Ideally you should check on your seedlings every day, to make sure that they have enough water and are growing well. Regular attention makes it easier to spot problems while they are minor and still easy to correct; issues that have remained undetected for a few days may well be easier to spot, and most will still be correctable.


  • Poor growth – if seedlings aren’t growing as quickly as they should then there are several potential causes. They may be suffering from low light or temperature levels, not have access to enough water for rapid growth, be overcrowded or lacking in nutrients.
  • Tall, spindly growth – low light levels are the most obvious cause of this problem, especially if water is abundant and the temperature is quite high. Plants may also be reacting to an over-abundance of nutrients.
  • Pale growth – Pale leaves could indicate a lack of light, an attack by pests or a nutrient deficiency.
  • Floppy seedlings – most often due to a lack of water, but if the growing medium is damp then it could indicate a problem with root growth, pests or disease.
  • Collapsing seedlings – seedlings that are simply keeling over are almost certainly suffering from the fungal disease ‘damping off’.

Pests and diseases

Grown indoors in controlled conditions, seedlings are protected from most pests and diseases. The key to healthy seedlings is to keep them clean – using clean containers, tap water and sterile seed composts keeps most diseases at bay.

Mouldy pots – if you make your own paper pots, or use cardboard tubes, then at some point you will find that they go mouldy. Often they sprout fluffy clouds of mould, but there are many fungal species that happily live on damp paper and cardboard, so yours may look different. The mould is unlikely to damage the seedlings in the pots, but living with unidentified fungi is not a good idea. Improving air flow and keeping the pots drier will help, but my solution is to water the seedlings with a weak solution of chamomile tea (I use tea bags, but you can grow your own chamomile if you want). Chamomile tea has anti-fungal properties that are quickly evident, but do wait for it to cool down before you use it!

Damping off – ‘damping off’ is the scourge of seedlings. It’s a fungal disease that attacks and kills seedlings rapidly. If it arrives in a seed tray then you can watch it moving across the tray like a slow wave, toppling seedlings like dominoes. Good hygiene helps prevent the disease from attacking, but it’s not fool-proof. Diseased seedlings have to be discarded. As soon as you see a problem, prick out any healthy seedlings to a clean tray of fresh compost, and space them further apart. Watering with chamomile tea may help prevent further problems.

Yacon seedling

Fungus gnats – fungus gnats are tiny little black flies that live in damp organic matter, which makes potting compost their number one choice. The adults do no damage to plants, but are annoying – although females run over the surface of the compost, males fly around. They don’t fly well, but as they like warmth and carbon dioxide they tend to fly towards humans and cups of tea. If you have a significant population then you’ll find it almost impossible to finish a drink without fishing a fly out of it. More importantly, their larvae chomp through plant roots and can cause problems for seedlings. If you have young plants that are failing to thrive it’s worth gently taking some out and seeing whether you have the larvae in the compost (they are tiny white worm-like things with black heads). If you do then transfer your seedlings to a clean home.

In theory, fungus gnats can be prevented and controlled by watering properly. Allowing the compost to dry out discourages the gnats, but could kill your seedlings. There is a biological control available, but I have never tried it. Yellow sticky traps positioned close to your pots capture the males as they fly around and reduce the population. Be careful how you position them as they are very sticky and will leave a residue on windows and stick to plant leaves. The ultimate solution is to move your seedlings outdoors as soon as possible, as fungus gnats are far less of an issue (and less of an annoyance) outside.

Aphids – aphids (greenfly, blackfly and similar sap-sucking pests) arrive on seedlings as if from nowhere, even indoors. They feed on plant sap, sucking it from leaves, and are most likely to congregate around new leaves and buds. One or two are not a big problem, but they rapidly reproduce and a large population can greatly affect the health of a plant. They can also spread diseases.

Small populations can be rubbed off with your fingers, or gently washed off. A sturdy plant will survive a blast from the hosepipe, whereas aphids will not. If you’re struggling to control the aphid population then there are oil- and soap-based sprays that will kill them off and are suitable for use in organic gardens. Again, if seedlings are old enough to survive outside then you may find that the cooler conditions slow the growth of the aphid population and natural predators (ladybirds and their larvae, for example) solve the problem for you.

Nutrient Deficiencies

Plants need three nutrients in large quantities (N, P, K – they’re called the macronutrients), and other minerals in smaller quantities (the micronutrients). There are also other minerals that some plants need some of the time. The roles of these nutrients aren’t always well understood – it’s an area of science that is still being explored.

Nitrogen (N)
Plants use nitrogen for growth, it is used in proteins and to make the green chlorophyll pigment they need for photosynthesis. A deficiency shows as slow, spindly growth and a serious case causes yellowing (chlorosis) of the leaves, with older leaves being affected first as nitrogen is concentrated around areas of active growth.

Phosphorus or phosphate (P)
Phosphorus is needed for the growth of roots and fruits, and seedlings use a lot of it to produce a good set of roots. Older plants recycle phosphorus they already have, so they need less. A deficiency is not obvious, but causes poor establishment of seedlings. You may also see brown patches on the leaves.

Potassium or potash (K)
Plants use potassium to protect against adverse conditions – cold, injury, drought and disease. It makes them more robust. A deficiency causes scorching on leaves, usually older leaves first.

Magnesium is an ingredient of chlorophyll, and a deficiency is another cause of yellowing leaves, starting from older leaves first. This chlorosis can also cause reddening of the leaves, as other pigments that are always there are revealed by the lack of green chlorophyll.

All plant cells need calcium in the course of their daily life and a calcium deficiency causes a general failure to thrive, with pale younger leaves that may have a tendency to curl inwards.

Sulphur, Iron and Magnesium
All used in the production of chlorophyll, a deficiency of any of these minerals will cause yellowing of leaves, usually beginning with younger leaves.

Boron is easily leached from peat, but may be less of an issue in peat-free growing media. A deficiency causes early death of growing points, leading to deformed plants and fruit.

Problems are most obvious on peat, sandy and very thin soils. Copper deficiency causes dark green leaves.

A zinc deficiency is not common, is usually associated with a high pH (very alkaline environments), and causes poor development of leaves.

There are a number of issues with diagnosing nutrient deficiencies. The first is that symptoms are very often not obvious until the deficiency is severe. Another is that, as you can see, several deficiencies could cause the same or very similar symptoms. And there are two sorts of deficiencies – a simple deficiency is caused by a lack of one particular nutrient. But an induced deficiency is either caused by the pH of the soil medium being wrong or by an imbalance of nutrients (an overabundance of one can affect the uptake of others).

If you are making your own potting mixes then it is worth using a pH test kit or probe to ensure that its pH resides in the ideal zone of between 6 and 7.5 (unless it’s for acid-loving plants, which we will discuss later in the book).

With purchased composts and mixes pH shouldn’t be an issue, and a balanced fertilizer will supply the basic N, P and K that plants need whether it’s organic or synthetic. A suspected micronutrient deficiency can be countered with a seaweed feed, as it contains a wide range of nutrients. The solution can be used as a liquid feed or (more dilute) as a foliar feed, sprayed directly onto leaves. Both have a rapid effect.

I suspect that the most common nutrient deficiency seen with peat-free composts is a nitrogen one. Peat-free composts are based on composted organic matter, whether it’s green waste or bark or something else. The composting process (and we’ll talk about that later, too) involves a balance of nitrogen and carbon, and while material is actively composting it ‘locks up’ nitrogen to do that and makes it unavailable to plants. Mature compost is stable and doesn’t have the same effect, but anything that is still rotting down has the potential to cause a nitrogen deficiency. A supply of nitrogen-rich fertilizer in some form will easily correct the problem.

Pampered seedlings outgrow their pots, begin to compete with one another and need to move on. They have to be prepared to face the harsher outdoor environment, and in the next section we will be looking at how ensure your seedlings become young plants ready to face the world.