Pythium is a water-borne pathogen that causes damping off, crown rot, and stunted growth. Dark Heart Lab services can test your grow for pythium.

By Tera Pitman, M.Sc.

You just completed your weekly irrigation system check. The nutrient mix is optimized and at the right rate. The water pH is within range, pre- and post-nutrient injection. The irrigation schedule is optimized, and the potting media is not too wet or dry. This was the week 5 check, and you are worried about what you are seeing overall. Why are so many plants struggling and falling behind in growth?

Figure one: Plants infected with pythium.

The foliage isn’t telling you a lot other than there is stress so you check a couple pots for roots at the drainage holes, but you do not see any in the pots of the weak plants. You decide to dig up some roots and look for differences between the healthiest looking plants and those that are stressed. In the healthy plant pot the roots are numerous, white, and have healthy looking root hairs. In the pots with weak-looking plants the roots are fewer, off-white to brown, brown spots are noticeable, and roots hairs are absent on many of the roots. The problem may be Pythium infection.

Figure 2: Damping off

The most common symptoms of Pythium in the greenhouse or indoor facility is damping off. 1 It is most noticeable when infecting new cuttings or young plants. The plants develop water-soaked crowns and fall over, or the cuttings never grow roots and collapse. When plants are larger when they are infected, crown rot may not occur. The roots may be heavily impacted, but the crown and aerial portions show stress but no obvious symptoms. Through late summer and autumn, we have talked to growers who are seeing these later Pythium outbreaks negatively impacting their operations. The infected plants grow slower than their healthy counterparts and show signs of stress (leaf yellowing, plant stunting, and red stems or petioles) that can be confused with nutrient deficiency. When the lighting is flipped to flower production the plants become more stressed and produce smaller and fewer flower clusters. Overall, finding Pythium in the greenhouse, either in your young or mature plants, can heavily impact production and yield. What can you do about it?

Figure 3: Plant crown showing pythium symptoms

First, you need to know where the Pythium spores are coming from. Spores are produced in water and are not airborne. The most common route of entry is contaminated water. Pythium, and its cousin Phytophthora, are Oomycetes and not true fungi.2 They are more closely related to kelp and diatoms than Fusarium and Botrytis, two fungal pathogens that can also impact Cannabis. They have cell walls made of cellulose. Many Pythium species that cause root and crown rot in the greenhouse can also grow in wet, biologically rich environments like rivers, streams, and reservoirs.3 If your operation gets its water from a surface source you should think about pathogens coming in with that supply. Oomycetes produce spores that have flagella, which allows them to swim through the water towards its next food source, such as those healthy cannabis roots. The first step in controlling Pythium is filtering or sanitizing the water entering your operation. Use in-line filtration, ozone sterilization, or UV sterilization to kill any pathogens in the water.1,4,5 Once your supply is spore-free you will have to clean your irrigation pipes, lines, capillary mats, holding tanks; anything attached to the irrigation system can harbor biofilm that Pythium can grow in. PVC pipe elbows and joints, line junctions and splices, all those nooks and crannies are places where biological material builds up over time and can be colonized by hyphal growth. Over time the Pythium can mature and start releasing zoospores that then end up in your plants. Proper irrigation line sanitation between production cycles is important to reduce or eliminate sources of water pathogens.

A more obscure mode of arrival is potted plants. Your greenhouse is connected to a municipal supply, but the place you bought plants from is not. New plants can harbor pathogens in their substrate, whether it is coconut coir, potting mix, or rock wool. Any water recirculation, capillary mat, or flood tray use within your facility will carry the pathogen to other plants, causing a head-scratching outbreak.

Another potential source of Pythium is recycled potting media. If the media is improperly sterilized between use soil and water pathogens can build up and infect subsequent plants. This includes the genera Phytophthora, Pythium, Fusarium, and Verticillium (more on other pathogens causing root rots later). Make sure your recycled media is autoclaved, steam treated, heat treated, or composted appropriately before reuse. You may want to include periodic soil testing for some of the hardier pathogens. On a similar note, wash all pots between use. Any residual potting media can harbor pathogens that are waiting for the next plant to infect.

How do you know Pythium is the problem? By testing samples, of course. Plant root samples can be sent for molecular or serological analysis. Soil and water samples can be filtered and used for biological assays to look for the pathogen.3 How do these tests work, and what kind of testing is offered by Dark Heart?

Many plant disease labs offer testing services for root infecting pathogens. The most common, and the type available at Dark Heart Lab Services, is a molecular assay that tests for specific DNA sequences in the sample.3 We use primers in a quantitative polymerase chain-reaction (qPCR) assay that amplify a region of the mitochondrial DNA that is unique to members of the genus Pythium. If you are not sure which pathogen is causing root rot, you can request multiple tests for the same sample. Molecular assays require very little DNA to run, so one sample can be used for many tests.

If samples test positive for Pythium, you should initiate regular screening in your production plan until the problem is resolved. This should include testing symptomatic plants to be aware of the ongoing issue and water sampling to pinpoint and address the point of entry. Water samples from various points in your system should be tested to localize issues, then a cleaning regiment implemented. Repeat water testing after irrigation system sanitation. If your water samples test clean but you are still identifying infected plants, trust the plant information. If new plant infections are occurring, then the pathogen is still entering or residing in the system. If you currently use a water purification system, contact the manufacturer to discuss how to modify the system parameters to address spore survival.

Questions? We are here to help. You can reach us at:

Figure 4: Roots infected with pythium; pythium under magnification.

Figure 1. Symptoms of Pythium infection on older plants. A: side view of an infected plant showing necrotic older leaves and general chlorosis. B: top down view of the canopy with leaf chlorosis very apparent.

Figure 2. Damping off symptoms in cuttings. At left, a full tray and additional plugs impacted by the disease. On the right, a closeup of individual cuttings. Wilting and apical necrosis are typical for damping off. When the cuttings are removed from the rock wool brown lesions and little or no root development are noticeable on infected cuttings.

Figure 3. A: Plant crown at the soil line showing brown lesions and cracking. B: The same lesion as A with the epidermis scraped away, revealing the Pythium infected tissue.

Figure 4. A: Root masses of young plants from one-gallon pots. On the left, roots infected with Pythium myriotilum; right, uninfected roots. B: Closeup of infected roots from a plant in rock wool showing discoloration on some roots and lack of root hairs. C: Microscope image of Pythium growing on nutrient agar.



  1. Punja ZK, Collyer D, Scott C, Lung S, Holmes J, Sutton D. Pathogens and Molds Affecting Production and Quality of Cannabis sativa L. Front Plant Sci. 2019;10:1120. doi:10.3389/fpls.2019.01120
  2. Redekar NR, Eberhart JL, Parke JL. Diversity of Phytophthora , Pythium , and Phytopythium Species in Recycled Irrigation Water in a Container Nursery. Phytobiomes J. 2019;3(1):31-45. doi:10.1094/PBIOMES-10-18-0043-R
  3. Schroeder KL, De Cock AWAM, Lévesque CA, Spies CFJ, Okubara PA, Paulitz TC. Molecular Detection and Quantification of Pythium Species: Evolving Taxonomy, New Tools, and Challenges. doi:10.1094/PDIS-03-12-0243-FE
  4. Choudhary CE, Burgos-Garay ML, Moorman GW, Hong C. Pythium and Phytopythium Species in Two Pennsylvania Greenhouse Irrigation Water Tanks. Plant Dis. 2016;100(5):926-932. doi:10.1094/PDIS-07-15-0836-RE
  5. Schuerger AC, Hammer W. Use of cross-flow membrane filtration in a recirculating hydroponic system to suppress root disease in pepper caused by pythium myriotylum. Phytopathology. 2009;99(5):597-607. doi:10.1094/PHYTO-99-5-0597


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