Troubleshooting Seedling Problems

Although we love popping beans over here, there are some challenges when growing from seed. Whether that’s the initial germination process and dialing it in, or the transition period where viable, germinated seeds move from the germination phase into the early vegetative stage.

During this week or two of life, cannabis seedlings can be very picky and having the right environment during this phase of growth is substantially more important than having an ideal environment later on in the vegetative stage.

That’s because small seedlings have limited roots, meaning they rely more on the absorption of moisture through their leaves than larger plants where the roots are more established and can carry more of the load.

In this article, I’ll cover some of the most common problems encountered during the first 2 weeks of growth after the seed has sprouted, and offer some solutions to avoid or fix these problems.

Stretchy Growth

Severity: Mild to Moderate

If you’re seeing excessive stretch to your seedling, there’s a couple of common causes. The good news is that it’s easy to fix, the bad news is that once you notice it’s often too late to completely rectify.

Too Light Light

The most common cause of stretchy, or ‘leggy’ seedlings is incorrect light. Whether that be light that isn’t bright enough, or lights that are placed too far away from the plant. I don’t recommended guessing your light metrics unless you’re already experienced. Instead, use a free PPFD meter app on your cellphone to gauge the light at plant level.

These apps aren’t always very accurate, but they do provide a useful gauge. Alternatively, consider a cheap, but trustworthy light meter like the UNI-T UT383 which will give you a LUX value to indicate the amount of light your plant is getting. Make sure to place it at the same height as the plants though, as light drops off with distance.

For the seedling phase, aim for a PAR reading of around 200 (16,400 LUX).

Incorrect Light Cycle

Less commonly, bad light cycles can also cause stretch. Although it may seem contradictory, having your plants under 24 hours of light can also increase stretch. During these first two weeks, a standard 18/6 light cycle will work, but I have also found success using 20/4 in the first week or two.

Collapsed Plant

Severity: Moderate to Extreme

There’s nothing quite as disheartening as opening your tent only to see your seedling has collapse under its own weight and is laying sideways on the medium.

This is typically caused by one of two issues:

Excessive Stretch

The first is only of moderate severity and that’s a plant that’s stretched too much from incorrect lighting and hasn’t managed to establish a strong enough stem or root system to hold up its weight. In this case, the plant can be propped up using a stick and catered to until it is strong enough to hold itself up.

Consider potting the seedling deeper during your next transplant, as it will allow you to bury some of the extended stem and improve its hold.

Damping Off

On the more extreme end, damping off is another common cause of seedlings collapsing under their own weight. Once this occurs, the plant will almost never recover and instead die within a few days. But before you start worrying, there’s an easy way to tell the two causes apart.

Look near the base of the stem for signs of a narrowing. When a plant is infected, it will usually have a small narrow area on the stem, almost as though someone has pinched it.

Damping off is a form of fungal infection that small plants can be quite prone to and can be caused by Pythium, Phytophthora, Rhizoctonia or Fusarium. This is especially true when the medium is overly saturated, which promotes the proliferation of these fungi and fungus-like organisms. Ultimately, when one is warned about the risks of overwatering seedlings, this is usually what is trying to be prevented.

To avoid damping off, ensure moderate watering practices and avoid overly stale or saturated air.

Burnt Tips

Severity: High to Extreme

Although burnt tips is more common later in the growing stage as cultivators push their EC up, it can also occur with seedlings for various reasons. These are the most common:

Too Much Feed

When feeding a young seedling one has to be careful not to overfeed, especially with Phosphorous and Potassium, which are both prone to causing tip burn in younger plants. Slowly ramp up to your vegetative feed, rather than rushing in with the nutrients in the first week or two of life.

Exactly how much you should feed will depend on the medium you’re using and the nutrient line. However, many manufacturers will specify a specific dose for early veg or seedlings. If yours doesn’t, start at 50% for the first few days and slowly increase it over the course of the first week or two.

Acidic Medium

An overly acidic medium can cause burnt patches on the leaves that can look a lot like overfeeding. This is a common symptom for new growers who are attempting to use garden store potting soil. Keep in mind that cannabis wants a pH of around 5.8 to 6.3 for ideal growth, while some soils are made for plants that prefer a pH range as low as 4.0

If you suspect your soil is the problem, try removing the plant and its roots in a safe way and transplanting it into a medium with a more suitable pH range. There are soils designed specifically for cannabis (Freedom Farms, Orgasoilux, Organics Matters, etc).

Hot Soil

A hot soil can also cause these symptoms. Much like the leaf burn we see from overfeeding, this is a result of too many nutrients in the medium. Similar to acidic mediums, these soils are usually those found at garden stores and they will often have a lot of bark used in them.

Even some cannabis soils can be a little hot for seedlings, which is why some growers will mix their soil with coco/perlite in the early stages of growth to reduce some of that nutrient excess.

Letting the medium dry out too much between feeds can also spike the EC and cause even coco/perlite mediums to become excessively hot and show similar symptoms.

Slow Growth

Severity: Mild to Moderate

Slow early stage growth can be natural, sometimes due to the genetic makeup of the plant. Not everyone is born to be a runner and not every seed will be a keeper. There are often runts (not to be confused with the strain Runtz), which may grow slowly. These plants are sometimes tossed out early by pheno hunters looking to only keep the strongest plants around.

But since it’s not just genetics that can impact the rate of growth, one also needs to consider other common reasons like bad soil quality (incorrect base pH or contains incorrect organic material for cannabis).

It can even be caused by a combination of less than ideal factors, for example too little humidity combined with some feeding issues can also cause slow growth.

Most of the time that I receive slow growth questions, the problem lies in the medium or the watering cycles. Chronic underwatering can significantly slow down growth, while also not always showing symptoms above soil.

Another common problem is root damage, sometimes growers may damage the root in its initial transplant which can cause stunting. For regular photoperiod plants, they may recover sufficiently, but autoflowers can suffer quite badly from slow growth in the first two weeks, and can result in very small yields.

Drooping Leaves

Severity: Mild to Moderate

Drooping leaves is one of the most common symptoms found in seedlings and usually indicate one of two problems: overwatering and underwatering.

Determining which it is can be tricky, as the symptoms can overlap. Underwatering tends to produce soft, floppy leaves and overwatering causes hard, rigid petioles that create downturned leaves. However, this is usually not as evident with small seedlings and isn’t always accurate.

Chronic underwatering or excessive dry-backs can cause a combination of both. This is where the grower will wait too long before re-watering and then water heavily when they do give water. For small seedlings its better to keep the medium moist and once the first inch has dried, to water again with only moderate amounts of water.

If you notice your leaves turning down, try and establish if you’ve been watering excessively or perhaps waiting too long between each watering cycle. In soil, there’s a fine balance to strike but in coco/perlite you can always water a little more than you think without issues, assuming you have sufficient drainage on your pot.

Leaf Discolouration

Severity: Mild to Severe

Leaf discolouration is a common symptom with a lot of possible causes. To identify the cause of your leaf discolouration, you will need to be quite particularly about its nuance. For example, a slight nutrient deficiency can cause discolouration, but so can underwatering or overfeeding.

Nitrogen Deficiency

One of the most common causes of yellow leaves in seedlings is a lack of Nitrogen in the root zone. Nitrogen is the most fundamental macro nutrient for young plants and its what drives its growth. When nitrogen deficiency is present, you will often notice the cotyledons first start to go yellow, followed by some yellowing of the true leaves.

If you notice this problem, ensure you’re giving the plant sufficient nitrogen and that your pH is within the range where nitrogen uptake can be facilitated.

Chronic Underwatering

Chronic underwatering where the medium is left to dry out excessively between waterings can cause plants to show various signs of discolouration, ranging from yellow to brown. These seedlings can die quite quickly if the roots are left without water frequently.

These dry backs can also spike the EC of the medium, causing nutrient burn and discolouration to the tips of the leaves.

pH Imbalance

An incorrect pH range can cause a range of symptoms, one of which is discolouration to the leaves. This may be seen as light brown marks, yellowing etc. The reason for the variability is because an out of whack pH range means a lot of micro and macro nutrients may be uptaken and the symptoms you see is a result of a consequential deficiency.

Burn From Liquid On The Leaves

Accidentally spilling nutrients on your leaves while watering under light, or giving your plants a foliar spray can also cause some leaf discolouration. Be careful when watering to only get nutrients in the soil and not on the plant itself, when it sits under light with water or nutrients sitting on the plant it can burn them and cause some discolouration.

Spots or Marks on Leaves

Severity: Moderate to Extreme

First thing first, if you notice any spots or unusual marks on the leaves, you should immediately be inspecting the plant to rule out pest problems. Look closely at the undersides and tops of leaves. Not all spots or odd marks indicate pests, but they are one of the most common causes of this symptom.

Having pests at any stage of growth is worrying, but during the first few weeks of growth it’s especially important to note, as small plants respond more negatively to stress than larger, established plants.

Thrips

Thrips are one of the most common cause of odd markings on leaves. They are a prevalent pest, and can reproduce very quickly in warm conditions. To identify thrips, look for signs of silvering on the tops of leaves, which is often scattered across different areas of the leaf surface.

If you notice thrips in the early stages of growth it’s actually better than noticing them later on as they are unlikely to have enough space to hide on the plants. Manually killing them and using a sticky trap may be enough to get rid of them. However, there are options like Spinosad or Micronized Sulfur, both of which I’ve used with success to get rid of them. But keep in mind that these may cause damage to small plants with too strong dilutions or when sprayed with the lights on.

Spider Mites

Spider mites can be a real challenge to deal with and are usually first noticed when the grower sees some small spots, clumped together on the top of the leaf. Unlike Thrips which are frequently also found on the tops of the leaves, spider mites will often stay on the underside and avoid detection for a long time.

The difference between them and Thrips in presentation, is that they don’t cause a silvering effect on the leaf and instead appeals like several pin pricks.

Taking action immediately is important in avoiding some real dire problems when the plant enters flower. To get rid of them, there are a lot of options on the market and the option you go with will depend on your growing preferences. For me, I have successfully gotten rid of them by rotating micronized Sulfur and Spinosad in 1 application every 3 to 4 days until they are gone (and then done a week or two extra just for safety).

Aphids

Aphids can cause symptoms similar to Thrips, and differentiating the two may prove challenging for new growers. Aphids are a bit easier to treat though, and opting for a pesticide of your choice (safe ones, of course) – can help to get rid of them.

To differentiate from Thrips, the easiest way may be to turn over the leaf and look for groups of bugs congregated together. Aphids are usually found in groups, but may not be in an early infestation.

Other Causes

If you see some spots on your leaves, always make sure there’s no pests – but if your pest search comes up clear, another possible cause is foliar sprays or nutrients that have splashed up onto the leaf. Accidentally getting nutrients onto your leaves while they are under light, can also cause some odd patchy markings to occur.

Other symptoms may be related to nutrient deficiencies, with calcium deficiency being one of the most common causes of spots on the leaves, outside of pests. However, this is more common in older plants as the drive for micronutrients increases.

Mutated Growth

Severity: Moderate

Mutated growth is a relatively common occurrence in young cannabis seedlings and can have several causes, ranging from genetics to issues in the root zone or environment. However, genetic mutations are a common cause.

While mutated growth is for the most part something one wants to avoid, there are several mutations that have gone on to become sought after. For example, the strain Freakshow is an example of a mutated plant that grows different to most cannabis.

Here’s a few examples of types of cannabis mutations:

Polyploidy: Extra sets of chromosomes causing larger or oddly shaped leaves.
Fasciation: Flattened or ribbon-like stems.
Whorled Phyllotaxy: More than two leaves per node.

Twisted Leaves

Severity: Mild

Twisted leaf growth can have a few causes, but often in young seedlings it’s caused by one of two problems:

pH Inbalance

Believe it or not, but incorrect pH values can do more than just cause deficiencies, it can also cause plants to have twisted leaves. If you’re certain that you’re not chronically underwatering your plants, it is worth checking your pH to ensure that it’s within the 5.8 to 6.5 range.

Chronic Underwatering

Chronic underwatering is another cause of stress that can, in some cases, cause the leaves to twist a bit in the early growing stages. Young seedlings should not have a lot of dry back, especially in coco/perlite mixes where they perform best with a constant access to moisture.