The much-needed rain in Oklahoma finally arrived, bringing both opportunities and challenges for growers across the state. Recent rainfall events across most of the state have led to saturated soil conditions, creating highly favorable environments for seedling diseases in field crops. As planting progresses and early-season stands establish, growers are increasingly observing issues such as poor emergence, damping-off, root rot, and uneven stands in crops including corn, soybean, cotton, and sorghum.

Seedling diseases are caused by a complex of soilborne organisms, including fungi and fungus-like pathogens, often involving species such as Pythium, Phytophthora, Rhizoctonia, and Fusarium. These organisms thrive in cool, wet soils and can infect seeds and young seedlings before or shortly after emergence, leading to reduced plant vigor and, in severe cases, significant stand loss and yield reduction.

Accurately identifying the causal agents of soybean seedling diseases can be challenging, as multiple pathogens may infect plants simultaneously and produce similar symptoms. In addition, rapid decomposition of infected tissue can make pathogen recovery and identification difficult, often requiring laboratory confirmation. The most commonly associated soybean seedling diseases include Fusarium root rot (Fusarium spp.), Rhizoctonia seedling blight (Rhizoctonia solani), Phytophthora root rot (Phytophthora spp.), and Pythium seedling blight (Pythium spp.).

In addition, seedling disease symptoms can also be confused with abiotic stresses such as soil crusting, herbicide injury, or nutrient deficiencies. Therefore, field scouting combined with accurate disease diagnosis is essential to determine the most appropriate management practices.

This newsletter provides an overview of the most important seedling diseases in soybean in Oklahoma. However, similar symptoms can also be observed in other field crops. With continued variability in spring rainfall patterns, proactive scouting and early intervention remain critical tools for protecting stand establishment and ensuring optimal crop performance this season.

Fusarium root rot: this disease can be caused by several species of the fungus Fusarium. This disease can result in both pre- and post-emergence damping off, also leading to delayed emergence and stunting of infected plants. The root system of the infected seedlings is smaller with fewer secondary roots, along with light to dark brown discoloration on the roots, sometimes extending through the vascular tissue to the hypocotyl (Figures 1 and 5). Infection can occur in a wide range of soils and environmental conditions, and it’s often associated with stressful growing conditions. Biotic and biotic factors such as herbicide injury, high soil pH, iron chlorosis, nematode feeding, and nutritional disorders can all predispose plants to infection. In severe cases, seedlings may die before emerging. The causal agent of this disease survives in the soil or in the previous crop residue. Certain weeds can also host some of the Fusarium spp. as well. It's important to emphasize that soybean plants can be infected by Fusarium spp. at any point during the growing season, but stressed plants are more prone to infection.

Rhizoctonia seedling blight: this disease is caused by the fungus Rhizoctonia solani, that can cause both pre- post-emergence damping-off. The common symptoms associated with this disease include the red-brown, dry sunken lesions on the seedling hypocotyl (Figures 2 and 5). Symptoms of this disease often appear in patches in the field or affect entire sections of row within a field. Infection occurs over a wide range of soil conditions and typically does not occur after the seedling stage (V4). The pathogen prefers soils with light and sandy texture, with disease prevalence increasing in warm and moist environmental conditions. However, saturated soil does not favor disease development. The pathogen, Rhizoctonia solani, also has a broad host range and survives in plant residue as mycelium and in soil.

Phytophthora root rot: this disease is primarily caused by Phytophthora sojae, a water-loving, fungal-like organism belonging to the oomycete group. Symptoms of this disease include mushy and water-soaked stems and stunted or wilted seedlings (Figures 3 and 5). Infection is favored by wet conditions after planting, but is more common in warmer and saturated soils, typically after heavy rainfall events where there is water standing. Symptoms are most commonly observed in patches, particularly in low-lying areas of the field. Infection occurs via the roots, and from there the pathogen colonizes the roots and stems. Phytophthora sojae can infect soybeans at any point in the growing season, from seed to maturity. The pathogen can survive on crop residue or in the soil as structures known as oospores.

Pythium seedling blight: this disease is caused by several Pythium species, another group of oomycetes. Because of that, symptoms of Pythium seedling blight are similar to Phytophthora root rot. Symptoms of this disease include rotten, mushy seeds with poorly developed roots. Above ground symptoms may appear as water-soaked lesions on the hypocotyl or cotyledons and are most commonly observed in patches in low-lying areas of the field (Figures 4 and 5). This disease is more severe in poorly drained soils. Pythium can also infect across a wide range of soil temperatures typically preferring cool and wet conditions; however, some species are more prevalent in warm and wet conditions.

Management of Soybean Seedling Diseases

The organisms that cause soybean seedling diseases can survive in soil for many years, and in the majority, are able to infect other crops as well, such as alfalfa, corn, sugar beet, and wheat, as some species of weeds. Therefore, crop rotation may not always be effective in managing these diseases due to the wide host range of Fusarium and Rhizoctonia species and the longevity of Phytophthora and Pythium species. Planting soybeans in optimal environmental conditions that favor quick stand establishment of the seedling will reduce plant stress and mitigate disease risk. Improving soil drainage may also reduce stress and risk of pathogen infection. Optimal seeding rates and planting depths may also increase the rate of stand establishment to reduce the susceptibility of seedlings to various diseases.

Will Seed Treatments Protect the Seeds?

Yes. Seed treatments can help protect germinating seeds and young seedlings from pathogen infection during early growth stages. However, their effectiveness may vary depending on the specific pathogens present, environmental conditions, and the active ingredients used in the treatment. For example, Pythium spp. and Fusarium spp. require the use of seed treatment products with different modes of action for disease prevention. Seed treatment options to manage soybean seedling diseases can be found in the following link to publications found on the Crop Protection Network website: Fungicide Efficacy for Control of Soybean Seedling Diseases.

Conditions With Similar Symptoms

It is also important to consider that recent excessive rainfall across Oklahoma has resulted in prolonged saturated soil conditions. These wet soils can delay crop emergence, increase the risk of soil compaction; thereby restricting root development; and contribute to reduced plant-to-plant uniformity in early growth stages. As a result, it is essential to scout fields to determine whether poor stand establishment and slow crop development are associated with soilborne pathogens or are primarily due to abiotic stress factors. Other disorders that can cause similar symptoms as soybean seedling blights are “Fluopyram effect” and herbicide injury. For more information on those disorder visit Crop Connection Network - An Overview of Soybean Seedling Diseases.

Scouting for Seedling Disease in Field Crops

Fields should be scouted for seedling diseases and stand establishment should be evaluated shortly after emergence and again a couple of weeks later. Where gaps occur in the row, seeds should be carefully dug up to check for evidence of seed rot. Seedlings that have emerged but are collapsing due to damping-off may still be visible on or near the soil surface.

When conducting stand counts, it is important to record the growth stage of plants being assessed. If plants appear developmentally delayed, they should be carefully excavated and their root systems examined. Infected roots are typically brown, water-soaked, and decayed. In corn, the mesocotyl should also be inspected for signs of rot.

Differentiating between seedling diseases caused by Pythium and Fusarium species in field conditions is often difficult due to overlapping symptoms. For confirmation, symptomatic samples can be submitted to the Plant Disease and Insect Diagnostic Laboratory (PDIDL) at Oklahoma State University or by contacting Dr. Maira Duffeck (347) 205-2180.

Figure 1. Fusarium-infected soybean seedlings (Image credit: Loren Giesler).

Figure 2. Sunken, dry lesions near the soil line characteristic of Rhizoctonia seedling blight and root rot (Image credit: D. Mueller, A. Robertson, C. Bradley, T. Mueller, and M. Chilvers).

Figure 3. Early season symptoms of Phytophthora sojae infection include damping off (Image credit: C. Grau, C. Bradley, K. Black, and D. Mueller).

Figure 4. Pythium seedling blight may kill seedlings prematurely (Image credit: Crop Protection Network)


Figure 5. General symptoms of soybean seedling disease caused by different fungal pathogens. Symptoms may not always be typical, and diagnosis should be confirmed to select appropriate control (Image credit: Ashley Joyce).

References:

Alison Robertson. Scouting tips for seedling disease.