Soil-Borne Diseases and How to Effectively Treat Them

Person pulling out weeds in a garden
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Of all the problems plants are susceptible to, soil-borne diseases can be the most frustrating. The gardener can think they are doing everything right and yet their plants become sickly, stunted and near death. Soil-borne diseases are caused by microorganisms that survive and move about in the soil. Most cannot be seen by the eye and go undetected until the plant becomes ill.

For any disease to take hold, three things need to be present:

  1. A pathogen (the microorganism that causes the disease)
  2. A host (our plants)
  3. The right environmental conditions.

In the case of soil-borne diseases, the pathogens can remain in the soil for long periods, waiting for the host - our plants - to come along. The environmental conditions can vary widely. Some pathogens favor damp conditions, some like certain soil pH levels and others target tender, succulent growth.

While some pathogens are short term visitors, appearing when the host and conditions are just right, others are naturally found in the soil and persist for years. When their favorite plant is not available, they may turn to an alternative. That's why clearing all the plant debris out of your garden at the end of the season is recommended.

Many plant diseases have similar symptoms, like yellowing leaves or dark spots. It is important to try and finds signs of the actual pathogen, but these are not usually visible without magnification. If you are having a longstanding problem, it would be worth your time to take a sample into your local Cooperative Extension.

Types of Soil-borne Pathogens

Here are the common types of soil-borne pathogens:

  • Fungi - the most common soil-borne pathogens. However, not every fungus causes plant problems and while the vast majority do not, over 8,000 fungi species do. And most plants are susceptible to some type of fungus.
    • Root rots cause the root system to begin to decay. The pathogens infect the plant's roots and block the uptake and flow of water and nutrients through the plant. Symptoms may include wilting, yellowing, stunting, dieback and eventual death and can be confused with other problems such as drought and nutrient deficiencies. Some common root rot fungi include Cylindrocladium, Pythium, Phytophthora, and Rhizoctonia.
    • Stem, collar, and crown rots affect the plant at ground level. Symptoms are similar to root rots, but since the rotting start above the soil line, it can be easier to detect early. Common pathogens to watch out for include: Phytophthora, Rhizoctonia, Sclerotinia, and Sclerotium.
    • Wilt diseases, like Fusarium oxysporum and Verticillium spp. cause wilting of the plants, despite adequate water. There are also usually internal symptoms.
    • Damping-off diseases affect young seedlings. They can be caused by a handful of fungi, including Pythium, Phytophthora, Rhizoctonia and Sclerotium rolfsii. They can infect the plants at germination or shortly after, causing sudden death. This is why the use of garden soil for seed starting is not recommended.
  • Bacteria - less common pathogens (and most don't stick around long). Some examples: Erwinia (soft rot), Rhizomonas (corky root of lettuce) Streptomyces (potato scab, soft rot of sweet potatoes)
  • Viruses - rare, thankfully, and most require living plant tissue to survive, but they can also hitch a ride on fungi or nematodes and flow in on water. When a virus enters a plant cell, it can cause the cell to produce more virus cells. Lettuce necrotic stunt virus affects Romaine lettuce plants, causing stunting and yellowing and sometimes spotting of lower leaves, while newer leaves remain green and thick.
  • Nematodes - sometimes called roundworms, nematodes are unsegmented worms with round bodies and points at both ends. Some are parasitic, like the nematodes sold to feed on beetle larvae in the lawn. And some will feed on or in roots. This is especially problematic for root crops, like carrots. Root rot nematodes are probably the most familiar. They cause distortion and swelling of roots and can affect the plant's vigor. Needle nematodes feed on the tips of roots, causing branching and swelling. And stubby root nematodes caused - yes - short, stubby roots.
Garlic bulb pulled from the soil with white rot visible
White rot on garlic bulb, caused by soil-borne fungus Jo Whittingham / Getty Images

Controlling Soil-borne Diseases

We've read what soil-borne diseases actually are, now what can you do about them?

Getting rid of the culprits permanently is just about impossible, especially if they are common in your area. They can survive in the soil, even when their usual host crop is no longer present. Chemical control is not very effective or long term and it can get to be prohibitively expensive. However, you can cut down on populations and infestations in a few ways.

  1. Clean up all garden debris at the end of the season. At the very least, get rid of everything that was infected. Pathogens can feed on over-wintering plant material.
  2. Rotate where you plant vegetables in the same family. If this is impossible for space reasons, it might be wiser to skip planting it for a year or two. While this obviously isn't ideal, if the alternative is successively bad harvests, missing a year of potatoes doesn't seem so bad. Try planting in containers for one year and then switching back to your garden the next.
  3. Some annually occurring fungal problems can be prevented by treating with sulfur or copper early in the season Both are considered organic controls.

Soil-borne diseases will continue to frustrate backyard gardeners. As always, the best defense is a good offense. Planting vegetable varieties with resistance to common diseases can help to both limit the occurrence of problems and the spread of soil-borne pathogens. It is not always possible to find resistant varieties, but if you can, it will certainly give you an edge.

Wheelbarrow filled with pulled weeds
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Article Sources
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  1. Soil-Borne Fungal Diseases. Washington State University Extension

  2. A Quick Look at Plant Disease Caused by Nematodes. Michigan State University Extension

  3. Soil Borne Diseases. Department of Primary Industries and Regional Development Website

  4. Using Organic Fungicides. Purdue University Extension