An Overview of Fusarium Root Rot

Introduction

Fusarium root rot can cause significant soybean yield losses in the United States and Canada. This disease is estimated to have caused a total yield loss of nearly 172 million bushels in the United States and Ontario, Canada, from 1996 to 2024. At least 10 Fusarium species are associated with this disease, including commonly known pathogens such as F. graminearum, F. oxysporum, and F. solani, among others. However, F. virguliforme, the causal fungus of sudden death syndrome (SDS), is not considered part of the Fusarium root rot complex. Because Fusarium root rot symptoms can be easily confused with other diseases, this article aims to improve understanding, diagnosis, and management of this disease.

Symptoms

Fusarium root rot can cause symptoms at any soybean growth stage. Early symptoms include post-emergence damping-off (up to the first trifoliate stage), root decay, browning of internal root tissues, and reddish-brown to black discoloration on the taproot and hypocotyl. In mature plants, infected roots often appear dark brown to black, may rot, and surface cracks may develop on the tap root. In severe cases, the growing tip of the taproot may die, resulting in stunting, taproot dieback, reduced nodule formation, and poorly developed secondary roots (Fig. 1). Aboveground symptoms begin as patchy chlorosis of the leaves and can progress to complete leaf yellowing and stunting, wilting, and premature defoliation of infected plants. Symptom severity depends on the extent of root damage. Fusarium root rot symptoms are often mistaken for those caused by other diseases (See Diseases with Similar Symptoms).

Disease Cycle

Fusarium fungi can survive in the soil for extended periods - up to 30 years in the case of F. oxysporum f. sp. cubense - by forming resting spores called chlamydospores. These spores remain dormant until environmental conditions become favorable for infection. In addition to soil, these fungi can also survive on crop residue, weeds, and seeds, which serve as a source of inoculum for the next growing season. Spores can spread through soil movement, water, and contaminated equipment or tools.

Soybean roots release natural compounds that stimulate germination of Fusarium spores. The fungus then enters the plant through small openings or damaged areas in the roots. Once inside, the fungus grows between root cells and can block the plant’s water channels (xylem), causing browning of the roots and wilting of the plant. Initial symptoms of infection include dark brown spots on roots and discoloration in the lower stem when split longitudinally. In severe cases, the fungus can cause extensive root damage, disrupt water uptake, and possibly release substances that contribute to wilting, yellowing of leaves, premature defoliation, and plant death.

Conditions Favoring Disease

Infection of soybean roots typically occurs early in the growing season when soil temperatures are 50 to 68°F (10 to 20°C) and conditions are moist to wet (20 to 100% water holding capacity). As the season progresses, hot and dry weather can reduce soil moisture, which may exacerbate symptoms in stressed plants.

The presence of soybean cyst nematode (SCN) and root-knot nematode (RKN) can significantly affect the development of Fusarium root rot. High SCN and RKN population densities enhance Fusarium infection and disease development, although the mechanisms behind their interaction are not well understood.

In addition to biological factors, several soil characteristics can influence the prevalence and severity of Fusarium root rot. Soil compaction limits the availability of water and oxygen necessary for healthy root growth, thereby increasing susceptibility to Fusarium fungi. Soil pH and texture also play a role. For example, Fusarium root rot caused by F. graminearum is the most severe in soils with a pH of 6 and a sandy loam texture.

Disease Diagnosis

Diagnosing Fusarium root rot in soybeans can be challenging, as symptoms are very similar to those caused by other seedling diseases, abiotic stresses, and nematode infection. Co-infection of roots by multiple pathogens is also common, further complicating field diagnosis. In many cases, laboratory diagnosis is required to distinguish Fusarium root rot from other causes of root and foliar symptoms.

Diseases, Disorders, and Other Issues Similar to Fusarium Root Rot

Flooding

Prolonged flooding can stress soybean plants by suffocating their roots and nodules, leading to yellowing, wilting, and ultimately, plant death (Figs. 2 and 3).

How to distinguish Fusarium root rot from flooding: Flooding injury often causes sloughing of the outer root cortex, exposing the white inner part of the root (a “rat-tail”-like appearance). In contrast, Fusarium root rot causes brown to black root discoloration and root decay.

Fusarium wilt

Fusarium wilt causes discoloration of the internal vascular tissue, wilting, and chlorosis in leaves  (Fig. 4).

How to distinguish Fusarium root rot from Fusarium wilt: Plants affected by Fusarium wilt have a brown discoloration in the vascular tissue (xylem and phloem) but usually have a healthy root system. In contrast, Fusarium root rot causes reddish-brown to black lesions and decay on the roots.

Iron deficiency chlorosis (IDC)

IDC symptoms typically appear as chlorosis in young trifoliate leaves and are often found in irregular patches (Figs. 5 and 6).

How to distinguish Fusarium root rot from IDC: IDC causes leaf chlorosis primarily in the upper canopy without root discoloration. Fusarium root rot may cause leaf chlorosis in the middle and lower canopy, and sometimes leaves in the upper canopy may appear scorched. Fusarium root rot is always accompanied by root decay.

Plant parasitic nematodes

Soybean cyst nematode (SCN)

SCN infection can cause yellowing and stunting with subtle or patchy symptoms (Fig. 7).

How to distinguish SCN infection from Fusarium root rot: The presence of SCN females and cysts on the surface of soybean roots is a key diagnostic indicator, whereas Fusarium root rot is characterized by the absence of visible nematode structures (Fig. 8). A positive SCN soil test from the affected area can also help determine if SCN is the main problem.

Root-knot nematodes (RKN)

RKN causes patchy stunting, chlorosis, wilting and plant death. Infected roots develop galls (Fig. 9).

How to distinguish RKN infection from Fusarium root rot: The presence of galls or knots on soybean roots is a key diagnostic indicator of RKN. Visible galls or knots are absent with Fusarium root rot. Diagnostic assessments can also be used to determine RKN presence.

Other root rot diseases

There are several root rot diseases, such as Pythium root rot (Fig. 10), Phytophthora root rot (Fig. 11), Rhizoctonia root rot (Fig. 12), and a root disease caused by Clonostachys rosea, that result in rotted roots, damping-off, wilting, and root discoloration. Rhizoctonia root rot symptoms can include reddish-brown lesions on affected plants. Plants infected by Clonostachys rosea have small pink to orange fungal structures on decaying roots (Fig. 13).

How to distinguish Fusarium root rot from other root rots: Identifying root rot pathogens in the field can be challenging. Additionally, multiple root rot pathogens may be present in a field simultaneously. Therefore, it is recommended to submit plant samples to disease diagnostic laboratories to confirm the cause of the symptoms and ensure accurate identification of the causal pathogens.

Red crown rot

Red crown rot manifests as reddish lesions on the lower stem, and patchy chlorosis and necrosis on upper leaves.

How to distinguish Fusarium root rot from red crown rot:Red crown rot causes a reddish discoloration on the lower stem and produces round, red structures (perithecia) on the crown and roots (Fig. 14), unlike Fusarium root rot, which does not produce perithecia.

Sudden death syndrome (SDS)

SDS symptoms appear as patchy chlorosis and necrosis between the veins of leaflets during the mid- to late reproductive stages. The veins of symptomatic leaves generally remain green.

How to distinguish Fusarium root rot from SDS: SDS causes discoloration in the cortex of the lower stem, but the pith remains white (Fig. 15). In contrast, Fusarium root rot can cause reddish-brown to black discoloration of the lower cortex and stem.

Disease Management

Host resistance

No commercial soybean varieties are known to have complete resistance to Fusarium species. However, some partial resistance has been observed against specific Fusarium species in certain varieties, though this resistance is not well characterized or widely used in current commercial varieties.

Cultural practices

Cultural management practices are often not effective at reducing Fusarium root rot because of the persistence of some Fusarium species in soil and their broad host range. Intercropping could be an option; for example, corn/soybean relay strip intercropping has been reported to significantly reduce Fusarium root rot caused by F. proliferatum compared to continuous soybean.

Planting into well-drained soils will reduce conditions favorable for Fusarium infection and help avoid soil compaction. Where feasible, improving drainage and minimizing plant stress from other sources - such as SCN and herbicide injury - can help reduce Fusarium root rot severity. Selecting soybean varieties tolerant to IDC may also be beneficial in fields prone to Fusarium root rot.

Chemical control

Fungicide seed treatments are available and labeled for the management of Fusarium root rot. Active ingredients with activity against Fusarium include azoxystrobin, fludioxonil, fluxapyroxad, ipconazole, mefentrifluconazole, prothioconazole, pyraclostrobin, and trifloxystrobin (Table 1). Effectiveness of these fungicides varies among species. There are no foliar fungicides currently effective for managing Fusarium root rot.

Table 1. List of active ingredients for managing the species of Fusarium responsible for Fusarium root rot as of February 2025. Efficacy ratings for active ingredients are available in Fungicide Efficacy for Control of Soybean Seedling Diseases.

NOTE: In some cases, the mentioned trade name may include multiple active ingredients in addition to the listed active ingredient specific towards managing Fusarium.

References

Bradley, C. A. 2008. Effect of fungicide seed treatments on stand establishment, seedling disease, and yield of soybean in North Dakota. Plant Dis. 92(1):120-125. Article | Google Scholar

Colombo, D. N., Rafi, N., Manoj, A., Fakhoury, A. M., Garcia-Aroca, T., Infantino, A., Leandro, L., Little, C., Petrovic, K., and Mathew, F. M. 2025. A diagnostic guide for Fusarium root rot of soybean. Plant Health Prog. (First Look). Article | Google Scholar

Dorrance, A. E., Kleinhenz, M. D., McClure, S. A., and Tuttle, N. T. 2003. Temperature, moisture, and seed treatment effects on Rhizoctonia solani root rot of soybean. Plant Dis. 87:533-538. Article | Google Scholar

Hartman, G.L., Rupe, J.C., Sikora, E.J., Domier, L.L., Davis, J.A., and Steffey, K.L. eds., 2015. Compendium of soybean diseases and pests (pp. 56-59). St. Paul, MN: American Phytopathological Society. Article | Google Scholar

Holliday, S., and Lux, L. 2025. Soybean seedling diseases. NC State Extension. Article

Sweets, L. E., Wrather, A., and Wright, S. 2008. Integrated pest management of soybean diseases. University of Missouri Extension. Article

Timmerman, A., Nygren, A., VanDeWalle, B., Giesler, L., Seymour, R., Glewen, K., Shapiro, C., Jhala, A., and Treptow, D. Soybean Management Guide. University of Nebraska-Lincoln. Crop Watch. Article

Webster, R. W., Becton, H., Mathew, F., and Baldwin, S. A. 2025. Phytophthora root and stem rot. NDSU extension. Article

Yan, H., and Nelson, B. 2022.  Effects of soil type, temperature, and moisture on the development of Fusarium root rot of soybean by Fusarium solani (FSSC 11) and Fusarium tricinctum. Plant Dis. 106(11):2974-2983. Article | Google Scholar

Acknowledgments

Authors

Nitha Rafi, North Dakota State University; Karthika Mohan, North Dakota State University; Athul Manoj, North Dakota State University; Febina Mathew, North Dakota State University; Maira Duffeck, Oklahoma State University; LeAnn Lux, North Carolina State University; Dylan Mangel, University of Nebraska-Lincoln; and Richard Wade Webster, North Dakota State University.

Reviewers

Tom Allen, Mississippi State University; Gary Bergstrom, Cornell University; Mandy Bish, University of Missouri; Travis Faske, University of Arkansas; Dean Malvick, University of Minnesota; Daren Mueller, Iowa State University; Alison Robertson, Iowa State University; Edward Sikora, Auburn University; Darcy Telenko, Purdue University; and Kiersten Wise, University of Kentucky.

Sponsors

This work was supported by the United Soybean Board (Project #24-210-S-A-1-A / 2411-210-0101). The authors also thank the United States Department of Agriculture - National Institute of Food and Agriculture for support.