Soil and weather conditions are critical during early soybean growth stages. Currently, central and northern Minnesota are experiencing below-average temperatures, and this trend is expected to continue through May 23, according to the National Oceanic and Atmospheric Administration temperature outlook. These conditions may increase the risk of seedling diseases caused by soil-borne pathogens.

Most soil-borne pathogens are already present in our soils. They wait for favorable conditions to infect seedlings and cause disease symptoms. Excessive soil moisture, cool soil temperatures, soil compaction and large temperature fluctuations can all increase the risk of root rot during emergence. Understanding field conditions and identifying symptoms early can help determine the cause of stand loss problems.

Conditions that favor soil-borne pathogens

Excessive soil moisture is one of the main factors increasing the risk of root rot in soybean seedlings. Saturated soils reduce oxygen availability in the root zone, stressing plants, slowing growth and weakening root defenses. Cool soil temperatures also slow germination and emergence, leaving seedlings exposed to infection for longer. Many pathogens infect soybean seedlings before emergence, especially when soil temperatures remain below 50–55°F. Soil compaction can further increase disease risk by restricting root growth, reducing water infiltration and keeping soils wetter and cooler for longer periods after rainfall.

Main pathogens associated with early root rot in Minnesota

The main seedling diseases of soybeans are caused by soil-borne pathogens, which spread primarily through soil and water. Across the Midwest, the most common causes of seed and seedling diseases are fungi and fungal-like organisms, including Fusarium spp., Rhizoctonia solani, Phytophthora sojae and Pythium spp. Other soil- or seed-borne pathogens, including Macrophomina, Colletotrichum and Phomopsis may also cause problems in some fields.

Phytophthora root and stem rot (Phytophthora sojae)

Phytophthora sojae is a fungal-like pathogen that can survive in soil for up to 10 years in association with soybean residue. Saturated and warm soils favor infection. Common symptoms include seed rot, brown stem and root rot, poor emergence and seedling death.

 

 

 

 

 

 

 

 

Pythium damping-off (Pythium spp.)

Pythium is also a fungal-like, soil-borne pathogen. Several species can infect soybean seedlings. Cool and wet soils favor infection, although some species may also infect plants under warmer conditions. Symptoms include seed decay, pre- and post-emergence damping-off and soft, water-soaked lesions.

 

 

 

 

 

 

 

 

 

 

Rhizoctonia root rot (Rhizoctonia solani)

Rhizoctonia solani is a common pathogen with a wide host range. Different strains may respond differently to soil conditions, making field diagnosis difficult. The most common symptoms are associated with hypocotyl lesions, reddish-brown cankers and damping-off.

 

 

 

 

 

 

 

 

 

Fusarium root rot (Fusarium spp.)

Fusarium seed and seedling blight are caused by a complex of different species. Some species are favored by warm, dry soils, while others may infect seedlings under cool, wet conditions. Common symptoms include root discoloration, seedling blight and stunted growth.

 

 

 

 

 

 

 

 

Disease management

Once symptoms appear, soil-borne pathogens are difficult to manage. However, several practices can help reduce the risk of early seedling diseases. Planting in soil warmer than 50°F can improve emergence and reduce the risk of infection. Using good-quality seeds adapted to local field conditions is also important. Managing soil compaction and poorly drained areas can help reduce saturated soil conditions favorable for disease development.

For managing Phytophthora Root and Stem Rot, selecting resistant varieties remains one of the best tools available. Dr. Megan McCaghey, University of Minnesota, is currently developing county-level maps to help farmers identify resistant genotypes adapted to their conditions.

After planting, scouting should focus on compacted areas, wet spots and lower field areas where disease pressure is usually greater. Evaluating emergence and early establishment in these areas can help determine whether soil-borne pathogens are affecting the crop.

If conditions improve after planting and the soil warms and dries, replanting may still be a viable option in some situations. According to Dr. Dean Malvick, University of Minnesota, seed treatments can help reduce damage caused by soil-borne pathogens. Products containing mefenoxam or metalaxyl may be effective against Pythium and Phytophthora. Products containing fludioxonil or strobilurin fungicides such as azoxystrobin, trifloxystrobin or pyraclostrobin may help reduce damage caused by Fusarium and Rhizoctonia.

Early scouting and accurate diagnosis are essential for determining the cause of stand loss problems and selecting the best management strategy. If you observe emergence issues this season, reach out to your agronomist, county educator, Extension specialist or the Minnesota Soybean team for support.