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Root Diseases of Greenhouse Crops


The two most common causes of root impairment of greenhouse crops are fertilizer toxicity and plant pathogenic fungi. In some cases, fertilizer toxicity predisposes plants to disease. An accurate diagnosis is necessary to manage the problem effectively.

Abiotic Causes

Abiotic (non-living) causes of root disease include excessive soluble salts, ammonium toxicity, and suffocation due to overwatering.

Most commercially available fertilizers are in the form of salts. When excessive amounts of salts accumulate in the soil solution, they desiccate plant roots.

Ammonium toxicity may occur when fertilizers containing urea or ammonium sulfate are used. Excessive levels of ammonium may also occur following steaming of organic soils, especially those containing manure. The conversion of ammonium to nitrate is carried out by soil microorganisms which are virtually non-existent in soilless media. The conversion can also be inhibited by certain pesticides, cool wet soil, low pH, excessive soluble salts, and poor aeration.

Roots must have oxygen or suffocation will occur. Soil composed of very fine particles is dense and has few air spaces. Similarly, a waterlogged soil contains little air. Plant pathogenic water molds thrive under saturated conditions.

Root Diseases Caused by Fungi and Fungus-like Organisms

Extensive root decay will result in wilt, but earlier symptoms can be seen by removing the pot and examining the roots. Healthy roots are generally white and firm; decayed roots may be water-soaked in appearance and/or darkened and easily macerated between the fingers. Some root colonizing fungi will move into the stem and cause canker or "black leg". Several fungi and fungus-like organisms can cause root diseases in greenhouse crops: four of the most common are described below.

All of the organisms described below are natural inhabitants of the soil and form survival structures that allow them to survive in soil for many years. They can also persist in soil and crop debris in the greenhouse.

Pythium is one of the most common pathogens found in the roots of greenhouse crops and is often associated with excessive nutrient levels or ammonium toxicity. The genus includes more than 100 species which vary in their pathogenicity to plants and sensitivity to fungicides. Many Pythium species have wide host ranges and can also cause damping-off, crown rot, and stem rot. Pythium is favored by high fertility and high moisture. Many greenhouse isolates of Pythium are resistant to metalaxyl.

Phytophthora, a related organism, is generally more pathogenic than Pythium but is less frequently encountered. The pathogen most often causes root and crown rot, but it can also cause foliar blight. Like Pythium, Phytophthora is favored by excess moisture and excess nitrogen fertility. Unlike Pythium, species of Phytophthora are more aggressive, more likely to be host specific, and less frequently found in greenhouses. The most likely source of origin is plant material. Optimum conditions for disease  development are saturated soil and high nitrogen fertility.  The pathogen is not likely to be seed-borne in commercial seed, and it does not travel easily through the air for long distances. It is possible that contaminated irrigation water can introduce the pathogen to new sites. Prevention is the key to managing Phytophthora  because it is difficult to suppress with fungicides once it develops.

Both Pythium and Phytophthora are most destructive when soil moisture is abundant. They are not true fungi, but rather members of the Oomycetes (also called "water molds") and as such are controlled by completely different fungicides than true fungi like Rhizoctonia and Thielaviopsis.

Rhizoctonia is also a common cause of root disease and stem canker. Rhizoctonia solani causes damping-off, root rot, crown rot, web blight, and stem canker in numerous greenhouse grown crops. Unlike Pythium and Phytophthora, dry soil is more favorable for disease development. For this reason, Rhizoctonia is more active in the upper portion of the soil. This pathogen is usually a problem in the cuttings and small transplant stage. The presence of wounds caused by insects or mechanical damage can predispose plants to Rhizoctonia infection.

Thielviopsis root and stem rot is caused by Thielaviopsis basicola. The fungus can survive in infested soil for years as chlamydospores. These dark spores give infected plant parts a black coloration which has resulted in the common name, Black Rot. The pathogen has a wide host range among ornamental and vegetable crops, with pansy and Calibrachoa being particularly susceptible. Black Rot is most severe in cold, wet soils. Thielaviopsis is favored by alkaline pH and can be managed by keeping the pH of the media at 5.5 in crops that will tolerate it.

Sources of Root Pathogens

Fungi that attack root systems are natural inhabitants of the soil and thus have the ability to survive there indefinitely. They are easily introduced into the growth medium by soiled hands, tools, flats and colonized transplants. Greenhouse floors may also harbor pathogenic fungi so it is important to keep watering nozzles off the floor. When a soilless medium is amended with field soil, it must be treated to prevent the introduction of plant pathogens, nematodes, insects and weeds. Fumigation or steaming of soilless media is not recommended; however, when a soilless medium becomes contaminated with plant pathogens, root rot can develop quickly due to the lack of competing microbes. Fungus gnats and shore flies may introduce and spread these pathogens within a crop. Biological and chemical methods are available for controlling these insects. See


Carefully inspect incoming plant material for signs and symptoms of disease. Avoid overwatering and overfertilizing. Monitor and maintain proper media pH and EC. Control insect pests and eradicate weeds inside and immediately outside the greenhouse. Practice good greenhouse sanitation.

Pots or flats should not be re-used. If they must be re-used, they should be washed thoroughly with soap and disinfested in 10% household bleach or a similar agent. For some crops, protectant fungicides may be used from the beginning of the planting cycle and repeated at regular intervals. Products containing appropriate combinations of fungicides such as Hurricane or Banrot can provide a broader spectrum of activity. For a full listing of products, see the New England Greenhouse Floriculture Guide.


Robert L. Wick; updated by Angela Madeiras, 2019
Last Updated: 
October 2019