Identification and Management of
Mid-to-Late Season Soybean Stem and Root Rots

Soybean Disease Information Note 5
Stephen R. Koenning, Extension Plant Pathologist

[Introduction] [Diagnosis]
[Phytophthora Rot] [Pythium Root Rot] [Red Crown Rot (CBR)] [Southern Blight] [Charcoal Rot] [Back to Soybean Disease Notes] [Other Resources]


Several soil-borne fungi cause lower stem and root rot of soybean. These diseases usually result in the occurrence of dead or dying soybean plants in mid-to-late summer. Certain diseases are especially prevalent after periods of drought stress. Frequently, two or more pathogenic fungi can be found associated with these dead plants. Steps can be taken to reduce these diseases in future soybean crops if the disease is properly diagnosed.

The most common soybean root and stem rots in North Carolina are Phytophthora Rot, Pythium Root Rot, Red Crown Rot, Southern Blight, and Charcoal Rot. Each of these diseases may occur singly or in combination with the others. Damaging levels of plant-parasitic nematodes will generally cause these diseases to be more severe. In many instances, disease severity may be a symptom of other problems such as inadequate fertility, soil compaction, poor drainage, herbicide injury, high levels of nematode infestation, or low pH. Correcting these yield limiting problems is the first step toward disease management in soybean.

Obtaining Proper Diagnosis

Proper identification 'diagnosis' of the disease causing fungus is essential to formulating a management strategy. County extension staff may forward plant and soil samples to the NCSU Plant Disease and Insect Clinic for diagnosis if they are unable to identify the disease. Growers should provide as much information about the problem as possible on the forms sent to the clinic. Symptoms, patterns and distribution of disease, variety, crop history, as well as rates and methods of application of herbicides and fertilizers can aid in proper diagnosis. Soil pH, soluble salts, and nematode numbers, may be determined if a soil sample is provided with the plants. Plants which show all stages of decline and which are representative of the problem should be included. Dead plants may provide clues as to the exact nature of the disease, but are often inadequate to make an accurate diagnosis.

Common Root and Stem Rots of Soybean in North Carolina

Phytophthora Rot

This disease is caused by the soil-borne fungus Phytophthora sojae. This fungus is widely distributed in North Carolina, but is most important in heavy, poorly drained soils. It may cause a seedling disease or pre- and post-emergence damping off. This disease is most common after soil temperature increases and high rainfall results in soils waterlogged for long periods. It is especially prevalent in low-lying areas of the field. Soybean varieties differ in their tolerance and/or resistance to Phytophthora Rot. Therefore, symptoms may vary in their severity depending on the relative susceptibility of the variety planted. Symptoms on older plants are root rot, wilting, and death of plants. The stem of highly susceptible cultivars is usually dark brown, and this discoloration may extend from the base of the plant to more than 10 inches above the soil line. Leaves remain attached to wilted plants. The vascular and cortex tissue of the plant has a brown-to-black discoloration and "pith discing" may be visible in dead plants. The disease may appear to be restricted to low-lying areas of the field, portions of the field with heavier soils, or the entire field may be affected if poorly drained.

Management: Improve drainage, if possible. Varieties possessing high levels of resistance should be used in fields where Phytophthora Rot is identified as a problem. Rotations of two-to-three years with grain crops, tobacco, cotton, or non-leguminous crops are necessary if resistant varieties are not used. A seed treatment with a mefonoxam (Ridomil Gold, Apron) containing fungicide is effective against the damping-off phase of the disease, but an in-furrow application may be required if resistant varieties are not used.

Pythium Root Rot

Various species of Pythium cause root rots of soybean. Pythium spp. may cause disease at any time of the season, but seed rots and damping off diseases are most common. Symptoms caused by Pythium spp. are very similar to those caused by Phytophthora sojae. The determination of which fungus is the causal organism must generally be done in the laboratory. Diagnostic kits are available and can accurately distinguish between these organisms but are fairly expensive. Pythium Root Rot at mid-season may affect scattered plants, but economic losses in North Carolina are rare.

Management: This disease is difficult to manage because of the wide host range of the pathogen and its persistence in soil. If the problem occurs on a yearly basis, changing varieties and improving drainage may be effective. A seed treatment with a mefonoxam (Apron) containing fungicide is effective against the seed rot and damping off phase of disease. Root rots caused by Pythium spp., however, must be controlled by an in-furrow treatment (Ridomil Gold).

Red Crown Rot (CBR)

The fungus Cylindrocladium parasiticum, which causes CBR or Black Root Rot of peanut (PDIN-002) also causes a root rot of soybean. Symptoms usually appear late in the season, during or after pod set. Foliar symptoms are generally noticed with the onset of cool weather in the fall. Upper leaves may turn yellow and leaves will later become brown between the veins. Plants will defoliate early and petioles will drop with the leaves. The roots of affected plants will have a black root rot and stalk tissue will be grayish or reddish brown above the soil line for two-to-four inches. The presence of bright-red fungal structures (about the size of the head of a pin) near the soil line are a positive indication for this disease though they are not always present. Affected plants may be scattered throughout the field or confined to one area of the field. Infestations of cyst (SOY-001) and root-knot nematodes result in more severe disease in conjunction with C. parasiticum.

Management: Two or more years of non-host crops such as corn or cotton may be necessary to reduce the density of C. parasiticum microsclerotia to non-damaging levels. Do not include peanuts in a rotation with soybean if this disease is present in a field! Soybean is generally more tolerant of C. parasiticum than is peanut. Differences in soybean varietal responses to this fungus have been noted, but are not adequately documented. Nematode management through the use of appropriate soybean cyst nematode or root-knot nematode resistant varieties (SOY-006) may aid in suppression of Red Crown Rot.

Southern Blight

The soil fungus, Sclerotium rolfsii causes southern blight and is present in nearly all North Carolina fields. Disease is most common in sandy soils, however. Plants suddenly wilt and die during hot, humid weather. Leaves remain attached to the dead stem. A white mat of fungal tissue may appear on soil and the base of the stem. Fungal structures called sclerotia frequently cover the fungal mat. Sclerotia are spherical, tan or brown in color, and about the size of a mustard seed. Diseased plants are usually scattered throughout a field, although it is common for the disease to spread from plant-to-plant within a row during hot, humid weather.

Management: Soybean is generally tolerant to this disease and economic losses are rare in North Carolina. Growers should check for other soil-related factors such as nematode infestation, fertility or pH-related problems if disease is severe. Rotations with non-hosts (corn or grain sorghum) and deep plowing to bury crop residue are reasonably effective tactics for managing this disease.

Charcoal Rot

Macrophomina phaseolina is a fungus which is widely distributed in soils and may be either seedborne or soilborne. This fungus attacks a wide variety of plants, including cornsoybean, cotton, grain sorghum, and numerous weeds. It can attack soybean plants at any stage of development, but is most evident following periods of hot, dry weather. Infected plants have smaller leaves and grow slowly. Leaves of older plants turn yellow and wilt, but remain attached to the plant. A grayish or silvery discoloration of tissue under the bark of the upper tap root and lower stem are symptomatic on older plants. A reddish, brown-to-black discoloration of the vascular tissue may extend from the tap root up the stem. The distribution of infected plants may be scattered or uniform. This disease should be suspected if previous corn crops were also poor.

Management: The key to managing this disease is alleviation of plant stress. Charcoal rot is most common when soil pH and fertility are low and/or plants are under moisture stress. Correcting nutrient deficiencies and subsoiling, if a hardpan is present, will reduce disease severity. Corn and cotton are somewhat less susceptible to this fungus, so rotations of two to three years with these crops may prove beneficial.

Other Resources

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Soybean Disease Atlas
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North Carolina Agricultural Chemicals Manual
NCCES Educational Resources

For assistance with a specific problem, contact your local North Carolina Cooperative Extension Service personnel.

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Last update to information: May 2000
Last checked by author: May 2000
Web page last updated on November 2000 by A.V. Lemay.