Many soil-dwelling microorganisms are benign or beneficial, of course, but certain species of fungi, oomycetes, and bacteria are agents of plant disease. The diseases include root rots caused by fungi or bacteria, as well as wilt diseases, such as verticillium wilt of tomatoes and other vegetables, that affect a plant’s ability to move water through its stems. These organisms can persist in soil for years, infecting future crops.
Plant pathologists agree that the best way to deal with soilborne pathogens is to avoid them. “Prevention is everything from my perspective,” says Deborah Mathews, Ph.D., an assistant cooperative extension specialist at University of California–Riverside. Here are six tips for avoiding trouble.
Inspect plants before you buy them. Pull them out of the containers and look at the roots. Are the roots white and healthy looking or dark brown and slimy, indicating root rot? Do they have galls caused by root-knot nematodes? If there are any signs of trouble, put the plant back and find a healthy one instead.
Practice good hygiene. “Don’t move soil around. Because if it’s a soilborne pathogen and you take soil and move it to a different site, you’ve just spread the pathogen with it,” says Pat Nolan, a plant pathologist with the County of San Diego, California. She also recommends cleaning your gardening tools before using them in a different planting area. “The pathogens can be transported on your dirty tools.”
Don’t overwater. “Moisture is your enemy with most fungi. Overly damp conditions promote fungal and oomycete growth,” warns Mathews. Oomycetes are organisms that act in ways similar to fungi but differ from them genetically. “If you see your plant wilt, your first instinct is to give it more water,” says Mathews. Before you do, check to see whether the soil is already moist. Most plants are best able to ward off root-rot organisms when grown in well-drained soil. If your soil is heavy clay, increase its porosity by adding organic matter to the top 6 to 12 inches. Also, keep mulch away from the crowns of plants, as it holds moisture and can cause rot.
Plant disease-resistant varieties. Some crop varieties are bred to withstand specific pathogens. When a vegetable has built-in resistance to diseases or pests, this information may be listed on the seed packet in abbreviated form. Abbreviations include V, F, and N, which indicate resistance to verticillium wilt, fusarium wilt, and pathogenic nematodes. “The best way you can prevent the host from getting sick is to plant one that isn’t capable of getting sick,” says Mathews.
Rotate your crops. Some soilborne diseases affect closely related vegetable plants but not crops from other plant families. (Examples of related crops are the brassicas, or cabbage family; the nightshades, which include tomatoes, potatoes, peppers, and eggplants; and cucurbits, including melons, squash, and cucumbers.) When related crops are planted in the same spot in successive years, pathogens in the soil don’t have to go far to find their host plant of choice. Crop rotation breaks the disease cycle by denying pathogens a suitable host. Nolan recommends a rotation of at least 3 years.
Keep your crops healthy. “Happy plants make more resistant plants,” says Mathews. But what happens if a soilborne pathogen gains a foothold in your garden despite your precautions? Step one is diagnosing the problem—often the most difficult step. Start by checking in with a local master gardener group, cooperative extension, or agricultural university, to see what kind of diagnostic help they offer.
“Once you have the diagnosis, then you can figure out what kind of measures you want to take,” says Nolan. “If it’s a soilborne organism that’s going to stay in your soil forever, like verticillium or nematodes, you can’t really get rid of it. If it’s something that goes away after a while, you can plant a different crop for a while.” Another option is solarization—using solar energy to heat the soil and kill pathogens—although that means covering your garden in plastic during the hottest months instead of growing the heirloom tomatoes you love.
Even if you cannot figure out what, exactly, infected your plants, you can still take measures to help ward off future problems. If a plant dies, says Mathews, pull it out and look at the roots. Roots that are dark brown, black, slimy, or mushy show classic symptoms of root rot. If the plant was in a container, discard the soil in the trash—not the compost pile. If the plant was in the ground, toss out the entire plant and its root ball, plus at least 4 inches of soil from around the plant.
As Nolan says, “Be aware of what kind of soilborne pathogens your plant may get. Knowledge is power—it helps you avoid things.”
Originally published in Organic Gardening Magazine December/January 2014.