Stem rot is a disease that attacks the stem itself, usually at or just above the soil line, and it is easy to recognise once you know what to look for: a dark, sunken, soft patch on the stem, often with a white or grey mould on it in damp weather, and a plant that wilts and collapses above the rot even though the roots look fine. The stem is the plant's highway, and when it rots through, everything above it dies. It is a common problem on tomatoes, peppers, cucumbers, beans, and many other vegetables, and it is particularly frustrating because the plant often looks vigorous until the day it falls over.

Several fungi cause stem rots, including Rhizoctonia, Sclerotinia, and Fusarium species, and they share a love of wet stems and still air. The rot often starts where the stem is damaged — by a stake rubbing, by soil splashing, by an insect bite — or where the stem stays wet because the plant is crowded and the air does not move. Some stem rots produce hard black resting bodies in the stem that survive in the soil for years, so the disease can return to the same bed again and again. The control is about keeping stems dry and intact, giving plants air, and removing infected material promptly.

What stem rot looks like: symptoms

  • Dark, sunken patches on the stem: brown, black, or grey sunken areas on the stem, usually at or just above the soil line, that feel soft when pressed.
  • White or grey mould on the stem: in damp weather a white, fluffy mould may grow on the rotted area, and in the case of Sclerotinia, hard black resting bodies like small rat droppings may form inside the stem.
  • Wilting above the rot: the plant wilts above the rotted section even though the soil is moist, because the stem can no longer carry water upward.
  • Collapse: the stem may break or collapse at the rotted point, and the plant falls over, often with the top still green.
  • Yellowing and leaf drop: leaves above the rot yellow and drop as the stem's transport fails, and the plant stops growing.
  • A foul smell in wet rot: some stem rots produce a soft, wet rot with a musty smell, especially in warm, humid weather.
  • Girdling: the rot may spread around the whole stem, girdling it completely, which kills everything above it within days.

Stem rot usually starts at a wound or at a point where the stem stays wet, and it spreads along and around the stem over days to weeks. The first sign is often a small dark patch that is easy to miss, and the plant may look normal above it for a while. As the rot spreads around the stem, the wilting begins, first on warm afternoons and then permanently, and the stem weakens until the plant collapses. In warm, wet weather the whole process can take a week; in cool, dry weather it may take a month. The disease is worst in crowded, humid plantings and in greenhouses, where the air is still and the stems stay wet.

Which plants get stem rot

Stem rot attacks tomatoes, peppers, eggplants, cucumbers, squash, beans, peas, lettuce, and many other vegetables, along with flowers such as zinnias and dahlias, and houseplants kept too wet. Sclerotinia stem rot, also called white mold, is a particular problem on beans, lettuce, tomatoes, and cucurbits, and it attacks hundreds of species. Rhizoctonia stem rot is common on seedlings and young plants of many kinds. The host range is wide enough that the disease is best thought of as a condition — wet, damaged stems in still air — rather than as a problem of any one plant.

Conditions that favour stem rot

Stem rot needs wet stems and still air: rain, overhead watering, and heavy dew all keep stems wet, and crowded plants that dry slowly are hit hardest. Wounds from staking, pruning, insects, and hoeing give the fungi an entry point, and plants that are overfed with nitrogen have soft stems that are easier to invade. The fungi survive in soil and in plant debris, and some produce resting bodies that survive for years, so a bed that has had stem rot before is at risk again. Warm, humid weather favours most stem rots, though some, such as Sclerotinia, prefer cool, damp conditions.

How stem rot spreads

Stem rot spreads through soil and water, in splashing rain, and on hands, tools, and stakes that touch an infected stem and then a healthy one. The resting bodies of Sclerotinia survive in soil for years and germinate when conditions are right, so the disease can appear in a bed that has not grown a susceptible crop for several seasons. The fungi also travel in infected transplants and in debris, and they spread by direct contact where stems touch each other in a crowded planting. Wind is a minor carrier compared with water, soil, and contact.

How to tell it apart from lookalikes

Stem rot is often confused with crown rot, but crown rot is centred at the soil line on the crown itself, while stem rot can occur higher up the stem and often shows a distinct sunken patch with mould on it. Damping off is similar but attacks seedlings, while stem rot attacks older plants with firm stems. Bacterial wilt also causes sudden wilting, but it does not produce a dark, soft, sunken patch on the stem. Cutworm damage severs the stem cleanly, while stem rot leaves a soft, rotted section. If the stem has a dark, sunken, soft patch with mould on it, stem rot is the most likely answer.

Prevention: cultural steps that work

  • Space plants generously and prune for airflow so stems dry quickly after rain or watering.
  • Water at soil level, in the morning, and avoid wetting the stems and the lower leaves.
  • Stake and tie plants loosely, so the ties do not rub and wound the stem, and check the ties as the plant grows.
  • Mulch to reduce soil splash onto the stems, and keep the mulch a few inches away from the stems themselves.
  • Avoid wounding stems when hoeing, pruning, or staking, and wash tools between plants.
  • Rotate crops so the same family does not return to the same bed year after year.
  • Remove and dispose of infected plants and debris promptly, and do not compost diseased material.

Treatment step by step

  1. Remove the affected plant or, if the rot is limited to a single stem on a multi-stemmed plant, cut out that stem well below the rot and dispose of it with household waste.
  2. Improve airflow by thinning crowded growth and spacing plants, so the remaining stems dry quickly.
  3. Stop overhead watering and switch to watering at soil level, in the morning.
  4. Mulch the bed to reduce splash, and keep the area around the stems free of fallen leaves and debris.
  5. If the rot is small and high on the stem, you can sometimes cut it out and let the plant continue, but a rot at the base that girdles the stem means the plant will not recover and should be removed.
  6. Clean tools and stakes after handling an infected plant, and do not reuse a stake from an infected plant without washing it.
  7. At the end of the season, pull up annuals and clear all debris from the bed, so the fungi and their resting bodies do not overwinter there.

What recovery looks like

Recovery from stem rot depends on where the rot is: a plant with a small rot high on a side stem can recover well once the stem is removed and the air improves, and it will often go on to produce a normal crop. A plant with a rot at the base that girdles the main stem will not recover, because the transport to the whole top is cut off. The recovery of the bed is the more important story: a bed that is spaced, staked, and watered at soil level will usually stay free of stem rot even where it was a problem before. The sign that the plan is working is a planting that grows through the season with no dark patches on the stems and no sudden collapses.

When a plant is beyond saving

A plant is beyond saving when the rot has girdled the main stem at the base, when the plant has collapsed, or when the rot keeps spreading despite improved airflow and dry stems. A plant with a rot on a single side stem is not beyond saving — remove that stem and the plant can carry on. A bed is not beyond saving, though a bed with a history of Sclerotinia stem rot may need a long rotation, since the resting bodies survive in the soil for years.

Frequently asked questions

Can I save a tomato plant with stem rot at the base?

Almost never. A rot that girdles the main stem at the base cuts off water to the whole plant, and the plant will not recover. Remove it promptly so it does not shed spores onto its neighbours, and check your local extension service if the problem keeps returning.

What are the black lumps inside a stem with white mold?

They are the resting bodies of the Sclerotinia fungus, and they can survive in soil for years. That is why the debris from an infected plant must be disposed of, not composted, and why rotation matters.

Why does stem rot hit my cucumbers every year?

The fungi survive in the soil and in debris, and they return in the first wet spell. Thorough autumn cleanup, rotation, spacing for airflow, and watering at soil level are the ways to break the yearly cycle.

Can I compost a plant with stem rot?

No. The fungi and their resting bodies can survive in home compost, so composting an infected plant returns the disease to the garden. Bag the plant and put it with household waste.

Does staking prevent stem rot?

Good staking helps, because it keeps the stems off wet soil and lets air move around them — but ties that are too tight can wound the stem and cause the very rot you are trying to prevent. Tie loosely and check the ties as the plant grows.

Getting help and going further

If you are unsure which disease you are dealing with, take clear photos of the symptoms and check your local extension service — they can confirm a diagnosis from a sample and advise on the varieties and the timing that work best in your area. You can also try our plant disease checker to narrow down the problem, and browse the guides hub for related disease guides. For growing advice, see growing tomatoes. For growing advice, see growing cucumbers. For growing advice, see growing green beans. Related guides: crown rot, root rot treatment, damping off seedlings. Whenever you remove diseased material, dispose of it with household waste — do not compost diseased material, since home compost rarely gets hot enough to kill the organisms that cause these diseases. Good record-keeping helps too: note the date, the weather, and the variety when a problem first appears, so you can spot the pattern next year and act earlier.