Rhizoctonia root rot and stem canker management in tomato production

Rhizoctonia root rot and stem canker caused by the soilborne fungus Rhizoctonia solani can be a significant challenge in Wisconsin tomato production, especially under cool soils, excessive moisture, compacted soils, or where tomatoes follow susceptible vegetable crops. Disease symptoms often begin shortly after transplanting and include stem constriction at the soil line, poor root development, uneven vigor, lower stem lesions, and eventual plant decline. Management is most successful when an integrated approach is used that combines cultural practices with biological or fungicidal protection.

Key integrated management recommendations for both conventional and organic systems

• Use vigorous, disease-free transplants with well-developed root systems.
• Avoid transplanting into cold, saturated soils (plant into >60°F when possible).
• Promote rapid root establishment through raised beds and good drainage.
• Avoid excessive soil compaction and overwatering immediately after transplanting.
• Rotate away from susceptible hosts for 2–3 years when feasible. Hosts include many vegetables such as potato, bean, pepper, lettuce, cucurbits, and brassicas.
• Minimize fresh undecomposed organic matter immediately before planting, which may favor pathogen activity.
• Use plasticulture or mulches to warm soils and reduce moisture fluctuation.
• Maintain balanced fertility; excessive ammonium nitrogen can favor disease development.

Organic Certified Rhizoctonia Management Program

• Biological transplant drench at planting. The most consistent organic suppression of Rhizoctonia in vegetables typically comes from biological antagonists applied directly to the transplant root zone. Active organisms include: Trichoderma harzianum, Trichoderma virens, Bacillus subtilis, Bacillus amyloliquefaciens, Streptomyces lydicus. Common OMRI-listed examples may include chitosan formulations, RootShield PLUS+, Double Nickel, Actinovate, Regalia, and Serenade Soil. Other inputs that may be useful on the foliage to reduce disease include hydrogen peroxide and peroxyacetic acid formulations. Applications are most effective when they are applied directly in the transplant water, placed into the root zone, and followed by warm conditions favoring rapid root growth.
• Soil health and organic matter management. Organic systems benefit greatly from microbial competition and improved soil structure. Recommended practices include: i) incorporate well-composted organic matter well ahead of transplanting, ii) utilize cover crops that improve soil aggregation and microbial diversity, iii) avoid excessive fresh poultry manure or unstable composts immediately before planting.
• Anaerobic soil disinfestation (ASD) or soil solarization. For high-value organic tomato systems with chronic disease pressure, ASD using carbon sources and tarp sealing can reduce Rhizoctonia pathogen inoculum (and other pathogens in the soil). Soil solarization may provide partial suppression during warm Wisconsin summers. A nice summary of ASD based on their extensive work at Ohio State University can be found here from Drs. Anna Testen and Sally Miller: https://ohioline.osu.edu/factsheet/hyg-3315
• Essential oil or natural product additions. Some growers have observed suppression using thyme or clove oils, mustard-derived biofumigant products, or compost extracts. These materials are generally supplemental and less reliable than biological root-zone protection.

Conventional Rhizoctonia Management Program

• In-Furrow or transplant water fungicide protection. The most reliable conventional suppression comes from targeted fungicides at transplanting. The effectiveness of fungicides after transplanting is variable. The fungus infects at and below the soil line. As such, if you can direct application to the lower stem region, you can reduce disease. Once infected, only fungicides with some systemic activity will be effective. The modification of environmental conditions to improve drainage, reduce cool/wet soil persistence, is best in addressing this disease.
• SDHI fungicides (Most effective group, FRAC 7) are among the strongest tools against Rhizoctonia. Examples include Fontelis (penthiopyrad), Aprovia Top (benzovindiflupyr FRAC 7 + difenoconazole FRAC 3), and Priaxor Xemium (pyraclostrobin FRAC 11 + fluxapyroxd FRAC 7). These materials can suppress root rot, stem canker, and improve transplant success. Applications should target the transplant root zone through i) transplant water, ii) directed spray, iii) or in-furrow placement.
• Strobilurin fungicides (Provide suppression, FRAC 11) are good tools against Rhizoctonia and other diseases. Examples include azoxystrobin (example Quadris), trifloxystrobin (example Trilex), pyraclostrobin (example Cabrio EG), and Veltyma (pyraclostrobin FRAC 11 + mefentrifluconazole FRAC 3). Strobilurin fungicides have shown activity against Rhizoctonia in many vegetable crops when applied in-furrow or banded at planting. Contact fungicides including chlorothalonil (example Bravo) are registered for Rhizoctonia in tomato and can protect above ground plant parts.

Biological and reduced-risk integration

Many Wisconsin growers can improve consistency by combining conventional fungicides, biological transplant drenches, and soil health management. This integrated strategy can reduce fungicide dependence, improve root vigor, and moderate environmental stress impacts.

Wisconsin-Specific Disease Risk Conditions

Rhizoctonia risk is highest in Wisconsin when transplants are set in cool spring soils, planting in soil that had previously been cropped to potatoes or snap beans, soils remain saturated after rainfall, or rapid temperature or moisture fluctuations occur which slow root establishment. Years with prolonged cool and wet May conditions often show the greatest transplant losses. Because Rhizoctonia is strongly influenced by environmental stress, the best outcomes generally occur when fungicides or biologicals are paired with practices that accelerate rapid transplant rooting and minimize early-season stress.

Example of an organic program:

1. Raised beds + plastic mulch
2. Well-composted organic matter incorporated weeks before planting
3. RootShield PLUS+ transplant drench
4. Avoid overwatering first 10–14 days
5. Rotate with small grains or grasses when possible

Example of a conventional program:

1. Raised beds + plastic mulch
2. Transplant water application of Velum or Quadris
3. Supplemental biological product in transplant water
4. Balanced fertility and irrigation management
5. Crop rotation and residue decomposition management