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Plant Stems Turning Black (Causes and Treatment)

Seeing your plant’s stems begin to turn black is the last thing you want to see. Is it a telltale sign that your plant is about to die? 

Stem rot, blight, stem rust, bacterial canker, and other stem infections are common causes of blackened plant stems. Other possible causes include pest infestations and stem and leaf spots. They are usually the result of poor cultural practices such as overwatering, a lack of light, and temperature stress.

Keep calm for the time being because, once the underlying cause has been identified, the majority of problems are straightforward to resolve.

What Causes Plant Stem Turning Black?

[1] Early Blight

The term “blight” refers to a group of fungal infections that cause plant stems to turn black. The name comes from the fact that early blight appears early in the growing season. This is usually in the early to mid-spring.

The fungus Alternaria solani is the most common cause of early blight. The fungus is usually found in soil, but it can also live in dead plant matter. In the moist conditions of early spring, the spores will germinate.

The infection begins as small, irregularly shaped brown spots or wounds on parts of the body that are close to the ground or soil. 

These irregular spots expand to form concentric rings around a dead tissue bull’s-eye. They will appear on the lower stems, leaves, and fruits of the plant.

The wounds will grow, turn black, and eventually cover the entire stems. Affected leaves will begin to yellow, then turn brown, and eventually fall off. Fruits will suffer a similar fate, developing black cracks and dropping.

Plants that are stressed, weakened, or malnourished are frequently affected. Damp conditions and warmer temperatures of 80-85 °F (27-29 °C) hasten stem blackening.

Early Blight on Stem

Control and Management

  • Remove and discard any plant debris to prevent the spread of the fungus.
  • Stake or prune your plant regularly to boost aeration and stop fungal infections. It’s vital to sterilize your shears or cutting instruments after each trim.
  • Avoid wetting the foliage of your plant. Irrigating your plant early in the morning should help the leaves dry out sufficiently.
  • Treat your plant with a copper-based fungicide (Check the latest price on Amazon here). Repeat application after every seven to ten days, as long as necessary.

 [2] Late Blight

Late blight, as the name implies, is a fungal infection that occurs much later in the growing season. In most parts of the United States, it appears in September or October.

Late blight, like early blight, begins in the soil. Stems, fruits, and foliage near the soil are the first to turn black or dark brown. It first appears on older branches and leaves, which develop water-soaked grayish-green lesions.

As the infection spreads, these lesions will enlarge and turn black. Some white cottony growths may form near the lesions. Infected fruits may develop black lesions as well.

Infected foliage usually turns yellow and then develops large black patches before falling off the plant. The affected leaves may also appear scorched or bleached.

As the condition worsens, the entire stem will be affected and turn completely black. If left untreated, your plant will most likely die in a matter of weeks.

The Phytophthora infestans fungus causes late blight. It grows best in moist, warm weather, with daytime temperatures ranging from 70-80 ˚F (21-27°C). It also prefers cooler nights.

Control and Management

  • Take drastic measures to prevent the spread of blight. Remove and destroy all infected parts. It would help if you did not reuse the cutting tool without sterilizing it.
  • Avoid reusing the growing medium.
  • Water your plant early in the morning hours and avoid overhead irrigation
  • Treat your plant using a copper-based fungicide or a broad spectrum bio-fungicide (Check the latest price on Amazon here).

[3] Stem Rot

Stem rot is frequently associated with root rot. Both are caused by fungi that infect the stem and roots in excessively moist conditions. This can occur as a result of waterlogged or soggy soil caused by overwatering, poor drainage, or excessive humidity.

Wetting the stems and leaves when irrigating your plant is another culprit. This is particularly true if you use overhead irrigation. Fungi from the Phytophthora and Fusarium genera are the most common pathogenic factors for stem rot.

Typical symptoms include stem swelling, softening, and turning brown, then black. The roots may also drown, die back, and begin to rot. They’ll be brown or black in color and mushy between your fingers.

Affected stems typically wilt and collapse, killing your plant. The leaves generally turn yellow, develop brown spots, wilt, and drop.

Stem Turning Black Due to Stem Rot
Stem Turning Black Due to Stem Rot

Control and Management

  • Stem rot is usually an indication of a late-stage fungal rot disease. Your chances of saving your plant are almost slim.
  • Your best bet is to clean your plant of all infected parts. Trim off any diseased roots, stems, foliage, and flowers (if affected).
  • Treat with fungicide, then repot your houseplant.

[4] Alternaria Stem Canker

Alternaria stem canker is a serious fungal disease caused by the Alternaria fungus. These unsightly, oddly shaped cankers mostly appear on stems near the soil. They can, however, harm fruits, leaves, and even flowers.

Alternaria stem canker symptoms include dark brown or black stem cankers. Circles may encircle these irregular lesions. As they spread, they will enlarge and darken.

You may also notice some black or brown zones between the leaf veins. Toxins released by the fungus cause these symptoms. Infected leaves typically wilt, become limp, and then fall off.

In temperatures around 77°F (25°C), the infection spread quickly.

Alternaria Stem Canker
Alternaria Stem Canker

Control and Management

  • The spread of the stem canker is encouraged by overhead irrigation and high humidity. You should increase ventilation to reduce humidity.
  • Prune and discard all affected plant materials
  • Treat your plant with any fungicide formulated for black fungus mold. I recommend a broad-spectrum product containing cyprodinil and fludioxonil. 
  • Avoid both overhead watering and handling wet plants

[5] Bacterial Canker

Bacterial canker causes black sunken watery or sticky lesions on your plant’s stems. They typically appear early in the spring season. These lesions frequently expel a pungent sap, causing the surrounding area to become moist and turn black or reddish-brown.

The foliage above the affected stems will show signs of stress as well. Yellowing, curling, and dead spots will appear on the leaves. If the bacterial infection is severe enough, the foliage will fall off.

Growth frequently stalls, resulting in stem dieback. Your plant will eventually die.

The pathogen responsible for the stem canker is Pseudomonas syringae. The opportunistic bacterium enters through wounds caused by cuts, injuries, etc. Bacterial canker is quite aggressive in wet and cool conditions.

Control and Management

  • Remove wilted, dead, or affected stems and leaves.
  • Make a habit of pruning during the flowering period. Avoid pruning in fall and spring.
  • Treat pruning cuts immediately using a grafting wax (Check the latest price on Amazon here).
  • Check soil pH. Adjust with lime if the growing medium is too acidic
  • From experience, I’ve found copper sprays to work well against bacterial cankers. If it has phosphorus acid, even better.

[6] Botrytis

Botrytis is a gray mold that appears on the stems as large tan or grayish patches. Botrytis spores are fuzzy or dusty gray and grow on wet foliage and stems. They germinate and thrive in a humid environment with cool temperatures.

Spores enter the tissue via breaks in the leaves and stems. These grayish patches will eventually merge and form black blotches on the stems. It most commonly affects older and lower stems.

Botrytis can also wreak havoc on flowers and foliage. It will cause grayish mold to speckle the leaves, obstructing photosynthesis.

It spreads rapidly and causes affected areas to collapse. Leaves and stems that are affected will wrinkle, droop, and wither.

 Botrytis Disease on Plant
Botrytis Disease on Plant

Control and Management

  • Remove infected plants from others immediately.
  • Trim off moldy parts and discard them properly. Don’t forget to clean your tools, hands, and gear to prevent the transfer of fungus spores.
  • Relocate your plant to a better-aerated, warm spot with less humidity
  • Let your plant dry completely before applying a fungicide spray
  • Avoid injuring your plant (Source: Pennsylvania State University)

[7] Black Stem Rust

Back stem rust is one of the most common fungal diseases that wilt plant stems. They are more commonly exposed parts of the stems. Rust can also be seen on leaves, fruit, and flowers.

Stem rust causes spore pustules that are initially white and then turn yellowish-green. They will eventually turn rusty brown or black and suffocate the entire stems. Warm temperatures, high humidity, and low light encourage their spread.

Common symptoms include:

  • Black spores visible on stems and foliage in late summer and fall
  • Black cocky blotches on infected stems
  • Affected leaves turn yellow and drop prematurely
  • Heavy infestation can cause stunting of growth

Control and Management

  • Good sanitation is necessary to curb the spread of the spores
  • Pick up and carefully discard fallen plant debris
  • Steer clear off overhead watering and wetting the foliage
  • Applying fungicides that contain pyrethrin, sulfur or copper will help control the stem rust

[8] Spring Black Stem and Leaf Spot

Spring black stem and leaf spot is a fungal disease that flourishes in wet spring conditions. Fungus Phoma medicaginis is responsible for spot disease.

Black spots appear primarily on stems and foliage as symptoms. These lesions appear quickly on stems and turn black. The entire stems may become blackened as they grow and coalesce.

Lesions on the foliage are typically irregular in shape and expand to form large blotches. Infected leaves wilt and fall off the plant, turning yellow. If the black lesions on the stems and leaves become too numerous, your plant will succumb to the disease.

Control and Management

  • Prune away infected leaves and stems as soon as you see black spots or lesions
  • I highly suggest planting cultivars resistant to spring black stem and leaf spot.
  • There are many different fungicides on the market claiming to control spring black stem and leaf spots. I still suggest using a systemic or a broad-spectrum fungicide.

[9] Summer Black Stem and Leaf Spot

Summer black stem and leaf spot is a fungal disease that thrives in warm, humid environments. It’s caused by the fungus Cercospora medicaginis. It overwinters in contaminated foliage and stems.

Symptoms include:

  • Brown spots with wavy edges appear on foliage first. They can turn silvery or grayish and be trimmed with yellow
  • Brown lesions appear on stems. They will ultimately turn black
  • Loss of lower leaves

Control and Management

  • Warm temperatures and too much humidity facilitate summer black stem and leaf spots. So, it’s best to take your plant to a cooler area with less humidity.
  • Trim away infected parts and discard them carefully
  • Application of copper hydroxide fungicides can help control the summer black stem and leaf spot disease.

[10] Insect Infestation on Stem

Some common pests can also settle on the stems and cause them to turn black. It’s often seen if the infestation is due to sap-sucking insects. These include mealybugs, scales, aphids, whiteflies, and true bugs.

These pests often excrete a sticky, sugary substance. Called the honeydew, this gooey paste is a favorite feedstock for mold growth. As a result, the stems, leaves, and even flowers will become sticky and develop black sooty mold.

Another common sign is the appearance of ants. They do also love eating the honeydew and may even protect the responsible pest.

Insect Infestation on Stem
Insect Infestation on Stem

Control and Management

  • Control measures will depend on the type of pest
  • Prune and isolate any infested plant
  • You can manually handpick or dub some bugs like mealybugs using alcohol-containing cotton swabs.
  • A strong water jet can also help remove most bugs like whiteflies, fungus gnats, mealybugs, and aphids.
  • For treatments, consider applying insecticidal soap, neem oil, or pyrethrin insecticides.
  • I also prefer using natural predators like lacewing larvae and parasitic wasps.

How to Prevent Plant Stems Turning Black

  • Ensure good ventilation – space out your plants, prune them, and stake your plants to improve aeration
  • Practice good sanitation – Avoid handling plants when wet, remove & discard debris, and sterilize cutting tools after every use.
  • Good watering habits – Avoid overhead irrigation, don’t wet foliage and water early in the morning.
  • Don’t reuse growing mediums.
  • Keep your plants healthy – Fertilize accordingly, use a rich potting mix, give proper light, and avoid low light.
  • Isolate infested or infected plants immediately.