Best fungicide for root rot

by Matt Gibson

So you may have overwatered your plants once or twice. Then you start to see the leaves getting dull, turning yellow, and looking rather sick. You take steps to correct the watering issue, but the plants don’t bounce back. Chances are, your garden is suffering from root and stem rot. These types of garden rot is caused by one of two issues. Either your plants got waterlogged due to overwatering or improper drainage or a fungus in the soil attacked and infected the roots.

If the crown or major roots are affected, your plants are in for some dark times, and without immediate help, they will wither away and die. There are some actions you can take to save them, but if the roots are too far gone, it’s best to discard, disinfect, take preventive measures against future attacks of fungal disease, and start again.

Not sure whether root and stem rot is the culprit? Smell the base of your plant around the root area. If it smells awful and moldy, it’s probably root rot. Remove the plant from the soil. Do the roots look white, firm, and healthy? Or are they brown and slimy? If they are brown and slimy, root rot is most likely the cause.

Symptoms of Root and Stem Rot

If you notice that your plants are slowly wilting and the leaves are turning yellow or dull for no known reason, your plants may be affected by root and stem rot. The wilting and dulling of color may happen quickly or over the course of several months.

Check the roots of one of the plants by removing it from the soil and feeling the roots with your hands. If the roots feel mushy and look dark instead of a creamy white or tan, you probably have root rot issues. Sometimes, infected roots will fall off when you touch them. Some healthy roots can be black or dark-colored, but they will still be firm to the touch, not mushy or limp. However, most healthy roots will be light-colored, which means that they are functioning well and are not suffocated by waterlogged soil with insufficient drainage.

Healthy roots have smaller feeder roots, or rootlets, which can be easily spotted when checking the root system. On plants affected by root rot, the feeder roots will no longer be attached. Usually, if the roots are affected by rot, the crown of the plant will also begin to turn brown or darken in color.

Treating Root and Stem Rot

In order to treat plants affected by root rot, swift action must be taken to save your crops. If you caught the problem early enough, there’s a good chance that you can address the issue and give your plants a fighting chance to bounce back. Remove the affected plants from the soil, and gently wash the roots under running water. Wash away as much soil as possible, and don’t worry about any affected roots that fall off in the process. Try and be as gentle with the plant as possible while you’re treating them, though.

Using a sharp, clean pair of gardening shears or scissors, cut away all of the remaining roots that are affected. This may involve removing the majority of the root system if the plant is severely impacted by rot. If so, reclean the scissors with rubbing alcohol after removing infected roots, and then trim back one-third to one-half of the leaves on the plant. Because the plant will not need to support as much top growth once it’s trimmed, it will have a better opportunity to regrow the root system and get back to good health.

Resume treatment by disposing of all the soil in the pot that the plant was in. If the plant was not in a pot, you may consider potting it now and treating the garden bed soil with a fungicide and/or solarization. After throwing out the soil from the pot, wash the pot thoroughly with a solution that is one part bleach and nine parts water. If you have fungicide on hand, dip the remaining roots in the fungicide to kill off any fungus that may be lingering around. Now that the root rot has been treated and the pot has been sanitized, repot the plant in fresh, clean potting mix.

Make sure that the plant’s new container has good drainage, and only water it when the top of the soil is dry as a bone. Allow the plant five to seven days to regrow its root system before adding any fertilizer, as it may shock or stress the recovering plant.


There’s no getting around it: all badly affected plants need to be removed and destroyed. Only try to treat moderately affected plants. If you were planting in containers, the control process is a simple fix. Toss out all impacted soil, as you don’t want to risk recontamination. Thoroughly clean all containers with a bleach solution that is one part bleach and nine parts water. Don’t forget to clean any and all tools that you used during the process of decontamination, including your gloves and even shoes.

If you were gardening in the ground or in garden beds, control may be a bit more difficult and time-consuming process than you had hoped, but it’s not impossible. One method you may want to consider is a fungicide soil drench. This can be a costly process, and you will want to get help from a professional if this is something you want to look into. The recommended approach to prevent future problems is soil solarization.

Soil solarization is the process of covering your soil with a tarp so that it heats up to more than 125 degrees Fahrenheit, killing off any fungus and bacteria that the soil may be harboring. Not only does soil solarization kill fungus and bacteria, it also wipes out a wide range of other pests that can wreak havoc on your garden beds, including nematodes and noxious weed seed. Plus, heating up your soil using solarization also stimulates the release of nutrients from the organic matter that is present in the soil. So after the solarization process is complete, your garden beds will be ready to produce like never before.

First, till the top layer of the soil. Then, rake the top layer until the surface area is smooth and even. Because wet soil conducts heat more efficiently than dry soil, water the area you plan to solarize until it is damp—but not so overwatered that it becomes soggy, as too much water will keep the temperature from reaching the level needed to kill off the fungus. Once you have a garden full of tilled, level, damp soil, you’re ready to cover it with tarp.

If you live in a warm climate area, cover your garden beds in clear plastic tarp for four to six weeks during the summertime. Ideally, the top six inches of soil will reach temperatures of up to 125 degrees Fahrenheit. If you live in a cooler climate area, use a black tarp instead of a clear tarp, as black tarp will attract the sun’s rays and increase the temperature underneath. In cooler climates, you will also want to leave the tarp in place for eight to 10 weeks, giving it more time to kill off all the fungus, bacteria and pests in the soil.

Preventing Root and Stem Rot

The only true way to fight root and stem rot is prevention. The two main components that lead to rot are temperature and oxygen. Plants, like all living things, need to be able to breathe in order to function properly. If the roots can’t breathe, the plant can’t grow. Prevent this lack of oxygen by making sure that roots are planted deep beneath the soil and that the soil is packed in loosely enough to allow oxygenation. If you are using a hydroponic or aeroponic growing system, make sure your air pump and air stones are large enough to keep water bubbling to allow plentiful amounts of oxygen to reach the root systems.

Hot temperatures are another thing that can lead to mold and mildew infestation. Unfortunately for outdoor gardeners, there’s not a lot that you can do to change the weather, so if you live in a warm climate area, consider adding rocks underneath the soil to improve drainage, and add mulch on the top layer to cool off the soil underneath. Use cool water when hydrating your plants as well, as hot water and hot weather is a bad combo for mold and mildew. Indoor gardeners may simply want to turn up the air conditioning during the summer months and provide plants an environment with proper ventilation.

Root and stem rot is not an uncommon problem, nor is it the end of the world. However, now that the problem has been identified, it’s time to work on a solution. Treating, controlling, and preventing root rot can be an arduous process, but anything worthwhile takes a bit of blood, sweat, and tears. If root and stem rot have taken hold of your garden, don’t give up hope—take up arms. You are now equipped with all the weapons you need to win the fight against rot and take your garden back.

Want to Learn More about Stem and Root Rot?

Gardening Know How Covers Treating Root Rot in Houseplants

GrowAce covers Root Rot: Prevention, Detection, Elimination

SFGate Homeguides covers How to Fight Root Rot

Texas A&M Extension’s Plant Disease Hand Book covers Stem and Root Rot

Veggie Gardener covers Root Rot

Weekend Gardener covers Root Rot

Weekend Gardener covers Will Soil Solarization Kill Fungus

How to Prevent Root Rot

Root rot is a disease of both houseplants and outdoor plants. It happens when the plant has to stand in soil that does not drain well. This leaves the soil wet and encourages pathogens which attack the plant’s roots. When the roots are infected, they can’t get the proper nourishment to the plant. Leaves wilt and become discolored. Eventually, the plant dies. When it’s pulled up, the roots are brown and rotten. Seedlings that have sprouted and seem healthy suddenly fall over, and the gardener sees that they are rotted at the soil line.

There is no cure for root rot. The plant needs to be pulled up and destroyed.

Preventing Root Rot

Keep the Ground Dry
The only way to deal with root rot is to prevent it. This means not watering the plant until the soil is dry. In an area where it rains frequently, the ground needs to be kept dry, and wet soil needs to be turned to allow water to evaporate. A good population of earthworms can also prevent root rot.

Add Perlite
Depressions in the garden that won’t drain well and hold water should be filled in, and the soil needs to be amended with perlite or mulch to help it to drain well. Watering plants before noon let them dry off in the afternoon and discourages the fungi that cause root rot. Plants should be watered from below. This keeps the fungi from being spread through water that splashes on the leaves.

Practice Good Hygiene
The gardener should try to avoid touching wet plants, for this can also spread disease. They should wash their hands after they’ve handled plants that they believe are sick and disinfect gardening tools.

If the gardener believes that the soil is harboring a fungus that causes root rot, one remedy is to shallow-plant seedlings. This encourages them to germinate early and gives them a better chance to survive. There should be good air circulation around the plants, and the gardener should employ three to five-year crop rotations.

Solarizing means heating the soil to around 130 to 140 degrees Fahrenheit over several weeks. Higher temperatures can kill beneficial organisms. To do this, the gardener loosens the soil in the middle of summer, drenches it with water and leaves it undisturbed overnight. The next day, the gardener covers the soil with clear plastic that is secured with rocks or bricks at the edges. They then let the soil heat up for about a month or a month and a half. Then, the plastic is removed and the gardener plants as usual.

There are fungicides that can kill the disease-causing fungi, but the gardener needs to be sure that they use the fungicide made specifically for the organism that’s the source of the problem. The gardener can send a soil sample and a part of a diseased plant to their local cooperative extension. Agents at the extension can identify the fungus and tell the gardener how best to defeat it.

What is root rot?

Root rot is a group of diseases that attack both indoor and outdoor plants, among which also cannabis. These can be caused by a number of different plant pathogens including bacteria (Acidovorax, Agrobacterium, Burkholderia, Clavibacter, Erwinia), nematodes (Tylenchulus, Pratylenchus, Heterodera, Globodera) and fungi (Rhizoctonia, Phytophthora, Fusarium, Pythium).

Most times, however, the condition is caused by a fungus, a microorganism that breeds easily by dispersing spores and sclerotia (a mass of mycelial filaments) and that can survive in the soil for long periods of time even under unfavourable environmental conditions.

One factor that contributes to root rot is poor soil drainage, as a well oxygenated substrate is essential to ensure healthy plant growth.

The disease mainly attacks seeds and seedlings – damping off is a common gardening problem – as these are more vulnerable and have a weaker immune system than full-grown plants.

Hydroponic systems are another common victim of root rot. This is because the tank containing the nutrient solution gets infected easily, contaminating the whole watering system and, ultimately, also the plants.

What are the symptoms of root rot?

Common symptoms include:

  • As the disease progresses, roots change from white to increasingly darker shades of brown.
  • Plants fail to correctly absorb nutrients.
  • Plant growth is stunted.
  • Leaves yellow gradually, as if affected by a nutrient deficiency.
  • Leaf margins become necrotic and curl, causing the entire leaf to dry out and fall.
  • Plants die.

Symptoms of Rhizoctonia:

Rhizoctonia often leads to damping off, and can cause healthy roots to decay from the middle up to the base of the stem. In some cases, the fungus can also attack the leaves.


  • Leaves grow to a smaller size and yellow gradually.
  • Plants become stunted and wilt.
  • The base of the main stem develops ulcers, and the leaves and stems show brownish spots.
  • Roots decay, gradually getting covered in a dark, viscous fluid.
  • If the humidity stays high constantly, a mass of filaments may emerge from the soil, invading the plant up to the leaves.

Symptoms of Phytophthora:

Plants affected by Phytophthora show stunted growth, along with symptoms similar to that of Pythium, but more severe.


  • Leaves wilt, yellow and drop off.
  • The base of the stem develops brownish/reddish ulcers.
  • The bark of stems and the leaves, too, turn brownish/reddish.
  • The roots become dark in colour – this can only be observed by digging them up.
  • The disease spreads quickly from plant to plant.

Symptoms of Fusarium:

Fusarium species attack the roots, the base of the stem and, occasionally, also leaf sheaths, which get covered in a dark, reddish rot. All of which leads to stunted plant growth.

Symptoms of Pythium:

Pythium infections, too, lead to stunted growth.


  • The plant loses vigour and wilts – partly or in full.
  • The corolla gets covered in a blackish, wet rot.

How to prevent root rot

  • Whether you grow indoors or outdoors, always try to verify the quality and origin of your substrate.
  • Use a well aerated soil mix to ensure proper oxygenation.
  • If you grow indoors, keep the grow room scrupulously clean at all times.
  • Check the cleanliness of the pots before sowing.
  • Water regularly, keeping to a strict schedule and avoiding overwatering.
  • Apply a root booster once a week to encourage a healthy root system.
  • Remember that poor ventilation and high humidity can easily lead to root rot.

How to combat root rot

Unfortunately, the diseases causing root rot are hard to eradicate completely. While the above measures may prevent the onset and progression of the disease, severe infections can only be addressed by discarding the crop entirely, starting from scratch with new, healthy plants. Otherwise, you can end up losing precious time applying treatments that won’t fully solve the problem, leading to weak, stunted, ill-looking plants.

Organic treatments: Gardening shops offer a wide variety of organic fungicides based on other fungi and bacteria, such as Streptomyces griseoviridis, which protect the roots against fungal attacks.

These biofungicides are effective against most root rot-causing organisms, and can also be used preventively on both plants and seeds. Usually supplied in the form of wettable powder, they can be applied to the substrate as a spray or soil drench, through capillary absorption or added to the tank of drip irrigation systems. Apply once every 2-5 weeks based on the severity of the infection.

Chemical treatments: If the infection is at an advanced stage, chemical products will prove ineffective. The only solution here is to discard the entire crop and start anew after thoroughly cleaning the grow tools and room, which should be further protected with a preventive antifungal treatment. You’ll see that your next grow will thrive like no other.

Happy harvesting!

Root Rot On Marijuana Plants

Root rot or Pythium is a type of root fungus that attacks the roots of marijuana plants that are already weak due to stress levels, disease, other damage, and nutrient deficiencies.

About root rot on marijuana

  • What is root rot
  • Signs of root rot
  • How to get rid of root rot
  • Root rot in hydro systems
  • Marijuana plant symptoms

Pythium is a parasite and it especially goes after seeds and seedlings – making it a terrible threat to your youngest, most tender plants.

Read this article and learn how to identify and treat root rot before it’s too late.

What is root rot

Root rot multiplies extremely quickly and spreads through giving off tiny spores that cannot be seen by the naked eye. These spores are the real threat, as they will take your marijuana garden from just one plant being affected to having your entire crop infected with root rot!

Root rot can attack plants that are growing in any system, including hydroponic, container, and soil-based growing systems. Although once the fungus has invaded it will be all over your garden, it is surprisingly choosy when it decides which specific plants to attack.

Tip: make sure to download my free Grow Bible for more information about how to prevent root root.

When it does spread, it does so underground, following a water trail between root systems. It germinates while traveling through this path so it is ready to spread once it reaches the roots of its new target. It then disperses itself through the plant’s tissue and creates resting spores that will soon germinate. This is how the fungus is allowed to continuously damage your whole garden, plant by plant.Back to top

Signs of root rot

The problem with this infection is that, since it travels underground and starts at your plant’s root system before hitting the rest of the plant, it is extremely difficult to detect until it’s too late. You will probably start paying attention when your plant’s leaves start wilting and turning yellow with brown edges. If you examine the roots, you will be able to notice the Pythium. Otherwise, however, the symptoms will just be like any other fungal damage.

If you do examine the roots, you will find them to be off color, soft, and watery. These are the signature symptoms of a Pythium infection. After a while, the most external layer will fall off the roots, making the stringy inside visible.

You won’t need to try so hard to see these symptoms if your plants are growing in a hydroponic system, of course, but there are ways to check within a soil setup as well. Simply dig down through the soil and look at the roots to see if they are damaged.

Healthy roots are always white or cream-colored, but Pythium-affected roots are brownish and might emit a mildew or rotting smell. You should check the roots for these signs as soon as your plant starts showing signs of wilting. That being said if your plant isn’t wilting it doesn’t necessarily mean it is not infected with the parasite – you always need to check the roots to be sure one way or the other.

After the wilting, other leaf-specific signs will probably follow, including burning, brown spots, yellow or white coloring, dying and dropping off of leaves, and strange signs of nutrient deficiencies in the leaves. The final symptom comes from the fact that, since it’s the roots where the problem arises, they are unable to function properly, including improper absorption of nutrients.

You may also take note that your plant has been taking in less water than usual. If this is the case alongside the above signs, you should jump into action mode to rid your plant of the Pythium. Not sure if your marijuana plants suffer from a Pythium infection? Check the article Marijuana diseases for a list with pictures of all possible marijuana diseasesBack to top

How to get rid of root rot

The main thing you should do (or maybe should have done) is prevent Pythium from happening in the first place. You first and foremost need to keep your growing site healthy and well-maintained, which will generally help lower the chances of the parasite invading your garden in the first place. The soil should be consistently well-drained and rich in nutrients – this will ensure that the Pythium cannot live happily in the soil, therefore discouraging it from invading at all.

Like most fungi, Pythium thrives in moist soil with warm temperatures (70 degrees Fahrenheit or higher) and high humidity. Be sure not to over-fertilize your plants. Instead, include a compost for your plant’s growing foundation – just make sure the compost has been aged correctly. A soil mixed with this type of compost is also more likely to keep pests and other diseases away because of all the good bacteria and nutrients.

Pest control is also a helpful way to prevent Pythium invasions. Some pests (i.e. the fungus gnat) carry fungus with them, so by keeping them away you will also keep your plants safe from contact with fungi. Make sure you don’t water your plants too much or too often. Make sure you let the top layer of your soil (about an inch deep) dry completely after each watering. This should keep the fungus gnats away.

Download my for more growing tips

Preventative measures with hydroponic growing systems will vary slightly from measures for a typical soil setup. The number one thing you need to worry about in a hydroponic growing system is cleanliness. Keep the environment and every piece of equipment used in the setup clean at all times.

When cleaning the system, use beneficial bacteria that has been added to your normal nutrient solution – this will work better than peroxide for preventing Pythium outbreaks. Peroxide kills the good bacteria as well as the bad, and you will need some of that good bacteria for fighting off infection. Hydroponic systems are particularly at risk from this fungus, simply because an infection would spread rapidly and would be basically impossible for you to stop.

You can also purchase root controls. If you do this, make sure the package specifies that it works for Pythium or root rot. And keep in mind that even some controls that claim to kill root rot will really take care of Pythium, so you really have to know what you’re buying. Other effective methods of control are copper treatments, oil sprays with clove, coriander oil, sesame oil, plus Trichoderma (a “good” fungus) and Marijuana Mold Control

If you have already confirmed the existence of Pythium in your plants by now, you will need to know what to do about it. Some growers prefer not to deal with it, so they simply discard the entire plant once they identify the fungus as the problem.

Download my for more growing tips

If you would like to save your infected plant, however, there are certain steps you can take. First, you have to treat the roots directly since they are the source of the problems. You also will need to change the environment itself so the Pythium no longer has the opportunity to spread and thrive. If you can’t complete the environmental changes, there is no point in trying – the root rot would simply return again and again, no matter what.

If you can change the environment as well as treat the roots, you should be aware that the affected roots will never recover. Because of this fact, you need to look to the new growth to see how your plant is faring with the treatment. You want to keep your eyes peeled for new white roots emerging. The same goes for the affected leaves – they will eventually die, but if your plant is recovering then, new leaves will look healthy and green.
Back to top

Root rot in hydro systems

To treat root rot and ensure it never returns to your hydroponic marijuana setup, you will first need to change the temperature of the growing space. This will also lower the water temperature in your reservoir, which is perfect.

By lowering the temperature, you are allowing more oxygen to be held in the water, which your plants need to properly combat this parasite. Increased oxygen intake also has the added bonus of speeding up plant growth in general. Pythium comes when the water temperature is too high (usually above 72 degrees Fahrenheit). If the temperature is kept 72 degrees or lower, you will greatly reduce the chances of root rot occurring. If you have a good supplement, however, higher temperatures will be okay.

As a second way of increasing your plants’ oxygen intake in a hydroponic system, you could purchase a large air pump and air stones. More bubbles and surface movement, in general, is useful in increasing the oxygen content of the water. Oxygen helps your plants grow, plus Pythium does not like water that has lots of oxygen, making this a twofold way of keeping your plants healthy.

Another option is to specifically add good bacteria to the water in a hydroponic system, which will help with any root-based diseases or conditions, as well as making nutrients more available for absorption by the plant.

Download my for more growing tips

In a hydroponic system, you need to be sure to consistently and frequently change the reservoir water. A minimum of every two weeks is a good rule of thumb, although many growers recommend even more frequent changes. Changing the water will allow your plants to have more nutrient access and will also avoid nutrient toxicities and deficiencies. Also clean out any dead matter (roots, leaves, etc.) right away and keep it out of your reservoir. Dead materials are a bacteria’s heaven – so don’t give them the chance to grow.

You also need to keep light away from your reservoir water and roots – it will heat it up too much, and that in combination with the extra light provides a great place for bad bacteria to grow. You can also prevent bad bacteria from getting into your system by cleaning all the equipment before you start growing. This will kill bacteria before it ever has the chance to infect your plants.

While some growers do it, it’s better to not use hydrogen peroxide (H2O2) to treat Pythium. It has only a temporary effectiveness (one day or so), meaning it would require daily treatments. For this reason, it might not work at all, and it will kill all the beneficial bacteria in the process. It is not recommended that you use hydrogen peroxide to deal with Pythium.Back to top

Marijuana plant symptoms

Leaf Color:

  • Brown or burnt edges
  • Pale color
  • New growths: yellow
  • Lower, older leave: yellow
  • Brown or dark-colored spotting

Leaf Symptoms:

  • Burnt leaf edges
  • Burnt leaf tips
  • Death of leaf tips
  • Curling under of leaves
  • Curling upward of leaves
  • Spots
  • Old leaves falling off
  • Slowed growth
  • Abnormal growth
  • Wilting or drooping leaves

Plant Symptoms:– Weak stems

  • Slowed growth
  • Wilting or drooping of entire plant

Root Symptoms:

  • Brown
  • Smelly
  • Mushy
  • Slowed growth

Pythium happens more commonly with indoor marijuana plants, so make sure from the get-go you are keeping the soil well-drained and the temperatures low enough. Since this infection is usually a result of watering your plants too much or too often, this should be considered for both indoor and outdoor grown marijuana plants. Pay special attention to how much your plants are absorbing, and make changes accordingly.

Remember that plants with strong genetics have less change of getting sick and are less vulnerable for pests and diseases. So make sure to buy cannabis seeds from a trusted seed bank.

Thanks for reading. Please leave comments or questions below and don’t forget to download my free grow bible.


The founder of I Love Growing Marijuana, Robert Bergman, is a marijuana growing expert that enjoys sharing his knowledge with the world. He combines years of experience, ranging from small-scale grows to massive operations, with a passion for growing. His articles include tutorials on growing…

Root Rot

Roots of vegetable plants may decline and die from a variety of causes. Unfavorable environments that result in either waterlogged or drought conditions are common causes of poor root health on vegetable plants.

There are also fungi in the soils that have the ability to infect roots and cause root rot. If major roots or the crown are affected by root rots or other problems, the entire plant can wilt and die rapidly. If only the small “feeder” rootlets are affected, the plant may decline slowly and appear generally sickly and unproductive. Sick or damaged roots may be present only on part of a plant’s root system, resulting in a one-sided appearance of symptoms on leaves and stems.


The first symptom of poor root health is usually dull foliage color. Sometimes leaves turn yellow and wilt. These changes may occur quickly or may take months to develop.

Examine plant roots directly to further verify the presence of root problems. Examination should be made soon after the plant is showing symptoms or just after it is killed, not after it has been dead for some time.

On healthy root systems white feeder rootlets are visible. With many root disorders, these tiny feeder roots are absent. Rotted roots will be brown and mushy. Outer root tissue can be easily pulled or slid off the inner root core with your fingers. The core will remain, looking like a tiny piece of white or brown thread.

Many of the root rot fungi, in addition to attacking small roots, also invade older roots and stem tissue. On soft-stemmed plants, the symptoms are visible on the surface of the stem, extending various distances up the stem from the soil line. Infections may be spotty or may cover the entire crown. Infections may first appear as brown streaks in the stems.


Root disorders and problems generally arise when plants are growing under unfavorable conditions. Management strategies, therefore, involve cultural changes aimed at increasing plant vigor. These include improving soil drainage and use of proper planting techniques. It is especially important to consider these management strategies in situations where plants have died and you intend to replace them in the same location.

Soil Drainage Improvement

Most root disorders can be prevented by providing good soil drainage. Most plants are attacked by pathogenic root rotting fungi when the base of the plant and roots are waterlogged for many hours. This is particularly true during the late spring and summer months, when the disease-causing organisms are most active.

Surface drainage problems can be easily prevented with planning. Soil surfaces should always slope away from buildings. Low areas sometimes cause problems because they cannot easily be graded to provide for adequate surface drainage. In such cases, drainage channels or underground drains may need to be constructed.

Good internal drainage, which is the movement of water through the soil, will influence the effective rooting depth and resulting plant vigor. Many gardens remain internally saturated because of underlying clay and rock layers. Sandy soils are generally well drained, but can be subject to dryness. Frequent light watering may be required because of their low water-holding capacities.

Internal drainage should be good on deep soils with sloping surfaces. Layers that restrict downward water movement, however, may cause poor internal drainage, even on slopes. This generally appears as a down-slope damp or soggy condition showing at the ground surface. Obviously, rooting conditions and plant vigor are adversely affected in such areas. Additionally, a slope may have good surface and internal drainage but often the base of the slope will remain wet for a long time. Placing a drain across the slope near its base or just above a damp spot on a slope will collect water from above and improve drainage.

Shallow underground water or high water tables are sometimes found in urban soil. If this standing water is below rooting depth, there is no problem. If it is shallow, underground drains may be installed to remove excess water. Expert advice should be obtained before these drains are installed.

Compacted layers of dense clay subsoil, or solid rock often cause internal drainage problems. A saturated soil area or perched water table will develop above the compacted layer or other barrier to water percolation. This zone is favorable for damaging root rot organisms unless it is deeper than the root system. If the soil below the compacted layer is found to be noncompacted, then the condition might be improved. This is done by removing the compacted layer through shoveling or back-hoeing and returning the soil to the hole. Drainage holes can sometimes be drilled through compacted layers to relieve or remove the perched water table.

Planting holes with drains can be built in rock or compacted soil to provide a desirable site for a particular tree or shrub. These measures are usually special cases. For good plant growth on such sites, they are necessary.

Planting to Avoid Root Rot

The planting hole should be at least twice the width of the root ball if potted plants are being used. The hole should be large enough to accommodate the roots without crowding. The sides of the hole should be rough and jagged. Check drainage conditions by filling the hole with water. If water drains in 24 to 28 hours it can be assumed that there is enough drainage. If water stands in the hole, corrective measures should be taken (see above), or only plants tolerant of poorly drained sites should be used.

Mix the removed soil to break up compacted layers and return some to the hole just prior to placement of the plant. Break some of the roots on the root ball surface of potted plants to encourage root growth into the surrounding soil. Make sure to straighten out any twisted roots to avoid girdling later on.

Place the plants so that they will be slightly higher after settling than they were in the container or nursery field. Never set the plant deeper than originally grown. Bring surrounding soil up to the old soil level. On poorly drained sites, it may be necessary to plant in raised beds. These beds may be bordered by rocks, old railroad ties, or other structural materials specially treated and designed for landscape use. Mulch the soil surface lightly to reduce the likelihood of heat and moisture stress.

Treating Root Problems

What can be done to save a plant that is already damaged? Certain fungicides are somewhat effective against root and crown rotting fungi in nursery or greenhouse production programs. Insufficient tests have been conducted to prove that they are effective in the landscape. Improving drainage, as mentioned above, can save some plants. Here are some other treatments which may help:

  • Avoid over-watering. A number of plants used in landscaping require little watering once they are established. Always allow the soil around plants to dry out a few inches below the surface before watering again.
  • Do not water the base of trees and shrubs directly. Water away from the trunks.
  • Improve moisture conditions around the crown of the plant by exposing the base of the plant to drying conditions. Remove some of the soil or the mulch. However, do not expose roots.
  • Do not fertilize plants during hot, dry weather periods.
  • Vertically mulch or core aerate to improve landscape soils. Vertical mulching will hasten drainage of excessive water, preserve necessary aeration during wet periods, improve water infiltration during dry periods, and promote the formation of fine feeder roots. Drill one-inch or two-inch wide, 18-inch deep holes in the soil on 12 to 20-inch centers under affected trees near the drip line of the branches (where fine feeder roots are located). Fill holes with a mixture of equal parts of peat and a coarse aggregate such as pumice or calcined (baked) clay particles.
  • Thoroughly water plants that will hold green leaves or needles through the winter in late fall if conditions are dry. Evergreen plants continue to need water throughout the year.
  • Fungicide drenches are generally not prescribed for root rot control of landscape plants. The reasons for this are that the cultural practices listed above will naturally control most of the associated infectious disease problems. Furthermore, fungicides are difficult to apply to the roots of mature plants and will not cure already infected roots.

Thielaviopsis basicola (Black root rot of tobacco and ornamentals)

Taxonomy Kingdom: Fungi Phylum: Ascomycota Class: Sordariomycetes Order: Microascales Family: Ceratocystidaceae Genus: Thielaviopsis Species: T. basicola Subspecies: T. basicola Scientific Name Thielaviopsis basicola
(Berk. & Broome) Ferraris Common Names and Diseases black root rot, Thielaviopsis root rot

Author: David Shew and Garrett Ridge, North Carolina State University

Scientific Name Synonym

Chalara elegans Nag Raj & W.B. Kendr.


Thielaviopsis basicola is a soilborne fungus in the phylum Ascomycota. T. basicola reproduces asexually by producing two types of conidia, endoconidia and aleuriospores. Endoconidia (also called phialospores) (7.5 to 19 × 3 to 5 µm) are single-celled hyaline spores with slightly rounded ends that are produced within elongate terminal phialides (Figures 1-3). If undisturbed, the conidia stick together end-to-end, forming long unbranched chains. Aleuriospores are darkly pigmented, cylindrical spores that contain 2 to 8 cells and measure 24 to 55 µm in length, with the terminal cell having a rounded apex (Figure 4). At maturity and before germinating, the cells fragment along the transverse septa, leaving two to eight short-cylindrical one-celled spores (6.5 to 14 × 9 to 13 µm) usually referred to as chlamydospores (Figure 5). Reproduction in this species is entirely asexual, but molecular evidence indicates that T. basicola fits within the teleomorph genus Ceratocystis.

Hosts, Signs, and Symptoms

Thielaviopsis basicola infects a wide range of hosts, causing root diseases on over 200 plant species. While primarily a root rot pathogen, symptoms may also include stem rot and damping off on some hosts. Black root rot is particularly severe on Japanese holly, pansy and other Viola species, and on tobacco. Other ornamentals commonly affected by black root rot are Madagascar periwinkle, calibrachoa, petunia, cyclamen, poinsettia, florist’s cineraria, and geranium. Many herbaceous perennials also are susceptible to black root rot, including Asarum, Heuchera, Tiarella, and Phlox subulata.

The primary sign observed on diseased tissue is the dark brown aleuriospores that appear black in mass. On susceptible hosts, the abundant sporulation can enhance the dark or black appearance of the lesion and gives the disease its common name, black root rot. When observed under magnification, both aleuriospores and endoconidia are usually present.

Above-ground symptoms of black root rot are typical of many other root rots or root problems and include chlorosis, defoliation, stunting, and wilting (Figures 6 and 7). Infected root tissue first develops dark brown to black elongated lesions (Figure -). The disease can quickly progress until much of the root system may take on a black discoloration (Figures 8 and 9). The cortical tissue collapses and the epidermis and cortical tissue may slough off, but decay is not as generalized as with Pythium or Phytophthora root rots. Co-infection with Pythium is common. Symptoms may include necrosis of the stem below the soil surface on some plant species. On poinsettia, longitudinal cracking of the stem may begin below the soil surface and extend up the stem.


T. basicola is a hemibiotrophic plant pathogen, with an initial biotrophic phase as it invades and colonizes living cells followed by a necrotrophic phase with the death of the plant cells. Chlamydospores of T. basicola can survive in soil for several years and serve as the primary source of inoculum. The fungus is spread when healthy roots come in contact with infected roots or infested soil and when aleuriospores are dispersed by splashing water. In the greenhouse, previously infected pieces of root that remain attached to pots, flats, and plug trays are an important source of inoculum for subsequent crops. Additionally, fungus gnats and shore flies can spread T. basicola, when feeding on root tips and other plant parts. Active black root rot infection sites are a preferred food source for these insects. Soil environmental conditions, especially cool soil temperatures (13 to 18°C) and pH values above 5.5, are critical for the development of black root rot. Temperatures that are unfavorable for the growth of the host may result in maximum disease severity. Movement of the pathogen from field to field is attributed to the movement of infested soil on equipment.

Geographic Distribution

M. J. Berkeley and C. E. Broome described T. basicola on peas and on Nemophila sp. in England in 1850. Thielaviopsis basicola has been reported from most regions of the world, most commonly in areas with cool and moist climates. The fungus is found in all major production areas for very susceptible crops.


In greenhouses and nurseries, incoming plants of susceptible species must be inspected to be sure that they are free from black root rot. This may be difficult in early stages of infection. Care must be taken that pots, flats, and potting mixes do not come in contact with native soil.

Environmental conditions are important for disease management and prevention. Soil temperatures should be favorable for the growth of the plant and soil pH should be kept low to limit disease development. In areas where pansies are used for winter color in the landscape, they should be transplanted only after the weather has cooled in the fall. Black root rot is generally more severe at soil pH values >5.6 and suppressed under more acidic conditions (pH < 5.2). In large nurseries or greenhouses, it may be possible to treat beds or bulk soil with aerated steam. All areas must be brought to a temperature of 71 to 82°C for 30 minutes. Steam treatment for used pots and flats is also recommended. For plastic items, the center of the stack should be held at 66 to 71°C for one hour. Chemical disinfectants can also be used.

Soil solarization with clear polyethylene tarps as well as soil flooding has been shown to be effective in reducing or eliminating T. basicola soil populations in field soils.

Crop rotation with grain crops is recommended for management of black root rot affecting tobacco. Leguminous cover crops and cotton are susceptible to T. basicola and should be avoided.

In tobacco, resistance is well characterized with complete single dominant gene resistance from Nicotiana debneyi and a number of sources of partial resistance in N. tabacum.

The incorporation of a biological control product based on Trichoderma or Pseudomonas into potting media could be beneficial for managing black root rot. Pseudomonas fluorescens strain CHA0, isolated from a suppressive soil, has been shown to be very effective in managing black root rot on tobacco. Other strains of P. fluorescens also have been reported to control black root rot.


Fungicide treatments for management of black root rot are protective in nature. Infected plants and those adjacent to them in pots and flats should be discarded. In the ornamentals industry, fungicide drenches with either thiophanate-methyl, fludioxonil, triflumizole, or thiophanate-methyl and etridiazole should be used preventatively or at the first indication of disease.

Sterol-inhibiting fungicides like flusilazole and triadimenol also have been shown to be effective in disease control for field crops. Fungicides with different modes of action can be applied in alternation, in tank mixes, or in pre-mixed products to deter the development and build-up of resistant strains. The use of a non-selective fungicide as the final spray of the season is strongly encouraged.

In greenhouses, benches need to be first cleaned and then sanitized between crops using a disinfectant based on one of a number of active ingredients, including sodium hypochlorite and copper oxychloride. Effective disinfestation of T. basicola from greenhouse surfaces is difficult to achieve.

Diagnostic procedures

The fungus is easily identified by its two distinct spore types. After washing roots, examine them carefully under the dissecting microscope for typical blackened sections and streaks. Often the shape of individual aleuriospores can be distinguished. If there is any doubt, suspect roots can be examined further at 100x. Caution: roots and crowns should always be examined before rinsing, which may remove evidence of other pathogens such as Cylindrocladium/Calonectria. If diagnosis is unclear, incubate affected tissue within a surface-sterilized carrot bait following this carrot bait protocol. If T. basicola is present, chlamydospores of the fungus will be visible, under magnification, in the carrot tissue.

T. basicola forms a gray-brown to black colony on most nutrient media, but is likely to be overrun by other soil fungi. Mycelial growth is greatest at 20 to 25°C and pH levels of 4.0 to 6.5. One of the most widely used selective media for T. basicola is the medium TB-CEN developed by Specht and Griffin. Diseased roots can be immersed in this medium for isolation, but it functions best when used for detection in soil assays (D. Shew, personal communication). Plates should not be discarded as negative until after at least 10 days of incubation.

Resources and References


  • National Institute of Food and Agriculture, U.S. Department of Agriculture, under Agreement No. 2011-41530-30708 as part of “Diagnostic Image Series Development for Supporting IPM in the Southern Region” (USDA-NIFA-RIPM-003351)

Black Root Rot of Strawberry

Skip to Management


1. Site Selection and Farming Systems

Choose a site with adequate aeration and drainage; rotate out of strawberries at least every 3 years into crops that are NOT hosts of Rhizoctonia spp., including crucifers and legumes. Sweet corn, sudangrass, and pumpkins are good choices.

Considerable research and practical implementation has been done in non-fumigant based management systems and in organic production systems. The most promising systems combine crop rotation with a cover-crop plus compost (CC+C) system or a method called Anaerobic Soil Disinfestation (ASD). The CC+C and ASD systems require considerable management but are consistent with organic and soil-health objectives. Detailed information is available for growers who wish to pursue these farming systems.

2. Use Disease-Free Plants and Host Resistance

These pathogens can be imported with transplants from both plug and bare root production systems. However, in our experience, the local soil population and soil management choices has more impact on the amount of BRR than plant source effects. Some tolerant cultivars exist but there are no resistant ones, since cultivars resistant to one pathogenic species are rarely resistant to others involved in the complex.

3. Monitor and Husbandry

Minimize stresses that exacerbate the problem. Maintain moisture and avoid temperature stress by mulching and using adequate irrigation. Use caution when applying herbicides, since injury due to over application may lead to greater black root rot susceptibility. Maintain organic matter and avoid compaction of the soil.


Fumigating the field prior to planting is highly effective. Fields with a history of strawberry production can experience a reduction in yield of 20-40% in the absence of fumigation and without other mitigation practices. Unlike other regions of the world, BRR is the most important issue in North Carolina and surrounding states. For more information on timing and use rates, see our strawberry IPM guide at for current recommendations.

Leave a Reply

Your email address will not be published. Required fields are marked *