Recently, I was asked by a colleague which disease pathogens I find most often in early emerging soybeans. To start, I am happy to report that as soybeans are planted earlier each year, more growers are using seed treatments. Fungicide seed treatments can offer control early in the season, but keep in mind that not all of fungicides within seed treatments specifically protect or are registered to be used against the oomycete fungi like Pythium and Phytophthora. There is always the chance of resistance to a seed treatment’s specific fungicide, but this has yet to be documented in “our neck of the woods.”

Second, my biggest pet peeve is that most think the biggest threat to early emerging soybeans is Phytophthora spp. In reality, we need to be watching out for Pythium infection. Recent survey work done by Midwest plant pathologists revealed that Pythium species are the more prevalent root rot pathogens infecting emerging soybeans. Historically, Pythium species were known to be more likely to infect early because they favor cooler temperatures (50 to 60⁰ F). However, this recent research also showed that some Pythium species may infect at warmer temperatures.

Finally, some soybean varieties may vary in their tolerance to Pythium, but to date there are no primary sources of genetic resistance that are in soybean varieties to protect against this disease. Therefore, our only defense against Pythium is seed treatments!

Don’t count Phytophthora out! This fungus is still with us and can infect soybeans at all growth stages. Some soybean varieties have sources of soybean resistance (genes) or tolerance available for control of Phytophthora. R-gene (single gene) resistance is the most common, because it is the easiest to breed and select for, but not all Phytophthora races will be controlled by R-gene resistance. Last year, with the heavy rains, I did witness a case where a Phytophthora species did overcome R-gene resistance within a soybean variety, but generally this is a rare occurrence.


Both Pythium and Phytophthora root rot pathogens can cause roots or hypocotyls to appear brown and rotted. In my opinion it is very difficult to make the distinction between Pythium and Phytophthora root rot within the field during early growth stages, and I am pretty at good at recognizing these diseases because of my training.

If I suspect root rot I use a microscope to examine oospores (spores) within roots (Pythium), a stereoscope to examine lemon-shaped sporangia growing on roots or hypocotyls (Phytophthora), or use a form of Enzyme-Linked Immunosorbent Assay (ELISA), a quick strip test used to detect antibodies or infectious agents in a sample (Phytophthora). But not all agronomists have the tools or skills to determine the species. Then it is best to send it to the University of Illinois Plant Clinic for diagnosis.

Both Pythium and Phytophthora spp. are more likely to infect plants that lack vigor or that are planted in a poor location in marginal conditions. Since both of these pathogens require moisture for infection, it makes sense that flooding and lower-lying areas of the field as well as clay soils that have a higher water holding capacity may be more at risk for Pythium and Phytophthora infection.
Control comes with good crop management. In addition to planting soybean varieties with high Phytophthora scores and using seed treatments, improving or adding tile drainage could offer some aid in some situations.

Stephanie Porter is a Sales Agronomist with Burrus® Hybrids with responsibilities that include educating growers and Burrus staff on all types of pests, weeds, diseases and other agronomic issues that affect corn, soybean and alfalfa production. Her territory encompasses Southern Wisconsin as well as Northern, Eastern and Southern Illinois. 

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About the Author: Stephanie Porter

As Outreach Agronomist for the Illinois Soybean Association (ISA), Stephanie supports research efforts and helps communicate both in-field and edge-of-field research and validation studies to Illinois 43,000 soybean farmers. She also helps lead the demonstration and adoption of conservation agriculture practices and raises awareness of best management and continuous improvement practices for conservation agriculture in Illinois. Stephanie has 23 years of experience that consists of agronomy, conservation, horticulture, plant diagnostics, and education. She has her bachelor’s in crop science and master’s in plant pathology from the University of Illinois. Stephanie is a Certified Crop Advisor and was named the 2018 Illinois Certified Crop Adviser Master Soybean Advisor. She also has experience with corn and soybean pathology research, crop scouting, soil testing, as well as crop consulting. Previously, she utilized her diagnostic training and collaborated with University of Illinois departmental Extension Specialists to diagnose plant health problems and prepare written responses describing the diagnosis and management recommendations as the University of Illinois Plant Clinic.