Soil-Borne Pathogens Can Cause Plant Blight and Disease

The Best Soil for Vegetable Gardens Biologically Suppresses Plant Pathogens

Soil-Borne Pathogens Can Cause Plant Blight and Disease

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By John Hibma – The crops we grow, especially vegetables, are subject to a number of different diseases and plant blight caused by soil-borne pathogens. Soil is full of organisms — both good and bad. The good organisms include worms, slugs, snails, beetles, ants, and spiders as well as gophers and moles and even snakes. We may not think of snails or gophers as “good organisms” but through their activity in soil, they benefit its condition making it healthy and capable of sustaining plant life. Soil microorganisms— whether big or small— don’t live passive lives in the soil. They actively decompose organic matter, recycle nutrients, fix nitrogen, detoxify pollutants and maintain soil structure. Healthy soil is the foundation of successful agriculture.

Unfortunately, soil can harbor many bad organisms that can cause plant blight and other plant diseases. These pathogenic organisms include molds, fungi, bacteria, and nematodes. In most cases, all soils whether they be healthy or marginal will harbor pathogens that may potentially limit and even destroy a field or garden. Soil-borne pathogens usually cannot be completely eradicated from the soil so they must be managed in a way that will limit the harm they inflict on a crop.

How many of us growing tomatoes have seen scabs on them or pulled up a growing carrot from the ground only to find it hideously misshapen? Or bell peppers that wilt before our eyes or the beans that are covered with a powdery plant mildew. If anyone grows a garden or has ever attempted to grow a garden, sooner or later they will probably experience the disappointment and frustration of plants that turn yellow and lack vigor or fruit that rots on the vine. On a larger scale, commercial vegetable growers can see entire fields decimated by a pathogen and lose many hundreds or thousands of dollars of potential revenue.

General symptoms of soil-borne pathogens include leaf blight, wilting and stunting, seed decay, fruit rot and root rot. Several of the more common vegetable diseases and plant blights found in the Northeast U.S. are:

Phytophthora blight: —this plant blight is caused by a water mold that will rot fruit and rapidly wilt and kill a plant.

Sclerotinia diseases—: caused by a fungus that produces brown or gray lesions on foliage and fruit.

Common scab—: caused by various Streptomyces species.

Verticillium—a: widespread mold that causes leaf wilt on many vegetable plants.

Nematodes—: worm-like organisms that attack the root structure of plants.

Pathogen distribution in soils that results in plant blight and disease is highly dependent upon the cropping history of a particular soil, such as the types of crops grown and whether or not there has been any crop rotation over the course of seasons. Soil moisture and temperature can also influence the level of pathogen loading. Many diseases are more severe with high soil moisture. Soil pH and nutrient levels will also contribute to pathogen infection. Probably the single largest factor contributing to high levels of soil-borne pathogens is the health and integrity of the soil itself.


Healthy soil is a combination of minerals, air, water, and organic matter. Minerals in the form of sand, silt, and clay make up about 50% of good soil. Organic matter— also known as humus —makes up only a small portion of soils but is critical to the transfer of the chemical ions that are necessary for plant growth and fruit and vegetable production. Well-structured and stable soils are an ecosystem all to themselves with their own balance and interaction of organisms. It’s this healthy environment around the “root zone” of a plant that allows for biological suppression of plant pathogens and prevents parasitism and damage to plants. Blight and disease are easier to fend off with healthy soil, bottom line.

Generally, the first sign that soil-borne pathogens are infecting a crop is an obvious yellowing of plants. Don’t assume its plant blight or disease. Ruling out water, fertility or mineral deficiencies comes first, followed by inspection of leaves, stems, and roots.

As with many things in life, an ounce of prevention is worth a pound of cure. In the case of Phytophthora blight, the parasite is transferred through water. Cucurbits, Solanaceae, and legumes are all susceptible to this mold so testing the water source for the oospores that cause Phytophthora is highly recommended as well as not over-irrigating and controlling field drainage so as to not infect a neighboring field. Rotating plants from one part of a field to another as well as disposing of culled fruits somewhere where they won’t re-infect a field will help manage this disease.

According to researchers at the University of California, Sclerotinia diseases must be managed with a combination of cultural and chemical means. It’s best left to the grower/farmer as to whether chemical management for diseased plants is an option or not. Sclerotinic activity favors high moisture and high humidity and cooler temperatures. Rotation of crops is another important tool in managing the sclerotial population in soils. Sclerotinia does not affect grain or grass crops so rotating fields with corn or small grains between seasons may help control sclerotinia.

Verticillium wilt is a wilting condition on the stem and leaves caused by a fungus that affects nearly all vegetable varieties. This disease affects the vascular system of plants limiting its ability to transfer nutrients. It’s spread in the ground through root systems. Spores can remain viable for over a decade which makes eradication from a field nearly impossible. One of the few ideas for plant fungus treatment is anaerobic conditions such as flooding, which of course, is counter-productive in many other ways.

Nematodes are microscopic worm-like organisms that live most of their life-cycle in the root systems of plants. Root-knot nematodes infect vegetables throughout the United States, impacting both the quantity and quality of marketable yields. Above ground symptoms include stunting and uneven growth. Carrots will be greatly misshapen with multiple forking; onions and garlic will have bulbs that are poorly formed and misshapen. The bloat nematode will affect onions, garlic, and leeks with stunting, withering and yellowing of leaves along with the swelling of the stems and bulbs.

Research from Cornell University recommends rotating onions, carrots, or lettuce with a non-host crop such as sweet corn and other grain crops to control nematodes. Sudangrass is a non-host to the root-knot nematode and when incorporated as a green manure will further suppress the soil population of this nematode. The use of cover crops grown between the main crops may provide an alternative management strategy. The use of pre-planting fumigants have been found to be very effective in controlling nematodes but are very expensive and their use is highly regulated.

Growers need to be aware that, when dealing with a soil-borne pathogen, the same management strategies don’t always work in all field situations to ward off plant blight and disease. Each pathogen and cropping system must be considered individually when developing a strategy to manage a pathogen. Once pathogens are detected, though, cultural practices such as crop rotation and bio-security measures are the most effective ways to manage the parasites. Introduction of resistant cultivars of a plant variety (when available) will also limit pathogen damage.

Once soil-borne pathogens have established themselves in soils it’s very difficult to eradicate them. Soils that are marginal in quality and health—meaning that plants have a difficult time getting established and growing —will be more inclined to contain soil-borne pathogens. Soils with higher levels of organic matter (humus) will support more of the good organisms and exclude the pathogenic organisms. Soil management practices may also have a negative effect on soil health which opens the door for pathogenic organisms to get a foothold. Increased tillage (plowing and disking) tends to decrease the soil’s biomass. The application of manure and compost will improve the humus levels in soil. A healthy soil has good tilth and drainage, is resistant to degradation and is resilient under adverse conditions. That soil will support a large population of non-pathogenic organisms and exclude those organisms that are pathogenic.

Originally published in Countryside 2012 and regularly vetted for accuracy.

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