Charcoal Rot (Crop Protection Network, 2015) is available to read online or obtain a print copy from your your local county Extension office.

Soybean plant pathologists discuss charcoal rot scouting and management series of videos>


Charcoal rot of soybean is caused by a soilborne fungus Macrophomina phaseolina. This disease had been considered primarily a southern soybean problem, but recently has emerged as a threat in the North Central region of the U.S. and Ontario, Canada, where weather trends favorable for disease development — such as warmer summer and winter temperatures and reduced rainfall — have likely contributed to its presence.

The fungus causes a general root rot in soybean, infecting the roots and lower stems. The name charcoal rot is descriptive of the small black fungal structures, called microsclerotia, on the lower stem of infected plants.Yield loss from charcoal rot is highly variable, but farmers can reduce crop injury by implementing best management practices based on a better understanding of this disease.

Plants of any age can be affected by charcoal rot. The initial infection occurs in the spring when soil moisture is high. However, symptoms remain latent unless stressful environmental conditions, especially hot, dry weather, occur during the mid- to late season as the crop begins to flower and form pods.

  • Scouting

    signs of charcoal rot in soybean stem

    See Charcoal Rot (CPN 1004) for a complete discussion and diagnostic photos of soybean diseases with similar symptoms.

    In the North Central region, visible symptoms, when they occur, generally do not appear until the later stages of pod fill. The characteristic sign of charcoal rot is the microsclerotia in root and stem tissue, and these may not be visible until maturity or plant death.

    Microsclerotia may be visible on the lower portion of the plant, often just under the outermost layer of stem tissue. To the naked eye, it will look as if the root or stem has been “peppered” with black spots (upper photo). Upon closer inspection with a hand lens, individual microsclerotia can be seen within the plant tissue (lower photo). See Scouting Soybean Stem Diseases, Crop Protection Network.

  • Symptoms

    Gray discoloration on the lower stem of a soybean plant affected by charcoal rot. To see an enlargement, go to: The Bulletin, University of Ilinois

    Symptoms of charcoal rot begin typically in the driest areas of the field such as sandy or compacted areas, or the tops of terraces. Infected plants wilt in the midday heat, recovering at night until the permanent wilt point is reached.

    Plants infected by the charcoal rot pathogen may have premature yellowing of the top leaves and premature leaf drop. This is easy to mistake for normal maturity. Look for unfilled upper pods and general low plant vigor. In some cases, the upper one-third of the plant may have only flat pods without seed.

    Beginning at flowering, a light gray discoloration develops on the epidermal and sub-epidermal tissues of both tap and secondary roots and lower stems. Scrape the outer tissues and use a hand lens to look for the presence of black microsclerotia - a diagnostic symptom of charcoal rot.

    Increased susceptibility to root rot
    In some cases, charcoal rot symptoms may appear in lower wetter areas of the field. In these instances, the soybeans usually will have symptoms of root rot from a previous infection of Pythium, Phytophthora or Rhizoctonia.

    The damaged root system decreases the ability of the roots to move water from the soil to the plant, putting the plant under moisture stress. In these situations, the charcoal rot fungus can be considered a secondary invader.

  • Agronomic impact

    • Results from controlled studies showed that infection by Macrophomina phaseolina can reduce plant height, root volume, and root weight by more than 50%.
    • Damage to the root system is most evident during the pod formation and filling stages, when demand for water and nutrient absorption is high.
    • Seeds of infected plants tend to be fewer and lighter as a result of the smaller root system.
    • Diseased plants will mature several weeks earlier, which further contributes to yield loss.
    • Root infection by germinating microsclerotia can occur very early in soybean plant development. Wyllie (1976) reported that M. phaseolina could infect up to 100% of soybean plants within 3 or 4 weeks after planting.

    View video: Martin Chilvers, field crops pathologist at Michigan State University, discusses current research on the effect of charcoal rot on soybean yield.

  • Risk Assessment

    Stress caused by excessive plant populations, soil compaction, improperly applied herbicides, nematodes, or other diseases avors the charcoal rot pathogen and increases the risk of infection.

    Unlike most soil fungi, which decline in activity when soils become too warm, the charcoal rot fungus is most active when soil temperatures are as high as 80-95° F (27- 35° C). Fungal growth and survival is favored by dry soils, conditions that weaken and stress the soybean crop, particularly during the reproductive growth stages.

  • Management

    charcoal rot field trial

    A checkoff-funded, multi-state field screening program for charcoal rot is now in place where breedling lines, germplasm, and commercial varieties are tested over different years and environments, including the midwest. Photo: A. Mengistu, USDA-ARS.

    Use varieties with the highest level of resistance available in a maturity group appropriate for your area.
    Plant the fullest-season varieties that are practical. Plants are most susceptible to charcoal rot at the beginning at flowering. The longer-season varieties tend to flower later and are in a vegetative growth stage during the early part of the hottest, driest portion of the growing season.

    Use no-till systems to increase soil microbial activity and conserve soil moisture, which can reduce charcoal rot.
    Soybeans direct-seeded in no-till systems typically have lower levels of charcoal rot compared to soybeans under conventional tillage.

    Rotate to non-host crops for 1 to 2 years in fields with a history of charcoal rot.
    Rotation to non-host crops such as wheat and other small grains for 1 or 2 years should be considered part of a charcoal rot management plan in problematic fields. Also, although corn, sunflowers, and other crops are hosts, research has shown that there are strains of the fungus that have host preferences. For instance, some strains prefer soybeans while others prefer corn or sunflowers. Therefore, rotation with any other crop can be beneficial and the longer the rotation, the better.

    Avoid excessive seeding rates to reduce crop stress and minimize loss to charcoal rot.

    Consider supplemental irrigation to slow colonization of the plant by the charcoal rot pathogen and reduce symptom severity during drought conditions.

    Fungicides do not provide protection
    No fungicide seed treatments have been identified that offer consistent control of charcoal rot.

  • Resources

  • Photo Gallery

    Close-up of microsclerotia of M. phaseolina

    Microsclerotia on stem tissue. Photo: Chris Little, Kansas State University

    Premature yellowing of plants infected with M. phaseolina. Photo: University of Illinois

    Soybean field with symptoms of charcoal rot

    Charcoal rot field trials. Photo: Alemu Mengistu, USDA-ARS