Pythium and Phytophthora root rot in closed hydroponic systems

Diseases of crops grown and closed hydroponic systems can be a problem and occasionally catastrophic. However, the presence of a pathogen does not necessarily mean that a disease outbreak will occur. Although not fully understood, there are fine balances in hydroponic systems involving climate conditions, biological control agents, etc. that can keep pathogens in check.

In open field conditions the soil temperature and moisture will fluctuate significantly throughout the growing season. On the other hand, the growth medium temperature and moisture are relatively constant in greenhouses. The nutrient solution temperature is the single most important factor governing development of zoosporic pathogens in hydroponics closed circuit systems.

Hydroponics is the ideal growing method to prevent and control root rot conditions and the control is also much cheaper, compared to soil sterilization. Unfortunately, closed circuit hydroponic systems provide ideal conditions for various root rots to develop. Monocrop plantings provide a high volume of hosts for the fungi to grow. Although a hectare of tomatoes is considered a monocrop system, there are many other bacteria that feed on the root rot fungi. So in open field conditions there is lots of competition. This is not the case with close circuit hydroponic systems. Pythium¹⁾“Featured Image created by OpenAI’s DALL-E.” was the most abundant genus in all production stages inside the greenhouse ecosystem²⁾McGehee, Cora & Louyakis, Artemis & Raudales, Rosa. (2024). Spatial variation of oomycetes and bacteria on surfaces, solutions, and plants from a commercial hydroponic greenhouse. Phytobiomes Journal. 10.1094/PBIOMES-08-23-0078-R..

The microclimate and environment around the roots are uniform which promotes rapid growth of the root rot fungi. The fungi might get washed away from the roots but they are re-circulated back and never leave the ecosystem.

The major root rot pathogens

There are a number of root rot pathogens that spread throughout a closed circuit hydroponic system. The most common and destructive are Pythium spp, Phytophthora spp and Fusarium spp. Other less known are Ralstonia solanacearum, Olpidium spp., and Plasmopara lactucae-radicis.

Other pathogens that cause disease in hydroponic crops are:

• Clavibacter michiganenese
• Colletotrichum coccodes
• Didymella lycopersici
• Erwinia spp.
• Verticillium spp. And
• Thielaviopsis basicola.

Although they do cause damage, so far it is not certain if they can spread throughout a closed-circuit nutrient system.

It is interesting to note that in a tomato crop Pythium aphanidermatum and P. morotola is more prevalent in summer while P. dissotocum is more active during colder or winter climates³⁾Kusakari, Shin’ichi & Tanaka, Yutaka. (1987). Root rot caused by Pythium spp. in tomato in hydroponics. Annual Report of The Kansai Plant Protection Society. 29. 31-34. 10.4165/kapps1958.29.0_31..

So why is Pythium so difficult to control. Shouldn’t there be at least some resistance to the pathogen by plants by now?

Pythium is a Chromista organism which has chlorophyll c, unlike other photosynthetic organisms which have chlorophyll a or b. This group includes organisms such as algae, protozoa, and some forms that are like fungi. Chromista organisms are extremely well adapted to water environments.

Pythium thrives in temperatures above 25°C⁴⁾Teixeira, Liliane & Zottarelli, Carmen & Kimati, Hiroshi. (2006). Temperature effects on mycelial growth and pathogenicity of Pythium spp. occuring in hydroponic lettuce. Summa Phytopathologica. 32. 221-226. 10.1590/S0100-54052006000300002.. So controlling nutrient solution temperatures you can indirectly control Pythium, to an extent. Between 20-25°C the destructive effect of Pythium is not so prominent, and plants show signs of nutrient deficiency which can be overcome with foliar feed. Above 30°C Pythium destroys all plant resistance and the plant dies within a week or two. At these high root temperatures, the roots are physiologically stressed and have little resistance to other pathogens.

Not all plants react equally to Pythium. JOHNSTONE etal (2004) ⁵⁾Johnstone, M. & Yu, H. & Liu, W. & Leonardos, Evangelos & Sutton, John & Grodzinski, Bernard. (2004). Physiological changes associated with pythium root rot in hydroponic lettuce. Acta Horticulturae. 635. 67-75. 10.17660/ActaHortic.2004.635.8. inoculated three lettuce varieties with Pythium dissotocum. The least resistant variety showed signs of infection within seven days of being inoculated. The more resistant variety recovered quickly in and the resistant variety was not affected at all. In my opinion none of the varieties would survive if the nutrient temperature was above 30°C because that is where Pythium is the most destructive.

Interestingly, bent grass (Agrostis) ⁶⁾Watanabe, Hideki & Kageyama, Koji & Taguchi, Yoshihiro & Horinouchi, Hayato & Hyakumachi, M.. (2008). Bait method to detect Pythium species that grow at high temperatures in hydroponic solutions. Journal of General Plant Pathology. 74. 417-424. 10.1007/s10327-008-0116-2., orange leaves and hemp-seed cotyledons⁷⁾Sánchez, J. & Sánchez-Cara, J. & Gallego, E.. (2000). Suitability of Ten Plant Baits for the Rapid Detection of Pathogenic Pythium Species in Hydroponic Crops. European Journal of Plant Pathology. 106. 209-214. 10.1023/A:1008773908813. can be used to identify Pythium within a day in closed hydroponic systems. This can be a valuable tool to test whether you have the disease or not. The precise method is a little daunting, but a good science lab should be able to assist.

Symptoms of Pythium and Phytophthora infection.

When tomato and other greenhouse plants are infected with Pythium or Phythophthora, they exhibit a variety of symptoms, particularly affecting the roots and the overall growth of the plant. Some common symptoms are described below:

Damping-off of seedlings: Damping-off is the symptom seedlings show when infected with Pythium or Phytophthora. It occurs either before seedlings emerge (pre-emergence) or after (post-emergence). In pre-emergence, the seeds may decay, or seedlings may die before they break the soil surface. In post-emergence, seedlings initially appear normal but quickly become water-soaked, wilt, and collapse at the base ⁸⁾Agrios, G. N. 2005. Plant Pathology.922..

Root Rot: Infected plants often have stunted or discolored roots. Healthy roots are typically white and firm, but roots affected by Pythium become brown, soft, and waterlogged. As the root system deteriorates, the plant’s ability to absorb water and nutrients is compromised. A classic symptom is the browning of the base of the seedling stem, especially with tomatoes and cucumbers. Leaves can become lighter in colour and necrotic around the edges⁹⁾Bogdan CVJETKOVIĆ, Zdravka SEVER. 2016. Journal of Plant Protection 5/2016, Vol. 16 / No. 5. Faculty of Agronomy, University of Zagreb, Department of Agricultural Zoology. Croatian Center for Agriculture, Food and Rural Affairs, Institute for Plant Protection.

Stunted Growth: Due to the compromised root system, affected plants often exhibit stunted growth. They may also appear to be in a state of perpetual wilt, even when soil moisture levels are adequate.

Wilting: Despite adequate soil moisture, the plants may wilt because the damaged roots cannot absorb water effectively.

Yellowing of Leaves: As the disease progresses, the leaves may turn yellow and drop prematurely due to the plant’s inability to uptake necessary nutrients.

Reduced Fruit Production: Very mild infected plants often produce fewer and smaller fruits due to the overall stress and reduced vigor of the plant.

Sources of Pythium and Phytophthora.

Understanding and eliminating the source of both Pythium and Phytophthora is the first way to control the disease and the cheapest.

Both Pythium and Phytophthora cannot be transmitted by air. They depend on water to stay alive and spread.

They are not transmitted by seed. There are many other diseases, mostly viruses that are spread by seed.

Growth medium is a major source of the disease. Peat is also known to host both Pythium and Phytophthora.

River sand, when used as ground cover for walkways is a source of infection. It is well known that Pythium aphanidermatum and P. dissotocum are found in river sand which is often used as growth mediums.  

The most obvious source of infection is water. Rivers, dams and boreholes are all contaminated with Pythium.

Some insects such as shore flies (Scaterlla stagnalis) and fungus gnats (Bradysia spp) can transmit various pathogens including Pythium.

Controlling and eradication of Pythium and Phytophthora

Let’s face it, you have Pythium and Phytophthora in your hydroponic system, especially if you are reading the article this far. Even if you have done everything you can, both these pathogens will be present. Impeccable care, hygiene and maintenance is required to maintain an acceptable level of infestation. The moment these pathogens are allowed to increase it becomes very expensive to clean the system. This usually involves shutting down part or the whole hydroponic system to disinfect. All the infected plants must be removed. I assume no grower has any interest in removing plants.

There are chemicals that control pythium and phytophthora but in order to use them commercially, they have to be registered in your country. So I cannot make any recommendations. I know in South Africa propamocarb hydrochloride and thiophanate-methyl can be used, but they are not registered on any vegetable crops grown in a greenhouse. A serious limitation of using unregistered chemicals is the lag period between application and harvesting, and off course a lawsuit but that is something else. The other risk is resistance of the pathogen with its own ramifications.

Hydrogen peroxide, chlorine dioxide and sodium hypochlorite are more efficient to clean plumbing pipes¹⁰⁾DISEASE MANAGEMENT IN SOILLESS CULTURE SYSTEMS, Journal: Acta Horticulturae, : 2010, ISSN: 2406-6168. At least there are no restrictions to the use of these chemicals inside the hydroponic system as long as they are not applied on the plants themselves.

It is quite surprising that surfactants at 15-20ppm controls pythium and phytophtora (Agral 90 and Kynogral 90). The concentration must be kept to at least 15ppm. Unfortunately both are not registered for use in hydroponic systems. Results indicate that Purogene® is the most effective for application into a gravel bed hydroponic system cultivated with lettuce¹¹⁾Roger Cuan Bagnall. 24 April 2008. ‘University of Pretoria – Department of Philosophy’. Control of Pythium wilt and root rot of hydroponically grown lettuce by means of chemical treatment of the nutrient solution. MSc (Plant Pathology). University of Pretoria, 2008.Microbiology and Plant Pathology..

There is renewed interest in radiation of soil with micro waves, called Anaerobic soil disinfestation (ASD)¹²⁾ PHYSICAL METHODS FOR SOIL DISINFESTATION IN INTENSIVE AGRICULTURE: OLD METHODS AND NEW APPROACHES, Journal: Acta Horticulturae, : 2010, ISSN: 2406-6168. The heat produced by the intense radiation is lethal to pathogens and pests. The disinfected soil or growth medium is mixed with new fresh mixtures that is not contaminated.

Slow sand filtration (SSF) is a reliable, low-cost solution to eliminate soil-borne pathogens in recirculating nutrient solutions¹³⁾Van Os, E.A. 1999. Closed soilless growing systems: a sustainable solution for Dutch greenhouse horticulture. Water Science and Technology 39:105-112.¹⁴⁾ Wohanka, W., Lüdtke, H., Ahlers, H. and Lübke, M. 1999. Optimization of slow filtration as a means for disinfecting nutrient solutions. Acta Hort. 481:539-544.¹⁵⁾ Runia, W.Th., Michielsen, J.M.G.P., van Kuik, A.J. and van Os, E.A. 1997. Elimination of root infecting pathogens in recirculation water by slow sand filtration. Proceedings 9th Int. Congress on Soilless Cultures, Jersey, p.395-408.. Both Phytophthora spp. and Pythium spp. Were eliminated from the nutrient solution by this method, unfortunately Fusarium spp., viruses and nematodes are only partly (90-99.9%) removed. Note that the pathogens were only removed from the water and not from the growth medium, pipes and roots.

Another clean non-toxic method is the treatment of infected water with Ozone (O3). Exposing a hydroponic nutrient solution with 10g/m³ ozone for one hour eliminate all pathogens and viruses ¹⁶⁾Runia, W.Th. 1995. A review of possibilities for disinfection of recirculation water from soilless culture. Acta Hort. 382:221-229. The problems is that people cannot be near the treatment tank as even 0.1mg/m³ ozone can cause severe irritation of mucus membranes in humans. The other impractical part is that the treated water must be left for one hour and not all growers have a big enough tank to store water that long. The process also reacts with iron chelates which leaves precipitates and must be removed. During this reaction iron (Fe) is removed from the water and must be replaced otherwise the plants will show Fe deficiency over time. The question is where to dispose of the iron deposits after the process¹⁷⁾E.A., van Os. 1 January 2009. ISHS. COMPARISON OF SOME CHEMICAL AND NON-CHEMICAL TREATMENTS TO DISINFECT A RECIRCULATING NUTRIENT SOLUTION, Journal: Acta Horticulturae, : 2009, ISSN: 2406-6168.