Root rot in plants: symptoms & treatment


For many years now, I have been growing various vegetables as a hobby in my spare time, which is what ultimately led me to studying horticulture. I find it fascinating to watch as plants grow from seed to fruit and to then finally be able to make use of the literal fruits of my labour.

Favourite fruit: Strawberries and cherries
Favourite vegetable: Potatoes, tomatoes and garlic

Sadly, root rot often ends the life of our beloved plants. Find out here how to correctly recognise, prevent and treat root rot.

root rot succulents
Root rot can be the end of a beloved houseplant [Photo: Stanislav71/]

Root rot is a common disease in plants. If the base of the plant begins to look soft and wilted, it can be one of the first signs of root rot. Unfortunately, all plants ranging from small plants in the garden bed to large trees can be affected by root rot. Usually, the root neck or even the whole root system will be affected by this disease and what remains is nothing but a soft, rotten mass.

Why do the plant roots start to rot and die in the first place? In most cases, bacteria and fungi are to be blamed for the plant damage. The exact causes of root rot, how you can recognise it and what to do to treat and prevent this disease will be explained in the following.

Root rot: possible causes

Root rot caused by fungi

Root fungi are one of the most common pathogens that attack and damage the roots of plants. Above ground, these types of fungi lead to wilting and chlorosis, i.e. the whitening or yellowing of the leaves. Most root rot can be traced back to different species of the common fungus Pythium or the oomycete Phytophthora, but there are many more fungi that cause rotting of the plant’s roots. Other well-known pathogens include Rhizoctonia, Fusarium or Phoma. However, it is often difficult to identify the exact cause of the disease, because the root system is underground, and the parts above ground usually only show symptoms of root rot in later stages of the disease. Here is a list of the most common fungal diseases and their symptoms:

phytophthora symptoms
Above ground root rot leads to chlorosis [Photo: Sarah2/]

Pythium induced root rot

  • The seedlings turn black at the base, rot and fall off
  • Roots grow at a slower pace and eventually rot
  • Root bark peels off
  • Plants wilt, turn yellow and start to rot
  • This disease is mostly caused by fungi belonging to the genus Pythium


  • Blackleg is caused by the soil-borne fungus Thielaviopsis basicola, also known as Chalara elegans
  • Roots turn brown and dry, while the root tips remain white
  • Leaves turn yellow and their growth slows down (however they do not die)
  • Commonly found in Cyclamen, chrysanthemums, pelargoniums, lettuce (Lactuca sativa), tomatoes (Solanum lycopersicum), legumes and elderberry (Sambucus)
  • In carrots (Daucus carota subsp. sativus), this fungus causes rot during storage. The fungus Chalaropsis thielavioides is a common secondary infection in carrots that may occur alongside this disease
Carrots with black spots
Blackleg attacks carrots in storage [Photo: Stella Photography/]


  • The pathogens invade the plants through root tips or wounds
  • They clog the veins of the plant and cause toxic substances to develop
  • They cause root rot in spinach (Spinacia) and onions (Allium cepa)

Early blight

  • Early blight is often caused by Alternaria species (Alternaria solani or Alternaria alternate cause this disease in potatoes)
  • Brown to black spots appear on the leaves, the stem also turns brown
  • Dark, caved-in spots start forming on the tubers and the potato tissue underneath loses its colour, hardens and dies off

Black scurf

  • Lettuce begins to rot due to Rhizoctonia solani starting at the lower leaves
  • Potatoes get stains and form a grey to white coating on the stems and the base can turn brown in the growing process
  • Potato tubers become deformed, develop spots and the core tissue dies off (also known as “dry core”)

Pink root

  • Caused by various Phoma species
  • Roots turn light pink, light purple (violet) or brown
  • Leaves change colour and plants with pink root can be pulled out of the ground quite easily
  • The species Phoma betae, for example, causes root rot in turnips (Beta) and may also cause decay in storage
tree root rot
Rotted roots can lead to plant death [Photo: Kritchai7752/]

Rot caused by Aphanomyces

  • Causes root rot in legumes, such as garden beans (Phaseolus vulgaris) or peas (Pisum sativum), or black root in radishes
  • The black root in radishes is caused by the fungus Aphanomyces raphani
  • Radishes (Raphanus) turn blue to black on the outside and, eventually, the inside rots away
  • After Aphanomyces infests the plant, bacteria or Rhizoctonia solani can also infect the diseased plants

Root rot caused by bacteria

Unfortunately, bacteria often join in when rotting occurs. However, bacterial rot can also develop by itself in damp weather. The following species are examples of bacteria that cause rotting:

  • Erwinia
  • Pseudomonas
  • Rhizomonas
  • Xanthomonas

An infection induced by bacteria is often caused by waterlogging in the soil. For this reason, bacterial rot is also referred to as wet rot or soft rot. As a result, moist patches tend to develop on carrots, onions and other plant parts that grow underground. What is more, wilting starts to occur, and the plants begin to rot and become mushy.

Late blight as a cause of root rot

Root rot on potatoes is caused by Phytophthora infestans. This fungus is very well known because it was one of the causes for the Great Irish Famine in the 19th century. When potatoes (Solanum tuberosum) are infested with blight, the stems turn brown and spots appear on the leaves. Above the ground, the plant dries up, while below the surface, the tubers rot. On tomatoes (Solanum lycopersicum), the fungus causes late blight and brown rot.

root rot disease
Late blight on tomatoes can be caused by fungi [Photo: Elena Masiutkina/]

Identifying root rot

Since there are so many different possible causes of root rot, it is often difficult to identify the culprit. In many cases, only a microscope or a laboratory would help. However, it is certain that signs of wilting are a typical symptom of root rot. Upon noticing this symptom, people tend to water the plants even more, which really results in exactly the opposite effect of what one would hope for. It is only when the plants have died, and they are taken out of the soil that the extent of the damage is fully visible. Therefore, we cannot stress this enough: the cause of death of most plants, including houseplants, is excessive watering and not drying out! Avoid waterlogging at all costs and you will most likely prevent root rot in plants.

In addition to wilting, both discoloration and chlorosis often occur on the leaves as a result of root rot. The roots also lose their usual colour and rot away. The same goes for root neck rot: it first discolours and then disintegrates. Once the roots rot, they can no longer provide support to the plants which makes it extremely easy to pull them out of the ground. Due to the damaged roots and the partially clogged plant veins, the plants no longer absorb the nutrients they require, and thus eventually die.

Root rot treatment and prevention

In the following, we summarised the most important tips for preventing and controlling root rot in plants:

Tip 1: Avoid waterlogging

In general, rotting can be treated by controlling the environment. Excess moisture promotes fungal infections, so avoid waterlogging and keep the soil or substrate loose and well-aerated. The more solid and moist the soil is, the more likely root rot will occur.

seedling in the rain
Waterlogging promotes fungal infection on plants [Photo: oksanika/]

Tip 2: Rotate your crops

If root rot occurs in the garden, it is crucial to pay attention to the crop rotation in the following year. Pathogens usually affect only specific crops or crop families. Therefore, make sure to change around the garden occasionally. If a potato plant rots, for instance, avoid planting potatoes in the same place in the following year. In fact, it would be best not to cultivate any members of the Solanaceae family there at all. Following a varied crop rotation and loosening up the soil can prevent root rot.

Tip 3: Beware of cachepots

To grow houseplants indoors, many people choose cachepots. Although these types of pots are decorative, houseplants are easily drowned in them. It is easy to overlook that there is still water in the pot and drown the plants without realising. Moreover, the stagnant moisture that often occurs in these pots, promotes an infestation of root rot pathogens.

Tip 4: Till the soil

With heavy garden soils, incorporating sandy material or compost is helpful. Organic materials increase the amount of humus and the soil’s water storage capacity.

Tip 5: Prevention instead of treatment

Precaution is better than cure and this is definitely true for avoiding root rot. Applying fungicides to cure root rot can have no effects whatsoever because the product won’t reach the fungi in the soil effectively. Nevertheless, there are various plant strengthening agents that can be used to impede rotting and promote a healthy growth of the plant. Unfortunately, although there is a lot that can be done in order to prevent root rot, it is usually too late for that when the situation has already turned acute. Therefore, it is recommended to maintain good conditions in the soil and keep up crop rotation in the garden beds. Furthermore, the plants can be protected from rotting with anti-rot agents.

natural remedies for root rot
By taking care of soil conditions you can prevent root rot [Photo: Mintr/]

Certain home-made extracts will help prevent root rot. Here are some examples:

  • Camomile extract: for this rot-proof extract, simply take a handful of dried camomile flowers (Matricaria chamomilla) and soak them in 1 to 2 litres of water for one day. Dilute the extract in the ratio of 1:5 before use.
  • Garlic extract: chop about 300 g of garlic cloves into fine pieces, brew the garlic (Allium sativum) in 5 litres of hot water. Next, let it steep for one day and dilute the extract in a ratio of 1:3. Finally, dip the root ball of the plant in this extract before planting in order to avoid root diseases.
  • Horsetail extract: combine 10 litres of water and 1 kg of fresh horsetail (Equisetum) and leave it to stand for one day before boiling the mixture for half an hour. Dilute the brew in a ratio of 1:5 and use it for treating soil fungus diseases.
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