An Overview of Soybean Seedling Diseases

Soybean seedling diseases are often the cause of reduced stand and can cause significant economic losses on an annual basis. Diseased seedlings are often less vigorous and severe stand loss may require replanting of affected areas. Seedling diseases are often more prevalent when wet weather occurs soon after planting. They are also more common in compacted and poorly drained soils or in areas where seedlings have been injured from herbicides.

Diagnosing seedling diseases in the field can be difficult since the symptoms of various seedling blights are similar, and seedlings often decompose quickly (Figure 1). This publication discusses the characteristics of the organisms that cause seedling diseases, describes injury symptoms that may appear similar to these diseases, and briefly addresses how to manage these seedling diseases.

The soybean seedling diseases that are most commonly observed on soybean are:

1. Fusarium root rot

2. Rhizoctonia seedling blight

3. Phytophthora root rot

4. Pythium seedling blight

Fusarium Root Rot (Fusarium spp.)

Many Fusarium species reside in the soil and can infect soybean. Infected plants may be stunted and spindly with brown or black lesions on the roots (Figure 2) and poorly developed root systems.

In severe cases, seedlings may die before emerging. Species of Fusarium can infect plants under a wide variety of environmental conditions. Fusarium root rot is often associated with stressed plants.

Rhizoctonia Seedling Blight (Rhizoctonia solani)

Rhizoctonia seedling blight is caused by the fungus Rhizoctonia solani. The characteristic symptom of Rhizoctonia seedling blight is a reddish-brown lesion on the lower stem or hypocotyl, usually at the soil level (Figure 3). Lesions on the diseased stem appear sunken (canker-like) and dry, and can girdle the hypocotyl.

This disease can occur over a wide range of soil conditions. Affected plants typically appear in patches or in rows in a field. Temperature and moisture requirements for infection and disease progression vary, although this disease tends to be common in warm and moist, but not saturated, soil. Stressed seedlings may be more vulnerable.

Phytophthora Root and Stem Rot (Phytophthora spp.)

Phytophthora root rot of soybean is caused by the oomycetes Phytophthora sojae and P. sansomeana. Infected plants appear alone or in patches (Figure 4).

The stems of Phytophthora-infected seedlings are typically mushy and water-soaked. Overall, infected seedlings will be wilted and stunted. These symptoms resemble those of many other seedling disease pathogens. Phytophthora sojae can also cause a stem rot of mature plants, characterized by chocolate brown stem lesions. Phytophthora root rot occurs across many environments, but is most common in warm (>60°F/15°C) and wet conditions.

Pythium Seedling Blight (Pythium spp.)

Pythium, another group of oomycetes, contains multiple species that can cause soybean seedling blight and seed rot. Species of Pythium cause symptoms similar to Phytophthora species.

Pythium seedling blight symptoms include rotten, mushy seeds or seedlings with poorly developed roots. Water-soaked lesions may be present on the hypocotyl or cotyledons (Figure 5).

Pythium seedling blight can occur across a range of temperatures, but high soil moisture increases the likelihood of disease and disease severity. Consequently, symptoms are most severe in poorly drained soils and areas prone to flooding. Recent research indicates that many Pythium species prevalent in the northern United States and Canada infect plants at a lower temperature range (50-77°F/10-25°C) than Pythium species in the southern United States (85-95°F/30-35°C).

Diagnosing Seedling Blights

Seedling diseases are difficult to correctly diagnose in the field, and are easily mistook for other problems (such as herbicide or environmental damage). In addition, seedlings may be affected by more than one seedling disease in a field at the same time.

For these reasons, we recommend sending injured soybean seedlings to a local diagnostic lab to confirm the cause before implementing a disease management program. Obtaining an accurate diagnosis is the first step in determining a management strategy. In addition, it may also be necessary to identify the species of organism (i.e. Phytophthora sojae vs. Phytophthora sansomeana) to customize management as fungicide efficacy and varietal resistance may vary depending on pathogen species.

Conditions With Similar Symptoms

A few examples of disorders that can cause similar symptoms as soybean seedling blights are listed here.

General Management

The organisms that cause seedling diseases can survive in soil for many years, and most are capable of infecting other crops such as alfalfa, corn, sugar beet, and wheat, as well as weeds. Therefore, crop rotation may not effectively manage these diseases. Short rotations of crops between soybean may also allow seedling disease organisms to build to high levels in the soil.

Seedling diseases may be more prevalent in no-till or reduced tillage systems since these soils typically warm up slower in the spring and retain more moisture. In these systems, additional practices, such as fungicide seed treatment, may be needed to manage seedling blights.

Fungicide seed treatments vary in efficacy, and products that control Pythium and Phytophthora diseases (such as ethaboxam, metalaxyl (-M), mefenoxam, and oxathiapiprolin), do not control Rhizoctonia and Fusarium species. Similarly, fungicides that are active against Rhizoctonia and Fusarium have little effect on oomycetes.

Additionally, fungicides may be more or less effective depending on the strain of fungus or oomycete, and
in some cases, a strain may have reduced sensitivity to fungicides. Therefore, it is important to accurately diagnose the seedling blights present in a particular field, if possible, down to the species level, and choose fungicide seed treatments accordingly.

Fungicide seed treatment efficacy guides are updated annually and available through the NCERA-137 soybean disease working group. For a current list, see Fungicide Efficacy for Control of Soybean Seedling Diseases (CPN-1020).

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Acknowledgments

Authors

Kiersten Wise, University of Kentucky; Carl Bradley, University of Kentucky; Loren Giesler, University of Nebraska; Bill Johnson, Purdue University; Travis Legleiter, University of Kentucky; Mark Licht, Iowa State University; Daren Mueller, Iowa State University; Martin Chilvers, Michigan State University; Anna Freije, Purdue University; Adam Sisson, Iowa State University; Albert Tenuta, Ontario Ministry of Agriculture, Food and Rural Affairs; and Heather Young-Kelly, University of Tennessee.

Reviewers

Tom Allen, Mississippi State University; Gary Bergstrom, Cornell University; Kaitlyn Bissonnette, University of Missouri; 
Emmanuel Byamukama, South Dakota State University; Ahmad Fakhoury, Southern Illinois University; Loren Giesler, University of Nebraska-Lincoln; Nathan Kleczewski, University of Illinois; Alyssa Koehler, University of Delaware; Chris Little, Kansas State University; Dean Malvick, University of Minnesota; Sam Markell, North Dakota State University; Berlin Nelson, North Dakota State University; Trey Price, Louisiana State University; Alison Robertson, Iowa State University; John Rupe, University of Arkansas; Damon Smith, University of Wisconsin-Madison; Darcy Telenko, Purdue University; and Lindsay Thiessen, North Carolina State University.

All photos were provided by and are the property of the authors and contributors except the cover photo and Figure 1 by Greg Shaner, Purdue University; Figure 3 by Tristan Mueller; Figure 4 by Craig Grau, University of Wisconsin-Madison; and Figure 8 by Bryan Young, Purdue University.

Sponsors

The authors gratefully acknowledge funding for this project from the United Soybean Board; the North Central Soybean Research Program; the North Central Integrated Pest Management Center, the United States Department of Agriculture - National Institute of Food and Agriculture, and the Grain Farmers of Ontario for their support. 

This publication was developed by the Crop Protection Network. The Crop Protection Network is a multi-state and international collaboration of university/provincial extension specialists and public/private professionals that provides unbiased, research-based information to farmers and agricultural personnel. 

This information in this publication is only a guide, and the authors assume no liability for practices implemented based on this information. Reference to products in this publication is not intended to be an endorsement to the exclusion of others that may be similar. Individuals using such products assume responsibility for their use in accordance with current directions of the manufacturer. May 2020