Root rot is a universal problem in commercial crops, yet our knowledge about it is fragmented. Understanding the root of the problem is at the foundation of effectively managing the disease. To be able to do that, you must learn about some of the microbiology that is running the show. Once you understand that, developing, integrating and optimizing treatments becomes easier, and you will be able to prevent root rot from developing in your plants.

To begin, let me introduce you to one of the main micro-organisms responsible root rot: Pythium spp. These fungi are widely spread around the globe and cause big problems in both indoor and outdoor gardens, whether you are growing in soil or hydroponically. Now we know who we are fighting, our mission is to analyze the pathogen to understand how it works so we can make its life unbearable.

What Causes Root Rot?

The Pythium spp. genus belongs to the family of Pythiaceae, which is in the oomycetes genus. Each species is able to produce zoospores (asexual spores that move) and oospores (thick-walled sexual spores) in infected plant roots and in the rhizosphere. These Pythium spp. are lethal. Why?

Well, they attack a wide range of host plants and they colonize frequently in soil, greenhouses, outdoor gardens and hydroponic systems—pretty much everywhere.

When the pythium’s zoospores encyst, they become immobilized. This makes the spores more resistant to extreme temperatures, desiccation and ionic environments. Oospores can survive for several months in fragments of dead roots, which may then be introduced and dispersed into gardens by infected transplants or reused media, polluted water, contaminated equipment and workers.

In The Annals of Applied Biology and Phytophatology Journal, researchers reported finding Pythium spp. oospores in the digestive tracts of larvae and adult fungus gnats and shore flies in North America. It is likely these insects help spread root rot in crops growing in warm and tropical climates.

During the infection process, mycelium (germinating oospores) form sporangia (zoospores), which encyst at the root surface to develop the germ tube that penetrates the root surface until the colony functions independently. Generally, the frequently penetrated areas are root tips, elongation zones and young root hairs, but most of all, root zones with increased root mucilage production.

Through a plant’s anatomy, we can link the root mucilage with the root apical meristem (RAM), a tissue that contains undifferentiated cells. These cells are capable of continued cellular division, which means RAM is required to provide new cells for root expansion and initiation of new organs, providing the basic structure of the plant’s body. If the root mucilage is colonized, the RAM is too.

Studies published in The Journal of Plant Pathology show the mucilage serves as a food base, enabling Pythium spp. to invade the roots, including old roots that zoospores normally do not infect. Under microscopic observations, the amount of mucilage was correlated with root browning, a necrosis reaction that develops in root tissues after they are infected and colonized by Pythium spp. and is associated with the accumulation of phenolic polymers.

Pythium necrosis is induced by an elicitor, which has a high degree of similarity with necrosis-inducing elicitors of Phytophthora spp. and Fusarium oxysporum. It is important to mention that qualitative and quantitative changes in mucilage and other exudates from roots at various stages of crop development appear to affect root-zone microbes, including Pythium spp. and other micro-organisms, both beneficial and harmful.

The Symptoms of Root Rot

Besides problems with their roots, crops affected by root rot often show signs of stunted shoots, wilted leaves and a reduction in flowering and fruiting productivity. Plants experiencing severe root rot often appear to be healthy, even though growth is stunted and roots are decaying. In most scenarios, stunted growth may go unnoticed for a considerable amount of time because all plants in the cohort are similarly affected.

The Treatment

The factors that make plants vulnerable to root rot include a low concentration of dissolved oxygen in the nutrient solution and a lack of oxygen in the soil, constant warm temperatures, high humidity, damp soils, excessive amounts of phenolic compounds and dark environments. If Pythium spp. grows under these conditions, it is good practice to control these conditions to prevent and even correct the disease.

Beneficial micro-organisms are one of the most effective ways to prevent and treat root rot. Options for bringing in good micro-organisms into your root mucilage include using aerobic bacteria (produced in compost teas), efficient micro-organisms (EMs), lactobacillus, mycorrhizae and trichoderma.

The key is to apply these beneficial solutions when a plant is a seedling or at first transplant and to keep administering the treatment with the same micro-organism to build up the root zone’s microflora throughout the plant’s lifetime. Just remember that using chemical fertilizers, chemical additives and chlorinated water can kill your happy micro-organism family.

Microbes have also been used to digest phenolic compounds and raise oxygen levels. A good choice is Bokashi, which usually has tons of actinomycetes that boost oxygen levels in soil systems and even in hydroponic systems, which typically have a low microbial diversity.

The most effective EM you can get is a local EM, which can be obtained from your local forest. To get it, fill a dish with wet rice and place it in a dark damp place in the forest for 2-4 weeks. Spring and fall are the two best times to do this. The longer you leave it, the more fungal the compound will be, and the shorter you leave it, the more bacteria-rich it will be. This is simply because bacteria reproduces faster than fungus grows.

The Growroom Set-up

When it comes to winning the battle against root rot, there are some things to consider when setting up your growroom. For instance, while some growers produce their own transplants, many people end up buying them from other growers. In some cases, the plant stock can be contaminated, and since many infected transplants are usually symptomless when ready for shipping to growers, the supplier might not even be aware of the problem. It is important to obtain plants from reputable growers—I can’t stress this enough.

Some growers reuse contaminated soil or rooting media such as slabs of stonewool or coconut fiber without sterilization, allowing for the carryover of various pathogens to the subsequent crop. In hydroponics, pipes, tubing, tanks and other plumbing components can be contaminated even when the systems are treated with disinfectants. Nutrient solution circulation is one of the primary ways Pythium spp. are dispersed in hydroponic crops.

Reports of severe epidemics are more frequent for crops grown in systems in which the nutrient solution is circulated amongst hundreds of plants before returning to the mixing tank, as opposed to highly compartmentalized systems such as stonewool slabs, where only few plants share a common root zone. While the buildup of root microflora is important in the fight against root rot, proper sanitation practices and using new materials and rooting media will help prevent the carryover of unwanted pathogens.


In warm, rainy outdoor climates, plants are highly susceptible to Pythium spp., Phytophtora spp. and Fusarium oxysporum. When the first rain falls after long periods of hot, dry weather, the rain will flood the soil, it will drain poorly and roots will suffocate. These dead roots produce phenolic compounds, which are probable carriers of oospores. It is important to use preventative measures in these types of growing conditions, such as mulching your soil to prevent it from becoming too hot.

When all is said and done, preventing and controlling root rot is not as difficult as it may seem, as long as you take these small steps to prevent the disease. Not only will your plants’ roots be disease-free, but using helpful bacteria and micro-organisms will allow your plants to be healthier and produce more. Just remember to use new materials when transplanting, be aware of the environmental conditions in which you are growing and adjust accordingly, and supply the right amount of helpful micro-organisms to keep your plants happy.