by hand (will be hiding in the ground at the base of its victims)
Leaves eaten on seedlings outdoorsVarious insects, slugs, etc.Hand pick slugs or apply slug bait; treat insects with insecticidal soap. Sometimes you have to resow
Seedlings blackened after a cold nightFrost damageResow

Keeping Fungus Gnats Under Control


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Fungus gnats: often more annoying than really harmful. Source: &

You’re sitting quietly in your living room and, suddenly, a tiny black fly zigzags in front of your face. You chase it off with a wave of the hand. Attracted by the CO2 in your breath, it soon comes back. You manage to squash it this time, but soon another one appears.

What is this insect? And where does it come from?

Many people mistake this tiny pest for a fruit fly (Drosophila spp.), and it is about the right size, but this particular little creature has no interest in fruits. Instead, it seems mostly to hang out around your firewood or your houseplants … that is, when it’s not flitting about your face.

The pest in question is a fungus gnat, a fly in the Sciaridae family of which there are some 20,000 species worldwide. Most of those that infest our houseplants are in the genera Scatella, Bradysia, Orfelia and Sciara, a rather useless bit of information, because it’s unlikely you’ll ever know the name of the exact species that shows up in your home.

A Family Portrait

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You’d need a magnifying lens to see this much detail on such a tiny insect as a fungus gnat. Source: Luis Miguel Bugallo Sánchez, Wikimedia Commons

The adult fungus gnat is a very small fly, rarely more than 4 mm in length, and usually black with transparent or grayish wings. You’ll often find several of them in the vicinity of a pile of firewood or around houseplants, but it also roams all over the house and, as mentioned, seems particularly interested in the air you breathe out.

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Fungus gnat larvae. Source:

The larva, which resembles a whitish, translucent, black-headed worm about 5 mm long, needs moisture to survive and will be found in some sort of moist organic medium, such as damp bark or potting soil.

How do fungus gnats get into your house? Well, adults may not be the world’s greatest flyers, but they can certainly be blown indoors or travel in on a pet or clinging to someone’s clothes. And it only takes one fertilized female to start a new horde!

That’s not the most common method, though. Most of the time, you (and yes, I’m pointing my finger in your direction!) brought eggs into the house by accident, either on firewood or when you bought a new houseplant or a bag of contaminated potting soil.

Most gardeners assume potting soils and seed starting mixes have been sterilized, but in fact, that’s almost never the case. Potting soil manufacturers instead use ingredients that are unlikely to harbor pests, but that do include some beneficial organisms: organic ingredients like peat, chopped bark and coir. They don’t want to sterilize their blends, as that would kill the beneficials. However, even if the potting mix is shipped out sans fungus gnat eggs, that doesn’t mean it will stay free of them.

When the bags of soil make it to the retail store, they often sit there for months and any tiny hole in the bag, even one no larger than a pin prick, is enough for female fungus gnats to lay their eggs in. Since garden centers inevitably host at least a small population of fungus gnats (they’re pretty much ubiquitous in humid environments), it’s not at all rare to bring home a potting or seed-starting mix already contaminated with fungus gnat eggs.

Good News, Bad News

The good news is that fungi are usually quite harmless.

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Adult fungus gnat. Source:

Other than annoying humans by their mere presence (who wants to see Aunt Mathilda swatting at gnats when she’s over for a visit?), adult fungus gnats cause no damage. Yes, they have mouth parts, but they neither bite nor sting. In fact, many even make themselves useful by pollinating flowers!

Even the larvae are usually not very harmful to plants. They mostly consume decaying plant matter they find in the soil mix as well as small fungi and algae. They’re especially attracted to the types of fungus found growing in overly moist soil. And here too, they can make themselves useful, because by digesting these products, they produce mineral-rich droppings plants can feed on.

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Some species of fungus gnat will attack plant roots if there is little else to eat. Source: Clipart Library &

On the other hand, especially when there is nothing else to eat, the larvae of some species (but not all) do attack plant roots. On a healthy plant, this is rarely very harmful, however. To start with, most houseplants produce more roots than they really need and in fact, a bit of fungus gnat pruning often stimulates the plant to develop a denser and more efficient root system! Plus, fungus gnats generally prefer dead or dying roots to live ones, especially tending to feed on roots that have been immersed in water too long and have started to rot. A mature plant has to be in pretty bad shape for fungus gnats to do any major damage.

Their effect on seedlings, on the other hand, can be much more serious. Young plants have very limited root systems and rather weak ones at that. In addition, adult flies can carry spores of harmful fungi, such as the dreaded seedling disease known as damping off. Plus, the small wounds fungus gnat larvae leave can serve as an open door for rot to set in. So, you really don’t want them chomping on the roots of your seedlings.

That’s why, even if the fungus gnats are not always very harmful, eliminating them is still the best policy … and if you discover they’ve found your seed trays, you need to get rid of them as soon as possible.

Know Thine Enemy

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Source: Knock-Out Gnats Granules

Indoors, fungus gnats can be present in any season and produce several to many generations a year. Although the adult seldom lives longer than 8 days, the female still has time to lay about 50 to 200 tiny eggs in moist potting soil or organic debris, preferably in the presence of fungi (it’s not for nothing they’re called fungus gnats: the odor of fungus attracts them). The eggs hatch in about 5 days and the larvae then feed for another 14 days. Next they pupate for 5 days. Following that, the adults emerge and the cycle begins again. The entire process takes about a month under normal indoor conditions, but can take place in as few as 17 days in a hot, humid greenhouse.

How to Control Fungus Gnats

Reduce Your Watering


Letting the potting mix dry out before you water can sometimes eliminate fungus gnats entirely. Source:

The first key to success in controlling fungus gnats in indoor plants is to understand that they absolutely need constantly moist potting soil during their larval stage. If you make a habit of letting your plants dry out a little longer, this will often solve the problem completely. In fact, many experts consider fungus gnats more a symptom of overwatering than a problem in itself.

Try applying the golden rule of watering. That is, water deeply, enough to moisten the entire root ball, then allow the soil to dry before watering again. Many gardeners discover that careful watering keeps fungus gnats fully under control.

Don’t be discouraged if this doesn’t seem to work at first: it takes at least a month to before the treatment will have reached all the stages of the insect’s life cycle.

A Barrier Between Soil and Air

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By covering the soil with sand or small stones (here: Growstone Gnat Nix top dressing, made from recycled glass), you can eliminate fungus gnats. Source: Growstone Gnat Nix

Another possibility is to make the surface soil unfit for fungus gnat larvae. Larvae live near the surface of the soil, no more than 1 ¼ inch (3 cm) deep, as they have to regularly move to the surface to breathe. Plus, they need moist, organic soil to live in. If you cover the soil with a ½ inch (1 cm) layer of sand or pebbles (there are even commercial products especially developed for this purpose, such as Gnat Nix), the larvae will no longer be able to live there … and besides, adults won’t be able to lay their eggs on such a dry medium either.

Trap the Adults


Light traps catch all flying indoor insects. Source:

To control adults, you can try setting out yellow sticky traps or, better yet, a light trap. I find the latter works like a charm!

Bring Out the Insecticides

It is also possible to drench the soil with an insecticide. Might I suggest one with few adverse effects on the environment, such as insecticidal soap or neem oil? It is also possible to make the soil less attractive to larvae by mixing diatomaceous earth or cinnamon powder into it.

Predators to the Rescue

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Knock-Out-Gnats brand Bti. Source:

The biological larvicide Bti* (Bacillus thuringensis israelensis), a bacterium usually used to manage mosquitoes, will help control fungus gnat larvae as well. Make a solution and use it to drench the potting soil. There are even formulations developed specifically for this purpose, such as Knock-Out-Gnats and Gnatrol, two professional products you can find on the Internet. You can also take MosquitoDunk type pellets, likely available locally, and crush them into powder to make a solution.

*Do not use Btk (Bacillus thuringensis kurstaki), designed for use on butterfly larvae, on fungus gnats. You need Bti, specific to Diptera larvae (flies).

Bti will only be effective when larvae are present in the soil. It has no effect against adults, eggs or pupae. Larvae, though, quickly consume the bacteria and die within 24 hours. It will likely be necessary to repeat the Bti treatment weekly for 3 or 4 weeks in order to eliminate all the pests as they cycle through the various stages of their life.

There are also other predators you can use to control fungus gnats, including beneficial nematodes like Steinernema feltiae or predatory mites like Hypoaspis miles. You can order these predators on the Internet.

Fungus gnats: often more annoying than really harmful and fairly easy to eliminate as well. Don’t lose too much sleep over them!20180111B Luis Miguel Bugallo Sánchez, WC

Damping Off Disease: Down But Not Out



When young seedling flop down as if pinched at the base, they’re suffering from damping off disease.

It’s always such a shock! Your seedlings germinate, start to grow and everything seems to be going so well, then one morning (it always seems to happen overnight), you awake to discover seedlings that almost seem to have been mown over. They’re lying on their side on the growing mix, with their stem blackened, apparently pinched at the base. But it wasn’t a person with nimble fingers who pinched back your plants, it was a disease called damping off.

This disease is not actually a specific disease, but rather can be caused by any number of soil-borne fungi, including Pythium, Rhizoctonia, Fusarium, Botrytis and Phytophthora, all of which present the same symptoms. Damping off spreads rapidly: entire trays can be killed back in just a few hours. Moreover, once the disease is apparent, it’s too late to save the fallen seedlings.

Less Common That It Used to Be


You have to treat damping off rapidly or it will spread

Damping-off is not as common as it once was. Ever since gardeners adopted so-called artificial soil mixes back in the 1970s (mostly composed of peat, coir, fine bark, vermiculite, perlite, etc., but no longer containing any “real soil” imported from outdoors), damping-off has become much less common. Artificial soils are sterile, or at least, close to being sterile and so are unlikely to harbor disease spores.

Damping off fungi are very common in outdoor soils. In fact, they’re found pretty much everywhere. If damping off doesn’t seem to occur all that often outdoors, it’s only because it tends to strike earlier than indoors, as a pre-emergence disease. Your seeds just don’t germinate at all and you never know that damping off was the cause.

Until artificial soils came on the market, most people simply dug up soil from their gardens to use in starting seedlings. Not only were such soils dense and heavy, allowing little air circulation and thus creating an excellent environment for fungal development, they also came pre-inoculated with a whole range of disease spores. Sowing seed back then was a race against time: the faster the seeds germinated and started to grow strongly, the less susceptible they were to damping off.

That said, fungal diseases are still readily spread indoors, though not as often directly though soil. Contaminated pots and tools, even watering cans, can spread them as can water splashing from one tray to another. Some diseases have wind-borne spores that can be carried by the slightest breeze, even indoors. So even the use of artificial soils doesn’t prevent damping off entirely… but it sure helps!

Once Symptoms Are Visible…

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Seedling pinched at the base by damping off. Photo: INAKAvillage211, Wikimedia Commons

Once you see seedlings mowed down by damping off, it’s too late to save them. The best you can do is to quickly treat the remaining seedlings with a fungicide such as chamomile or clove tea in the hopes of slowing the disease’s progress. In the past, almost every home gardener in North America had a bottle of No-Damp, a fungicide developed expressly to controlling damping off, at hand, but it is no longer available.


To help prevent damping-off, use only clean pots and tools. Wash any recycled containers well with water and bleach. Also wash your hands well if you’ve just come in from working in your outdoor garden. Consider opening a fresh bag of potting soil for your seedlings: a bag left open for a few months may have been contaminated by air-borne spores. And never use garden soil on seedlings.

So much for preventing contamination, but seedlings also readily outgrow damping-off, which usually only affects very young seedlings. Applying the best possible growing conditions will help the seedlings get off to a quick start and grow to beyond the stage where they are subject to it. Thus anything that stimulates rapid germination and fast growth also helps prevent the disease. That’s why seedlings should be placed under warm, humid conditions after sowing, in a growing mix that is moist, yet well drained.

Also sow the seeds at the recommended depth (this will vary from one species to another), never too deep, otherwise the seedling will take longer to reach the light… and that gives the fungus more time to get to it.


Starting seeds in a mini-greenhouse helps prevent damping off at first, as it stimulates fast germination, but once the seeds have sprouted, the covering has to come off.

Freshly sown seeds benefit greatly from being started in a mini-greenhouse, that is, with their tray or pot covered more or less hermetically with some sort of transparent material in order to maintain high humidity. This could be a clear plastic dome, a pane of glass, a plastic bag, a plastic bottle cut in half and placed upside down over the pot, etc.: anything that will let some light in while keeping the humidity high. This, combined with moderate light and warm temperatures around 75°F (24°C), gives ideal conditions for most seedlings to sprout and grow.

As soon as the majority of the seeds have germinated, though, give your seedlings a change in regime. High humidity and high temperatures also encourage fungus growth. So once the seedlings are up and growing, remove their mini-greenhouse and expose them to cooler temperatures, good air circulation, more moderate humidity, say about 50 to 60%, and also stronger light.

Fresh soil, good drainage, cleanliness, decent air circulation, humid air, intense light and moist but not saturated soil, they all add up to good growing conditions that will help keep damping off at bay.

When Damping Off Returns

In spite of the recommendations above, some gardeners have repeated problems with damping off: it just seems to come back year after year. If this is your case, here are some extra tips on preventing the disease:


Milled sphagnum moss

  • When sowing seedlings, instead of covering them with potting soil, use milled sphagnum moss (not peat moss). Sphagnum moss is a natural fungicide. Milled sphagnum moss (one brand is appropriately named No Damp Off) is not necessarily easy to find locally. I prepare my own by running dried sphagnum moss through my wife’s coffee grinder.
  • You could also try sprinkling the potting mix with cinnamon powder, another natural fungicide.
  • Water or spray your seedlings with cooled chamomile or clove tea. Both have proven antifungal effects.


    Treated seed is colored so it can’t be mistaken for untreated seed.

  • Sow “treated seed”, that is, seed coated in fungicide. This technique is not, however, considered acceptable in organic gardening circles.

I repeat that the treatments described will not save seedlings that have already been mowed down by damping off. At best, they simply slow down the disease and stop it from spreading.

With damping-off as in so many things, an ounce of prevention really is worth a pound of cure!20170406A