How to Identify and Prevent Stem Rot

Phytophthora blight (Phytophthora capsici) infecting green beans
Phytophthora blight infecting green beans

NY State IPM Program at Cornell University / FlickrCC BY-NC-SA 2.0

Stem rot on garden flowers, crops, or potted plants caused by fungi in the soil. Stem damage or wilt to members of the cucumber family (zucchini, squash, pumpkin, gourds) is often caused by the squash vine borer.

Diagnosing and controlling stem rot or wilt depends on which garden crop is affected. Here's how to control stem damage from both fungi and the squash vine borer.

How to Prevent Stem Rot

As with many fungal diseases, once a plant is affected, there is not much to be done. Once you notice stem rot, there is usually already damage to the roots or other parts of the plant. That’s why good gardening practices and preventive measures cannot be over-emphasized.

  • Improve Drainage. Soil-inhabiting fungi like the ones that cause stem rot thrive in moisture. Poorly drained soil, often in combination with warm temperatures, is an ideal breeding ground. Adding plenty of organic matter improves soil drainage. Another solution for excessively wet soils is to grow your garden vegetables in raised beds.
  • Plant Correctly. When transplanting seedlings, plant all the plants at the same depth so that none of them are buried in the soil.
  • Keep Soil Away From Stems. As you cultivate the soil or till make sure that you don’t toss any soil against the stems. Tilling the soil can bring the fungus closer to the surface.
  • Avoid Areas With Previous Rot Issues. While rotating crops in your vegetable garden is always a must because it helps control other plant diseases, in the case of Phytophthora capsici and Sclerotinia sclerotiorum, it does not help because these fungi are resistant to winter temperatures and can live in the soil year after year for a more than a decade. If you have a problem with any of the fungi causing stem rot, a fresh start with healthy soil in a raised bed might be the best solution.
  • Improve Air Circulation. Always ensure proper air circulation and give plants ample pace. In rows that are too densely planted, humidity gets trapped, which propels fungal growth, especially in warm weather. Thin seedlings as needed. A trellis is a good way to keep vines and foliage off the soil and improve air circulation.
  • Check Mulch. If you apply organic matter as mulch, make sure it’s fully decomposed. If your compost isn’t ready yet, you are better off using plastic sheets for mulching.
  • Start With Healthy Plants. Healthier plants are less susceptible to disease so make sure the plants get all the nutrients they need.
  • Control Water Usage. Don’t overwater, and avoid using surface water from ponds and creeks, which may be contaminated with Phytophthora capsici.

Stem Rot Caused by Fungi and Parasites

Sclerotinia sclerotiorum

Sclerotinia sclerotiorum (white mold) is one of the plant pathogens with the largest host range damaging more than 350 species. Garden crops susceptible to the fungus include beans, soybeans, cabbage, carrots, cucumbers, cilantro, lettuce, melons, onions, peas, pumpkins, squash, and tomatoes.

Sclerotinia sclerotiorum on a bean stalk
Sclerotinia sclerotiorum on a bean stalk Jymm / Wikimedia Commons / Public domain

Sclerotinia sclerotiorum can manifest itself in two distinct and opposite symptoms:

  • Water-soaked irregularly shaped spots on stems, leaves, and fruit. The fungus visibly spreads by covering the plant surface with a cotton-like substance, which is the mycelium of the fungus. Eventually, the entire plant turns soft, slimy, and will die out. 
  • Distinct but dry lesions on the stem, stalk, or branches. As the lesions grow, they girdle the affected plant part—or the entire plant, if the lesions appear at its base—and the plant turns first yellow, then brown, and eventually dies.

In either type of symptom, at an advanced stage of the disease, you might notice a small, compact mass that resembles black seeds. These are the hardened mycelium of the fungus.

Phytophthora capsici

In members of the cucumber family, stem rot may also be caused by another parasitic plant pathogen, Phytophthora capsici which causes Phytophthora blight. Water-soaked lesions on the vines become brown, the plant tissue dies, and the stem is girdled, which leads to wilting and dieback of the vine above the lesion.

The pathogen lives in the soil but is transmitted to plants primarily through water, such as rain or irrigation. In warm and moist weather, the fungus spreads rapidly and can kill a plant within a few days.

Rhizoctonia, Fusarium, and Pythium

The fungi Rhizoctonia and Fusarium, and the oomycetes Pythium, a parasitic plant pathogen, live in the soil and attack the plant, often in the seedling stage. Symptoms include spots on the lower part of the stem, in a wide range of colors: gray, brown, black, or vibrant red. The disease leads to root decay, wilting, dieback, and weakened plants.

Stem Wilt Caused by the Squash Vine Borer

A sudden wilting of your squash plants is not necessarily caused by any of the fungi above. It may also be the doings of the squash vine borer, whose larvae burrow into the stem. Upon looking closely, you might see tiny holes in the stem and sawdust-like frass. If that’s the case, find out how to control squash vine borer here.

Squash vine borer damage on a squash stem
Squash vine borer damage on a squash stem

Campwillowlake / Getty Images

Article Sources
The Spruce uses only high-quality sources, including peer-reviewed studies, to support the facts within our articles. Read our editorial process to learn more about how we fact-check and keep our content accurate, reliable, and trustworthy.
  1. Plant Disease: Phytophthora Root and Stem Rot. University of Nebraska-Lincoln

  2. Squash Vine Borers. University of Minnesota Extension

  3. Phytophthora in Vegetable Crops. University of Minnesota Extension

  4. Sclerotinia stem rot (white mold) on soybeans. University of Minnesota Extension

  5. Rhizoctonia root and stem rot on soybeans. University of Minnesota Extension

  6. Soybean seed and seedling disease. University of Minnesota Extension

  7. Pythium root and stem rot. Michigan State University

  8. Squash Vine Borers. University of Minnesota Extension