Understanding Pythium Root Rot

By Robert Linderman
Published: April 28, 2020 | Last updated: April 20, 2021 09:44:05
Key Takeaways

Pythiums are plant pathogens that cause damping off of seedlings, or nibble on the roots of older plants. There are pythiums everywhere in agricultural and landscape soils. They also invade soilless media, and attack plant roots in greenhouse production systems. Read on to figure out where they come from and how to get rid of them.

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Of all the soil-borne diseases I have encountered and researched in my career, pythium root rot is one of the most frustrating and difficult to get a handle on. There are pythiums everywhere in agricultural and landscape soils and they invade soilless media and attack plant roots in greenhouse production systems.


As a group, pythiums infect a huge range of plants, from turf grass and vegetables to fruit trees and conifer seedlings. Pythiums are known as young plant pathogens, causing damping off of seedlings, but on older plants they are often root nibblers.

There are many species included in this group and some are highly pathogenic. Others are less pathogenic and only become problematic when they seize the opportunity to infect otherwise compromised or stressed plants.


This makes assigning blame for the damage caused to roots difficult. Simply isolating pythium from the roots does not necessarily tell the whole story. It is necessary to consider many aspects of the crop production system to get a clear picture.

The underlying questions, for which the answers remain undetermined in many cases, is, “Where did pythium come from and how can I get rid of it?” In this article, I hope to address these questions by describing the biological nature of these pathogens.

Is Pythium Caused by a Fungus?

Originally, I learned pythiums and phytophthoras were fungi. However, the most recent genetic studies indicate they are not really fungi, but are more closely related to brown algae. I still call pythium a fungus. Pythiums and phytophthoras are called water molds because they thrive in wet soil or production systems. They survive in soil or water or in infected root pieces as resting spores called oospores.


When oospores germinate, they produce sporangia from which swimming spores that can move in free water are released in soil or in water that flows in streams or ponds or ditches. If pythium-contaminated water is used for irrigation, the pathogen has invaded your system. Once inside, it can infect some roots and then more roots, to the point where the root system cannot support the plant. The cycle is then completed and circles back to the production of more oospores.

Read More: Root Rot Remedies


Disease Symptoms of Pythium

As more and more of a plant’s roots become infected by pythiums, roots cease to function and above ground symptoms become apparent. These symptoms often include stunting of growth and brown or dead root tips. The outer portion of the root easily slips off, leaving a strand of vascular tissue exposed. Because of the weakened root system, plants may wilt at mid-day and turn off-green to yellow. Some might even die. Under the microscope, one can see the oospores of pythium formed in the root cortex and sporangia produced on the root surface. Pythium species cause a range of symptoms, including damping-off of seedlings, seedling root rot, root rot of cuttings, and root rot of larger plants grown in containers. Above ground, plants may be stunted due to poor root function and may turn off-green due to poor nutrient uptake.

Managing Pythium in the Garden

Once pythium infections have occurred, control is difficult. Prevention is definitely the best strategy. The pathogen source is either from the soil or potting medium, the plant propagule itself, the container or the irrigation water. Commercial potting media are not likely to be contaminated with pythium (although it has been reported), so no treatment is necessary. If potting mix is being reused, however, it must be pasteurized with heat (a maximum of 150°F for 30 minutes, as higher temperatures may kill some beneficial microbes). On a small scale, this can be accomplished in a microwave oven in a covered plastic container.

Read More: How to Improve Plant Growth with Micro-Organisms

Containers for planting might be contaminated from being used previously. They can be sanitized with household bleach (10% out of the jug for at least 10 minutes). Pythium is not likely to be carried on cuttings or seeds, so their treatment is usually not needed. If those potential sources are eliminated, only the irrigation water remains. Municipal water is treated with chlorine and would not be a source of pythium. Similarly, well water is not likely to be contaminated.

However, irrigation pond water or water that flows over the soil might pick up some pythium. Heat, ultraviolet light, ozone and chlorination can be effective treatments against pythiums lurking in water, but are expensive and require some training to be used properly. Slow sand filtration is an effective, simple and inexpensive method for removing pythium from water.

Having covered all of the primary sources of pythiums—potting media, used containers, plant propagules or irrigation water—it is essential to not introduce pythium thereafter. Pythiums can be lurking around, just waiting for some lapse in sanitation practices. It is important to disinfect all bench surfaces, potting benches, tools and equipment that will contact the potting mix.

Read More: Slow & Steady - Slow Sand Filtration for Hydroponics

If there is a history of pythium infections, it may be necessary to apply a preventative chemical or biological agent to the potting mix to prevent infections. Biological agents should be applied to the potting mix before, during or immediately after transplant. They can even be applied to plants in plug trays before transplanting.

The same advice would apply to chemical agents that might be used. Biological control agents and fungicides might have to be applied more than once to maintain adequate protection. Do not apply them at the same time. It is also worth noting there are some pythium populations that resist fungicides.

Many garden soils that have been used for a number of years could already have significant populations of pythium. Remember, pythiums are usually young-plant pathogens, so transplanting older plants could avoid infection levels that would affect the plants. Some pythiums require cooler temperatures and wet soil, so delaying planting could help get plants going without pythium infections.

Compost amendments often contain enough diverse microbes, including some antagonists, to help suppress pythium infections as well. Of course, fumigation of the soil will kill off the pythium in the soil exposed to the fumigants, but after the chemical is gone, the pythium can come back. Fumigation requires a professional applicator and poses significant human or other animal risks, so is not recommended for most gardens.

Another approach for the home gardener is to solarize the infected soil prior to planting. This entails covering the area to be planted next year with a clear plastic tarp, with the edges sealed. This has to be done the season before planting when sunlight and summer temperatures are hot enough to be effective.

The solar energy penetrates the plastic tarp and converts it to heat energy that is trapped and penetrates down the soil some distance, depending on how long the tarp is left on. At least one month is needed to have some effect on killing pathogens. Unfortunately, some good microbes might be killed as well, but on the plus side, so are some weed seeds. The soil must be prepared by tilling and irrigation before applying the solarization tarp. Next year, the solarized area is hopefully ready for planting.


Pythiums cause a large range of diseases on a huge range of plants, from seedling damping off, to root rots of many plants that result in stunted growth due to poor root function. They are soil- and water-borne pathogens favored by wet soil or potting medium conditions. They survive in soil by means of thick-walled spores that germinate and produce sporangia that release swimming zoospores and infect roots. Once roots are infected, new sporangia and zoospores spread the infection to other roots.

Management of pythium diseases is best done by prevention because once infections occur, not much works to stop them. Sanitation is required to avoid introducing the pathogen on the plant propagule, used containers, potting medium or in the irrigation water. Sanitizing tools and the work area is essential to avoid introducing the pathogen. Treatment of infected garden soil is difficult, but compost amendment and soil solarization are strategies both worth considering.

Read Next: The Kratky Method - A Simple and Fun Way to Grow


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Written by Robert Linderman

Profile Picture of Robert Linderman
Dr. Robert G. Linderman is a retired research plant pathologist and former research leader at the USDA-ARS Horticultural Crops Research Laboratory in Corvallis, Oregon. He is also a courtesy Professor Emeritus at Oregon State University. He has been in the industry for nearly 50 years and is currently the science guy for two companies: Plant Health, LLC and Santiam Organics, LLC.

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