Pathogen Profile: Pythium

We are introducing a new series on this blog called Pathogen Profile where each post focuses on a pathogen commonly found in hydroponic systems or is of concern to greenhouse growers. We hope that Pathogen Profile can be used to help growers better understand common plant pathogens in hydroponic and greenhouse systems so that they can be better managed.

Some of the things we cover in Pathogen Profile include: 

  • What kind of pathogen is it?
  • What kinds of plants do this pathogen infect?
  • How does the pathogen infect plants?
  • What general symptoms are exhibited in the host plants?
  • How is the pathogen potentially introduced into the greenhouse or hydroponic system?
  • How is the pathogen dispersed?
  • What environmental conditions allow for the pathogen to proliferate?
  • What can growers do to mitigate the pathogen?

The more information that growers know about plant pathogens, the more prepared and confident they will be to handle them. We hope the data that we gather from Healthy Hydroponics will fill in some of the current knowledge gaps regarding plant pathogens in hydroponics and greenhouse systems.

Important Notes
The information we present in Pathogen Profile is based on collating published peer-reviewed scientific literature and sources we think are reliable. This is by no means an exhaustive review of pathogens. Pathogen Profile gives a small glimpse of what is known about pathogens and we encourage growers to do more research on their own based on the pathogens in relation to their own crops and hydroponic systems. We are not plant pathologists thus the information presented in Pathogen Profile should not be used as professional advice to treat pathogens or to operate your hydroponic system. The cited work can be found at the end of the profile.


Our first Pathogen Profile is on Pythium as it is the most common pathogen that our growers have expressed concern about. This does not come as a surprise because Pythium is ubiquitous and known to cause root rot in a variety of greenhouse hydroponic crops. It is also not an organism that can be easily mitigated because of certain species’ ability to produce motile spores (zoospores), to withstand high temperatures, and the likelihood to aggregate in root zones.

What is Pythium?

Pythium is an oomycete (belonging to the phylum Oomycota in the clade SAR, domain: Eukaryota) colloquially known as water mould although it is not a true fungus. Several members of this genus are plant pathogens known to cause damping off in seedlings and root rot in a variety of plants. A particular species Pythium insidiosum is an animal pathogen causing pythiosis, a disease of the gastrointestinal tract or skin, in humans and other mammals [1, 2].

Although there are close to 200 species and strains of Pythium, P. aphanidermatum, P. dissotocum, P. irregulare, and P. ultimum are species that are the common culprits of crop loss in greenhouses [1, 3].

Host Plants

Many species of Pythium are generalists meaning they can infect a wide range of plants. Pythium has been known to infect hydroponic vegetable, fruits, flower, and ornamental crops including cucumber, tomato, sweet pepper, spinach, lettuce, arugula, strawberry, rose, chrysanthemum, antirrhinum, poinsettia, cannabis, and tobacco [1, 3, 4, 5].

Infection and Symptoms

Some Pythium species form zoospores (motile spores) which penetrate roots. The P. aphanidermatum and P. irregulare produce zoospores whereas P. ultimum produces few to no zoospores. The latter has been more commonly found to be a pathogen of plants in soil systems than in recirculating systems [1, 3]. Zoospores have been found to be attracted to root exudates produced by plants. A study of cucumber plants found that Pythium proliferation in roots was often found associated with roots that produced more mucilage than none [6].

There are two stages of Pythium infection of roots. Biotrophic phase: Pythium infected roots but overt symptoms in the host plant are not seen yet. Necrotrophic phase: Roots turn yellow/brown, root necrosis (tissue damage), plants are stunted. Usually, symptoms are observed above-root only when root rot is very severe thus it can be difficult to detect and control Pythium by observation early on [1]. 



There are a plethora of conditions that can cause Pythium proliferation. Temperature plays a role in the growth of most pathogens. Different Pythium species have various optimal conditions for growth and proliferation. Certain species such as P. aphanidermatum and P. helicoides can tolerate optimally high-temperatures of 35-40°C (95-105°F) but can also grow at lower temperatures [3]. On the other hand, P. ultimum prefers lower temperatures such as 25-30°C (77-86°F) [3]. Most Pythium species have optimal temperature ranges in which they proliferate but are able to survive and multiply at lower temperatures as well [1]. 

Oxygen level

Another factor that affects Pythium proliferation is oxygen level. Root rot has been shown to increase when oxygen levels in the nutrient solution are low [1]. Higher temperatures are usually accompanied by lower dissolved oxygen levels. 

Dispersal Factors 

Type of hydroponic system

There are a number of factors affecting the dispersal of Pythium. Firstly, different types of hydroponic systems, e.g. trough systems with no rooting substrate vs compartmentalized systems (slabs) have an effect on the rate of zoospore dispersal. For example, plants in nutrient film technique systems share nutrient solution directly upstream and downstream of other plants allowing a free flow of zoospores from an infected plant to others. In contrast, plants in rockwool slabs are compartmentalized and zoospore dispersal is immediate to only the few plants sharing the same slab [1, 7]. It should be noted that zoospores spread quickly in small and commercial-scale hydroponic systems [1].

Flow rate of water

On a related note, studies have shown that the flow rate of water influences the dispersal of zoospores. Zoospores travel shorter distances in slow-flowing water such as those near the root zone (rhizosphere) or in compartmentalized hydroponic systems [7]. Fast-flowing or mixing water can cause damage or lysis of zoospores thus killing them or removing their ability to sense potential infected roots (damaged or infected roots can release chemical signals that attract microorganisms). This suggests that Pythium may have a higher chance of aggregating in root areas and in growing substrates. However, it is important to note that zoospores have been shown to disperse overall fairly quickly through areas of small- and commercial-scale hydroponic systems [1]. 

Practices to control and manage Pythium 

The following practices presented here are adapted from Table 1 in this very insightful review on Pythium root rot in hydroponic crops by Sutton and colleagues [1].

There are two main routes to lower levels of Pythium: 1) The initial source of Pythium and 2) the dispersal of Pythium once it’s been introduced into the crop or hydroponic system.

Table 1. Practices to control and manage Pythium

Lowering initial source of PythiumWithin the greenhouse: 
crop residues, growth
substrate, hydroponic equipment and components, working surfaces, crevices
Steam, chemicals*, temporary acidification** of nutrient solution
Lowering initial source of PythiumInto the greenhouse and hydroponic system:
water, seedlings, transplants, insects, environment surrounding the greenhouse
Treat water used for nutrient solution, ensure transplants and substrates are pathogen-free [although this is hard],
using screens on vents to filter out insect acting as vectors carrying pathogens, and disinfecting workwear,
maintaining a weed-free and plant-free zone directly outside the greenhouse
Lowering rates of Pythium dispersalRecirculating nutrient solution Heat pasteurization, UV irradiation, membrane filtration, slow filtration, ozonation, activated hydrogen peroxide
Suppress PythiumRoot zoneBiocontrol, chemical pesticides, control of environmental conditions/parameters, covering between crop and roof to reduce dripping water

Things to consider not mentioned in the review

* Depending on the surface and material, certain chemicals can erode metals, please use chemicals as directed by manufacturers.

** Depending on your crop and again system equipment, can temporary acidification do more harm than good? 

What do we still need to know and manage Pythium?

We need an early detection and identification system of Pythium species for disease management. Since Pythium infects roots in the biotrophic phase without causing noticeable symptoms, it allows infection to go undetected for a period of time. Healthy Hydroponics’s approach to sequencing DNA in the hydroponic system can allow earlier detection of Pythium by sampling the root zone thus allowing growers to be aware and prepare for a potential Pythium outbreak in their system.

Furthermore, we need to know what are the environmental conditions or combinations of conditions that allow different species of Pythium to thrive. We know that higher temperatures (greater than 25°C or 77°F) and generally low oxygen levels encourage Pythium root rot. What are other environmental factors or nutrient levels that contribute to proliferation in hydroponic systems?

It is highly likely that Pythium can still become established in hydroponic systems even with strict precautions taken in a greenhouse due to its ubiquitousness and initial absence of  symptoms. Thus, growers need to be aware and vigilant of environmental conditions that allow Pythium to thrive. 

Works Cited

[1] Sutton, J. C., Sopher, C. R., Benchimol, R. L., Hall, J., Grodzinski, B., Liu, W., & Owen-Going, T. N. (2006). Etiology and epidemiology of Pythium root rot in hydroponic crops: Current knowledge and perspectives. Summa Phytopathologica, 32(4), 307-321. Retrieved from

[2] Vanittanakom, N., Supabandhu, J., Khamwan, C., Praparattanapan, J., Thirach, S., Prasertwitayakij, N., Louthrenoo, W., Chiewchanvit, S., & Tananuvat, N. (2004). Identification of emerging human-pathogenic Pythium insidiosum by serological and molecular assay-based methods. Journal of Clinical Microbiology, 42(9), 3970–3974. Retrieved from

[3] Moorman, G. W., & Daughtrey, M. L. (2002, February). Don’t Expect Pythium Root Rot to Always Act the Same. Greenhouse Product News, 36-38. Retrieved from

[4] , C. E., Burgos-Garay, M. L., Moorman, G. W., & Hong, C. (2016). Pythium and Phytopythium Species in Two Pennsylvania Greenhouse Irrigation Water Tanks. Plant Disease, 100(5), 926-932. Retrieved from:

[5] Punja, Z. K., & Rodriguez, G. (2018). Fusarium and Pythium species infecting roots of hydroponically grown marijuana (Cannabis sativa L.) plants. Canadian Journal of Plant Pathology, 40(4), 498-513. Retrieved from

[6] Zheng, J., Sutton, J. C., & Yu, H. (2000). Interactions among Pythium aphanidermatum, roots, root mucilage, and microbial agents in hydroponic cucumbers. Canadian Journal of Plant Pathology, 22(4), 368-379.

[7] Holderness, M., & Pegg, G. F. (1986). Interactions of host stress and pathogen ecology of Phytophthora infection and symptom expression in nutrient-film grown tomatoes. In 1242056571 921225957 P. G. Ayres & 1242056572 921225957 L. Boddy (Eds.), Water, Fungi, and Plants (pp. 189-205). Cambridge University Press.

Feature Image is adapted from root rot in Cicer arietinum (chickpea) from Bjornwireen.

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