Symptoms of Root and Stem Rot + How to Prevent It

You may have dealt with root and stem rot before if you’ve had a plant that was seemingly quite healthy, until it suddenly wasn’t and quickly died. Stem rot happens when a fungus takes over the root system of your plant, suffocating it and causing very fast wilting and decay.

Root and stem rot can be very concerning because most of the signs of it occur under the soil, in the root system, and aren’t noticed until the fungus has taken over the roots and is killing the rest of the plant.

Unfortunately, root and stem rot is a very nasty fungus that’s nearly impossible to treat, so the best method is to prevent it in the first place. Stem rot happens when the soil conditions are moist and dense enough for the fungus to develop. But, by following the tips outlined in this article, you can avoid the fungus taking hold.

1. dead spider plant leaves

What is Root and Stem Rot?

Root rot and stem rot are similar conditions that are both caused by a fungus that takes over the root system and causes the entire plant to decay. Since the fungus starts in the roots, this is often called root rot. However it quickly spreads to the stems and branches, which is why it’s also called stem rot.

Stem rot can happen to all plants in all different climates, however there are some correlations between the type of fungus and type of plant. There are a few different fungi that can cause stem rot as well as Phytophthora, which is technically a water mold and not a fungus.

Phytophthora is a very common cause of stem rot because it can live dormant in the water and therefore spreads easily through irrigation systems. In fact, the Phytophthora cactorum is the mold that caused the Irish Potato Famine by wiping out all the potato crops.

2. image of moldly water

Additionally, there are several fungi that can take over the roots and will send pathogens throughout the plant’s nutrition system, taking over the host. The two most common fungi that cause root and stem rot are Xylaria and Armillaria.

Xylaria mali and Xylaria polymorpha are often called Black root rot, because the fruiting mushrooms produced look like balck fingers sticking out of the ground! This fungus is more commonly observed affecting older trees that are at least 10 years old. However, it can remain dormant in root fragments in the ground for up to 15 years and from this can spread to young plants.

3. Xylaria polymorpha Croatia
Xylaria polymorpha- Croatia / Woluhar / CC 3.0 

Armillaria is known by the names of Honey Fungi, Shoestring Root Rot, or Openky and is often connected with stem rot in hardwood or pine trees, although it’s also frequently found attacking stone fruit trees. Yet Armillaria is also the most common fungus that provokes stem rot because it has a high tolerance for any soil type or plant host.

One more very common stem rot issue is called Texas Root Rot or Cotton Root Rot, and the fungi are Phymatotrichopsis, Phymatotrichum, or Ozonium. As the name suggests, this kind of stem rot is only found in the southwestern United States, but is certainly a problem when found.

These fungi don’t grow in colder regions and only grow in heavy alkaline soils, making the dry land of the southwest the perfect breeding ground. These fungi can also spread very quickly because they don’t discriminate when it comes to plant hosts- except, oddly, for pomegranate trees!

4. Armillaria mellea Honey Fungus UK 1
Armillaria mellea, Honey_Fungus,_UK_1 / Stu’s Images / CC 3.0

Some other common stem rot fungi include: Rhizoctonia, which is known to affect younger plants; Fusarium, a fungus that can harm humans if an infected crop is eaten; and Dematophora or Hypoxylon necatrix, rarer but intense fungi that can aggressively wipe out crops.

Regardless of the fungus or if there’s Phytophthora, stem rot is provoked when the soil is too damp and these fungi or molds begin to develop. However, this doesn’t mean that stem rot only happens in wet climates- it’s very possible to have problems with stem rot in dry climates and even more so with houseplants.

This is because stem rot fungi can develop due to several different factors that create the right conditions in the soil. In the next section, I’ll explain the various ways in which soil conditions may be suboptimal for your plants, yet just perfect for stem rot fungi.

5. hand holding dead potted plant

Causes of Stem Rot

The soil conditions that stem rot fungi like to live in are wet, damp, and moist in a tightly packed space. These conditions can be created in various different ways- and even more so considering different types of soil and plants.

The spores of fungi are pretty much everywhere and they’re likely already present in your soil, so the best you can do is to take care to prevent these conditions. The case is slightly different for the Phytophthora mold, since it lives and travels through water, but it thrives in similar conditions and you can still avoid it through the same preventative measures.

Too Much Water

One of the most common causes of stem rot is sitting water. This is more common with potted plants that don’t have drainage holes and hold in old water. However, this can also happen with plants potted in the ground that have air pockets in the soil that fill with water.

For both potted and in-ground plants, overwatering is the most common cause of stem rot. Stem rot is why overwatering is unhealthy for plants, because the excess water can stay in the soil around the roots and encourage fungal growth.

This issue is much more serious with potted plants, because plants that are growing in the soil can usually dispense the excess water in the surrounding area. With potted plants, on the other hand, there isn’t anywhere for the leftover water to go.

Additionally, many common houseplants- like the Fiddle Leaf Fig or Monstera Minima– are native tropical plants, so they’re used to water easily draining out. When they’re in a pot and are overwatered, their roots aren’t used to soaking up that much water, leaving water to sit in the pot and fungi develop.

6. close up of dead leaf

Issues with the Soil

Stem rot can happen even if you’re not overwatering or with plants growing directly in the ground. Despite the level of water you give your plants, if you’re not using well-draining soil then the water won’t drain properly and you can still have problems with sitting water.

This often happens when the soil is too compact from being squeezed into a pot or hole that’s too small. If your plant is sitting in tightly packed soil, this also means that its root ball will be more compact, making it easier for the fungi to take over the root system.

Along with tightly packed soil, the type of soil itself makes a big difference in preventing stem rot. It’s important to pay attention to the type of soil that your plant naturally grows with, as this is important in keeping the right moisture levels in the soil.

Some plants really thrive with a loamy and moist soil, but others prefer an acidic soil and therefore struggle to absorb excess water. This is why stem rot is really common with plants that are native to dry areas, because they’re so drought resistant and don’t tolerate overwatering as much.

Some plants need a mixture of different materials in the soil to make the root system looser and to increase drainage. The type and composition of soil in relation to the plant that you’re growing has a huge impact on how the plant can absorb nutrients in the soil, which will determine whether fungi can grow in the roots or not.
7. dried flower

Symptoms of Root and Stem Rot

Unfortunately, root and stem rot doesn’t have many distinguishable indicators- other than the sudden decline or death of your plant. There are, however, a few ways that you can interpret the various signs to know if you’re dealing with root rot or another disease.

While stem rot does give many indicators that your plant is struggling, these symptoms aren’t different enough from many other issues that it’s often difficult to know what might be the cause. Signs of decay from stem rot are very similar to those from underwatering, sunlight issues, or advanced pest infestations.

Root Problems

Honestly, the best way to know if you’re dealing with root rot is to see the roots directly, when possible. With smaller plants and houseplants, you should try to take the plant out of its planter or the soil so you can inspect its roots.

With large, outdoor plants that you can’t uproot, try to dig up the surface roots. Of course, you need to be careful not to damage the roots while you’re digging because that can expose the plant to many diseases.

If the minor, fine roots are orange, this may indicate that the major roots are rejecting and shedding off the minor roots to reduce the root system and fight the fungus. If root rot has already started growing, the roots will be brown and limp and might even smell moldy.

8. leaf with browning edge

Problems with Foliage

There are also many above ground symptoms that can signal to you that you might have a root rot problem. While these are general symptoms, you can determine if there’s root rot if you have a combination of these and can tell that you have overly damp soil.

You’ll definitely have issues with the plant’s foliage first, before it spreads to the stems or branches. The leaves will become yellow and then brown and appear mushy or very soft. This is distinguishable from underwatering- even though underwatering also causes yellowing leaves, the leaves become very dry and frail.

For plants that have specific fall foliage, they might turn this color too early when affected by stem rot. This happens because the plant isn’t receiving enough nutrients so it loses its ability to produce green leaves.

9. dead hydrangea flowers

Plant Growth Issues

You’ll also notice a significant decline in the plant’s health, since its roots are blocked from the nutrients in the soil so the upper half of the plant will be suffering- which takes on many forms.

Generally speaking, your plant will either slow down its growth or completely stop growing.  For example, you might see that your plant’s new growth is much smaller, or maybe that it’s not producing new growth at all.

If you have stem rot with a tree, it can spread easily between trees and this can lead to the overall canopy thinning out as the trees produce less leaves. You will also see that the branches or even parts of the trunk are sunken in.

For fruiting plants, your plant might create “stress crops” when it knows that it’s fighting off a disease. When a plant feels severely threatened by a disease or pest infestation, it might produce an extremely high amount of fruit or seeds if it’s preparing to die soon.

One more thing to note is that the fungal pathogen Anthracnose causes many of the similar symptoms of decay, but is not associated with stem rot. So, although you won’t see mold or mushrooms forming it will still cause your plant to intensely decay.

10. mushrooms growing on mossy tree

Mold and Mushrooms

There is one major giveaway that you’re dealing with stem rot and that is, of course, seeing mushrooms growing around the base of the plant. However, if the fungus has created mushrooms, that’s a sign that it has really developed and at this point you can’t save your plant. The best you can do is remove it quickly so the fungus doesn’t spread to nearby plants.

Specifically for the Armillaria fungus, you can actually see the fungus’ mycelial network growing on the bark, before it produces mushrooms. If you remove the bark from the roots, you’ll find that the roots are spongy with a stringy fungus growing on it- this is why the fungus is called Shoestring fungus. This mycelia becomes bioluminescent when the tree is actively decaying, so that would be another clear indicator.

With many types of fungus there could be a white mold that forms around the base of the plant. If you dig up the surface roots and first layer of soil and see some white mold, this is also a sign that stem rot has formed and developed quite a bit.

11. woman potting small tree

How to Prevent Stem Rot

Root and stem rot are known to wipe out the plants that they grow on because the signs of fungal growth aren’t clear until it’s too late. Even if you happen to catch stem rot before the fungus really takes over, it’s still very hard to completely get rid of the fungus.

This is why any experienced gardener or houseplant owner will tell you, do everything you can to prevent it in the first place.

This is also why our growing guides go so in depth with explaining the soil needs and how much to water each plant, because following these needs will really help you prevent stem rot.

Preventing Stem Rot with Houseplants

Stem rot is very common with houseplants, despite the perception that growing indoors will decrease the chance of fungal infection. This is because houseplants grow in confined pots and don’t have the same ability as in-ground plants to release excess water.

This also means that plants in container gardens are more susceptible and extra care needs to be taken with these as well to keep your fruits and veggies growing well.

12. houseplants lined up

The best preventative step you can take is to avoid overwatering! Many plants, especially tropical houseplants, are quite drought resistant and will survive periods of not being watered enough. Plus, most plants will communicate through their leaves that they need water.

In general, it’s much easier for a plant to recover from being too dry for too long, than to recover from a fungal infection. Typically, when plants are too dry, their roots will die and the plant will become less productive, but once watered again the roots will grow back.

However, this reversibility doesn’t apply to stem rot- even more so considering that we often don’t know about the fungus until it’s too late.

This rule varies for each plant, but it’s generally best to wait until at least the top layer of soil is dry before you water again. Check our many vegetable growing guides to see how much water your plant needs or read our complete houseplant watering guide.

It’s also very important that the plant has good drainage, since it is just sitting in a pot. You can do this by planting it in a pot with drainage holes and a drainage tray for excess water. Once the leftover water fills the drainage tray, you should dump the water into another pot so it’s not sitting with the plant.

13. putting rocks in a potted cactus
A woman adds rocks to her potted cactus to keep the soil dry and rough, which is perfect for desert plants like cacti.

Preventing Stem Rot in Outdoor Plants

There are many things you can do to avoid stem rot for your in-ground plants, but you should take extra care if you live in an area that is known to have fungal infection often.

A common oversight that happens during planting is to remove all dead pieces of wood or roots in the area where you’re planning to plant. These fungi can stay dormant in dead wood for several years, and if you don’t remove these pieces before planting fresh plants, the fungi can reactivate and grow on their roots.

As I explained earlier, compact soil or root balls create the perfect space for fungi to spread, so make sure you dig a large enough hole when you’re planting and don’t cram your plant in a space where it can’t grow. This also applies to houseplants- repotting them into larger pots is a very effective way to be proactive.

14. bush in front of fence

You can also use a mixture of different materials- like perlite, peat moss, or vermiculite– to add texture to the soil and make sure it’s loose enough to drain out water. Additionally, if you recently experienced a storm that washed away lots of soil, it would help to replace some soil to help your plants recover.

You should also protect your plants’ roots from any damage and address it if any occurs, so the roots don’t get infected while they’re exposed. This could be from any equipment that accidentally cut the surface roots or damage from heavy storms, but regardless the roots shouldn’t be left open.

Also, general maintenance like pruning and fertilization at the beginning of the growing season help keep the tree as healthy as possible. Healthy roots are more able to fight against fungal infections, and you can help them out more by adding some mulch around the root ball to keep the soil aerated.

However, make sure not to add in mulch right on top of the root ball or around the base! This is a common mistake that actually provokes stem rot, because the mulch retains moisture and puts weight on the base of the plant.

15. potato plant with phytophthora
Phytophthora_infestans_potato_Doré / Rasbak / CC 3.0

Checking for Phytophthora

It’s also good practice to check your water storage for Phytophthora, since it can easily spread through water. This can be devastating, but this method is fairly easy to check and if you use a large irrigation or rainwater system, you’ll want to check before distributing all this water.

Suspend or place a piece of fruit in your water storage and return in a day or two to see if there’s any signs of rotting. If so, this means there’s Phytophthora in your water system and you need to quickly disinfect the system.

Fight Fungi with Fungi

Lastly, one of the most effective ways to prevent stem rot fungi from taking over your plants is to have a healthy and thriving fungal ecosystem in the soil. Along with the nutritional benefits of healthy soil, having a diversity of bacteria in the soil helps prevent stem rot fungi from taking over.

The practice of using biocontrols involves using organic material to promote the useful bacteria and keep the harmful bacteria in check. Trichoderma is a fungus that is commonly used to fight off aggressive fungi. It grows well with the presence of lots of organic materials, like from compost or worm castings.

Lastly, by planting ground cover around your plants you’re adding an additional root system that can help absorb any excess water. Having another layer of plants also helps keep the soil pH at normal levels and the soil active with healthy bacteria.

16. potted plants with watering can

Remember to Take Care

The final word regarding root and stem rot is prevention. The best way to avoid stem rot is by following the care needs of your plants and keeping them as healthy as possible.

Stem rot fungi don’t stand much of a chance against a fully healthy plant with strong roots, but they do with plants that are already struggling. Especially considering that stem rot fungi lead to serious decline in plant health, if your plant isn’t at full strength you’ll likely lose it.

However, if you go easy with watering and make an effort to keep your plants in healthy soil, you shouldn’t have any problems with stem rot!

stem rot 1 stem rot 2

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