Managing Diseases of Tomato in the Midwest Using Organic Methods

eOrganic authors:

Daniel S. Egel, Purdue University

Amit Kumar Jaiswal, Purdue University

Sahar Abdelrazek, Purdue University

Lori Hoagland, Purdue University


To many organic tomato growers, diseases are the great unknown factor in production. Diseases seem to be able to strike at will, leaving the grower with few options. This article examines disease management, from cultural techniques to approved organic pesticides. Along the way, growers will gain an understanding of seed quality and the importance of soil health in organic production. For the most part, diseases common in the Midwest are used as examples. However, the principles of disease management apply to tomatoes grown anywhere.

Disease Prevention

While reacting to a disease observed in a field is sometimes necessary, using cultural techniques to prevent or minimize disease before it occurs is preferable. This section discusses cultural methods to prevent diseases of tomato.

Disease Resistance

One of the most important decisions a grower can make to prevent disease is what variety to grow. Most of us choose a tomato variety based on taste and texture—or more importantly, what consumers regard as important. However, another important factor is the disease resistance of the host.

Most information sources on tomato disease resistance list varieties as resistant and partially resistant, or highly resistant and intermediate resistant. Such language lets growers know that varieties may exhibit very few symptoms or none (highly resistant); or may have symptoms, but likely fewer (intermediate resistant) than a fully-susceptible variety.

For example, many hybrid tomatoes are highly resistant to one or more races of Fusarium wilt. Such varieties are unlikely to exhibit any symptoms unless an unusual race is encountered. On the other hand, varieties described as having intermediate resistance to early blight will likely show symptoms of this disease. However, an intermediate level of resistance is often sufficient to lower disease pressure, lessening the potential for loss of yield or quality.

The three most important diseases for which host resistance is desirable are Verticillium wilt, Fusarium wilt, and root-knot nematode. Resistance to all three is often called “VFN.” Most modern hybrids have Fusarium wilt resistance to one or more of races 1, 2 and/or 3. All three of these diseases are soilborne and can cause plant death or complete yield loss. Plants weakened by one or more of them also might be more susceptible to other diseases such as early blight.

Many growers and consumers prefer the taste and diversity of heirloom varieties to modern hybrids, believing that varieties lost flavor when breeding efforts began to concentrate on yield, shelf life and other factors. However, many heirloom varieties are susceptible to diseases, including those mentioned in the previous paragraph. Therefore, in growing heirloom or other varieties known to be susceptible to diseases, cultural factors to prevent diseases are even more important.

The best information about tomato disease resistance comes from seed companies, university extension, and your own experience. Reputable seed companies have data on their own varieties. Many universities have collected information about varieties from their own trials. It is a good idea to use information from all available sources when deciding what variety to grow.

Finally, experienced growers may observe differences in the amount of disease or the reaction to disease even across susceptible varieties. For example, there is no known disease resistance to timber rot of tomatoes. However, the open architecture of some varieties might result in lower humidity and thus fewer infections. Or, a variety with a vigorous root system might withstand feeding damage from root-knot nematode better than other susceptible varieties.

Figure 1. The tomato variety on the left is susceptible to leaf mold, while the variety on the right is resistant. Host resistance offers an opportunity to avoid some tomato diseases. Photo credit: Dan Egel, Purdue University.

Fall Tillage and Crop Rotation

Some pathogenic fungi or bacteria require crop residue to survive. As long as small portions of a tomato plant survive in the soil, the fungi or bacteria associated with the crop debris are still viable. Fall tillage—tilling in the crop at the end of the season—hastens decomposition of the crop debris and decreases survival of the pathogen propagules. While fall tillage and crop rotation do not eliminate the pathogen from the soil, they may reduce the severity of the disease in the following crop. Similarly, rotating away from tomato or another solanaceous crop helps reduce the amount of the pathogen that survives in crop residue by extending the interval between crops of tomato.

For example, if you grow a tomato crop with the disease early blight, fall tillage and a crop rotation of three to four years helps destroy much of the crop residue that might harbor the pathogen. On the other hand, if you wait until Spring to till in the crop residue and immediately plant tomato, early blight could be severe in the new crop. Fall tillage and crop rotation are useful management tools for many of the diseases listed in Table 1.

Figure 2. These tomato vines were not tilled into the soil in the fall, which may extend the survival of any pathogens in the plants. Photo credit: Dan Egel, Purdue University

Other fungal or bacterial pathogens can survive in the soil in the absence of crop residue. For example, the pathogen that causes Fusarium wilt can survive in soil without a tomato host for years. While fall tillage and crop rotation are always good management practices, they have minimal effect on some soilborne pathogens. Some pathogenic fungi produce structures that can survive in soil, such as white mold and southern blight. However, these propagules do not survive well if buried several inches under soil. Deep-plowing crop debris helps to bury the survival structures, known as sclerotia, lessening pathogen survival.

Other diseases are caused by pathogens that survive not in soil or crop debris, but insects. In the Midwest, there are fewer insect-borne diseases than in warmer areas such as the southeastern United States. Tomato spotted wilt virus (TSWV) is an example of a such a disease. The pathogen that causes TSWV survives from year to year in weed hosts or, in protected situations, in thrips which are also responsible for transmitting and spreading the disease. Impatiens necrotic spot virus (INSV) is a similar virus with a similar biology and management strategies. Fall tillage and crop rotation do not have much effect on insect-transmitted diseases such as TSWV and INSV. As in the case with other viral disease transmitted by insects, the disease may be managed by controlling the insect. TSWV can be managed by applying insecticides to lower the populations of the thrips. In addition, some varieties have intermediate resistance to TSWV.

Soil Health

Soil is the basis of the entire crop production system and habitat for millions of diverse organisms, each of which participates in ecological services such as breaking down organic matter, nutrient cycling, water retention and/or filtering potential pollutants. However, intensive agricultural practices and monoculture have reduced soil organic matter, reduced microbial diversity and activity, depleted soil nutrients, and increased soil acidification and accumulated salinity—all diminishing soil quality or health. This has contributed to an increase in plant diseases. Restoring and maintaining soil health are crucial for agricultural sustainability and ecological services.

A healthy soil balances physical, chemical, and biological processes that stimulate plant productivity, preserve environmental quality in the soil, and may suppress some soil diseases. A healthy soil has these features (see references for more information):

  • Sufficient organic matter
  • Good soil tilth and structure
  • Sufficient water-holding capacity and infiltration
  • Plant nutrient recycling and availability
  • No toxic chemicals that harm plants
  • Sufficient microbial diversity and beneficial microorganisms
  • Minimal weed, pathogen, and insect pressure

Healthy soils suppress plant disease. Farmers should follow soil management practices that minimize soil disturbances, increase soil organic matter, and diversify soil biota. They should utilize cover crops as much as possible to increase soil health. Common soil management practices documented for restoring/improving soil health and reducing plant disease in various crops, including tomato, are crop rotation, cover crops and green manures, organic amendments (compost, manure, and biochar), soil (bio) solarization, and conservation tillage.

Crop Rotation

In addition to disease management, good crop rotations can help increase soil organic matter and nutrients, soil microbial biomass and activity, and microbial diversity due to rotation of different plant families. Characteristics of a beneficial crop rotation include crops with extensive root systems, legume crops for nitrogen fixation, and/or Brassica and related crops for bio-fumigation. These include sorghum, Sudan grass, rye-vetch, pea, bean, cowpea, lettuce, radish, alliums, canola, rapeseed and mustards.

Cover Crops and Green Manures

Cover crops are grown primarily during the off-season to prevent soil erosion and nutrient losses by covering the soil and capturing nutrients not used by the crop. Cover crops also may be used to improve soil structure, reduce weeds, and improve soil fertility. For example, cover crops with extensive root systems help to break up hard-packed soil to improve structure while legume crops improve soil fertility because they can fix nitrogen.

Green manure crops are crops that are grown for incorporation into the soil while they are young and green to provide nutrients and improve soil structure; however, they serve as cover crops before termination. Cover crops and green manures may reduce water runoff and soil erosion, increase soil organic matter, increase microbial activity and diversity, and suppress plant diseases and weeds.

Cover crops often perform better with a mixture of species than just a single species. Good cover crops for organic farming systems include mixtures of barley, rye, wheat, hairy vetch, and crimson clover because of their relatively fast growth, competitiveness, and ease of mechanical termination. Brassica and related crops can be effective for disease management due to their bio-fumigation potential and enrichment of beneficial microbes. They have been used to suppress plant pathogens such as Verticillium, Rhizoctonia, Pythium, Sclerotinia, Phythophthora, Macrophomina and root-knot nematode (Meloidogyne spp.) in various crops. Their efficacy is variable and dependent upon timing of incorporation into soil. Certain cover crops may be better suited for your area—check your local extension service for recommendations.

Organic Amendments

Organic amendments such as compost, manure, plant residues, and biochar improve soil health and plant productivity and suppress plant pathogens. Compost, plant residues, and manure amendments have been reported to suppress soilborne and foliar diseases such as Pythium damping-off and root rot, Rhizoctonia diseases, Fusarium wilt, gray mold, late blight, and others in tomato.

In addition to potentially suppressing diseases, the use of compost and manure has been shown to improve soil structure and fertility, stimulate beneficial microbes and activity, release antibacterial and anti-fungal compounds during organic matter decomposition, and induce systemic resistance. Compost quality and its effect on plant health generally depends on the raw material used (preferably C:N 25 to 40:1), the composting duration (maturity), the composting process, and the concentration added to soils.

Recently, biochar soil amendments have been reported to improve soil health and plant growth and development. Biochar is a solid high-carbon co-product of biomass pyrolysis (decomposition brought about at high temperature). Biochar has also been shown to suppress foliar and soilborne diseases in various crops, including gray mold, powdery mildew, Fusarium crown and root rot, Fusarium wilt and bacterial wilt in tomato.

Soil Solarization and Bio-solarization

Soil solarization uses the sun's energy to heat the soil sufficiently to kill pathogenic microbes. The process involves covering moist soil with transparent plastic and exposing it to sunlight for 4–6 weeks. Soil temperatures under the plastic must reach a sustained 110-122°F. In the Midwest, solarization could be most useful in a greenhouse or high tunnel. For example, it might be possible to produce a tomato crop in a high tunnel from April to July and then carry out soil solarization in the high tunnel in August.

A similar technique known as bio-solarization, or anaerobic soil disinfestation, involves incorporating an organic amendment that decomposes rapidly under anaerobic conditions, generating compounds that are toxic to several soilborne pathogens. Bio-solarization can be effective against several soilborne plant pathogens that cause damping-off, Verticillium wilt, Fusarium wilt, white mold, and root-knot. Bio-solarization suppresses disease by inactivating pathogens' cellular processes, generating toxic organic acid and volatile compounds, enriching antagonistic microorganisms, and inducing the plant's systemic defense. It is most effective in warm and sunny climates, especially where the hottest part of the year is not the primary growing season.

Conservation Tillage

Conservation tillage is the practice of leaving some crop residue between crop harvest and the next planting to reduce soil erosion and increase soil organic matter. For example, the cover crop could be tilled under in certain rows, leaving an area between the crop rows untilled. This practice can have positive effects on soil health; however, conservation tillage also may risk increasing plant disease caused by the pathogens that can survive in crop residues for extended periods (crop residue-borne pathogens).


Maintaining proper sanitation in a field or greenhouse of tomatoes can reduce the occurrence of disease.

The Transplant Greenhouse

Greenhouses used for tomato transplant production should be cleaned and sanitized between generations of transplants. Seedborne diseases (see Seed and Transplant Quality) can survive on transplant trays in leftover debris, greenhouse benches, and other equipment. It is best to clean equipment, including re-used trays, to remove plant debris and media before sanitizing as the sanitizers cannot readily penetrate organic debris, allowing the pathogen to survive.

To avoid introducing diseases to the field via transplants, inspect transplants during growth for possible disease and remove affected transplants and possibly entire trays. If transplants are purchased elsewhere, inspect them on delivery (see Scouting and Disease Diagnosis). Do not reuse soilless mixes.

Figure 3

Figure 3. Used transplant trays, shown here, are among the tools, work surfaces, and equipment that should be cleaned and sanitized before use to minimize the introduction of pathogens to field or greenhouse tomato production. Photo credit: Dan Egel, Purdue University.

Cull Piles

Growers inevitably harvest fruit that is not marketable. Tomato fruit may be culled for many reasons. It might be rejected because of the presence of disease—even if the disease wasn't recognized. It is therefore best to move culls well away from production. Pruned foliage is best moved well away from production as well. Culls and prunings may be composted (see Making and Using Compost for Organic Farming). After proper composting, such material may be used as organic matter on the farm. However, material that is not properly composted might contain pathogens and should not be used on the farm.


Many of the tools used in a tomato planting may become contaminated with pathogens during use and may facilitate pathogen spread when used on healthy plants.

  • Shovels used in the field may have come into contact with soilborne pathogens such as Pythium and Rhizoctonia. Clean and sanitize such tools before use in another field. It is a good idea to dedicate tools such as shovels to greenhouse use only.
  • Pruners may have been used on a tomato plant with a disease such as bacterial canker. Regularly sanitize pruners between plants.
  • A diseased tomato plant can contaminate adjacent stakes. Sanitize stakes between seasons.
  • Soil clinging to cultivators used in a field contaminated with a pathogen can spread it to a new field. At the very least, wash cultivators after use in fields known to have a history of a soilborne disease.

Methods of Sanitation

Soap and water remove much of the debris that may harbor pathogens. However, washing is not always sufficient. Equipment and tools should also be sanitized. The chemical used to sanitize may include the active ingredients ethanol (70 percent), chlorine bleach (usually at the rate of 1 percent active ingredient), and hydrogen peroxide. Check with your certifier to see what can be used in your operation.

Airflow, Leaf Wetness, and Relative Humidity

Most foliar diseases require leaf wetness, or high relative humidity, for infection to begin. Tomatoes produced in a high tunnel or greenhouse situation will usually face higher humidity and less leaf wetness than plants grown in a field situation. For this reason, tomato diseases in a high tunnel or greenhouse are often different from those that may affect tomatoes in the field. To reduce humidity in a greenhouse or high tunnel, avoid the temptation to overcrowd tomato plants. There is seldom a need to place plants any closer than 4–5 feet between rows and 20–24 inches between plants in a high tunnel. Research in a high tunnel shows that tomatoes spaced any closer tend not to have higher yields, but instead have smaller fruit. Additionally, spacing them closer may lead to higher humidity and longer periods of leaf wetness.

Similarly, tomatoes grown in the field that are spaced too close together are more likely to remain wet from dew or rain. Most recommendations call for tomatoes spaced approximately 5 feet between rows and 18–24 inches between plants. Rows oriented parallel with prevailing wind will tend to facilitate drying.


Overhead irrigation may increase leaf wetness and the severity of foliar disease. Splash of overhead irrigation water may also spread pathogens from leaf to leaf. If overhead irrigation is necessary, time irrigations so the foliage is dry at onset and has a chance to dry before evening.

Seed and Transplant Quality

Tomato seedborne pathogens—including fungi, bacteria, and viruses—can be transmitted in or on tomato seeds. The resulting disease on seedlings, if planted in the field, may spread disease from one plant to another, introducing the pathogen to new production.

Most tomato diseases that can be transmitted on seed result in only a small percentage of infected transplants. However, even a few diseased transplants can provide enough pathogen inoculum to spread disease among tomato plants in an entire field, causing severe yield losses later in the season. Diseased transplants should be discarded. Growers should know which diseases are potentially seedborne, understand how to minimize the risk of such diseases, and how to manage the diseases. Consider the following strategies:

Exclude the Pathogen

  • Purchase seed that has been tested for the seedborne diseases important in your area. Although most vegetable companies cannot guarantee disease-free seed, purchasing seed that has been tested will minimize the risk associated with seedborne diseases.
  • Avoid bringing infected seeds or transplants to your field. Scout purchased transplants for possible disease symptoms on delivery. Regularly scout transplants produced in your own facilities.
  • If disease symptoms are observed in a transplant facility, discard all symptomatic transplants as well as several apparently healthy trays of transplants on either side of the diseased transplant tray. Alternatively, discard all transplants, sanitize the greenhouse, and replant.
  • Select seeds and transplants of disease-resistant cultivars for planting, if available. (See information about host resistance).
  • Clean and sanitize the transplant facility between generations.
  • If you plan to save seed from your field, scout regularly for disease symptoms. Avoid saving seed from infected plants or fruit.

Eradicate the Pathogen

Physical seed treatment, such as treating seeds with hot water or air, can help destroy seedborne pathogens and reduce the incidence of infection. See Organic Seed Treatments and Coatings for more information.

Manage Seedborne Diseases

If you are producing your own seeds:

  • Harvest tomato fruits when they are properly mature.
  • Sufficiently dry the seeds before storage, either in the air or with heated air treatment. Reducing seed moisture content to about 12 percent before storage has been shown to reduce seedborne pathogen inoculum and seed decay.

Most chemical seed protectants aren't an option for organic growers. However, biological seed treatments, such as amending seeds with microflora antagonists to the seedborne pathogen, are available for organic growers and can help reduce disease severity. An example is Mycostop® (active ingredient Streptomyces griseoviridis Strain K61), which is labeled for Pythium and Rhizoctonia diseases. 

Table 1: Prominent diseases of tomato and their causal agent, mode of survival, host resistance, and seedborne nature.


Causal agent


Host Resistanceb




Colletotrichum spp.

Crop debris



Most common on fruit close to the soil where mulch has not been used.

Bacterial speck

Pseudomonas syringae pv. tomato

Crop debris



Cool-weather disease compared to bacterial spot.

Bacterial spot

Xanthomonas spp.

Crop debris



Most strains are resistant to copper fungicides.

Bacterial canker

Clavibacter michiganensis subsp. michiganensis

Crop debris



Systemic within the plant.

Early blight

Alternaria spp.

Crop debris



Commonly starts on older leaves.

Fusarium crown rot

Fusarium oxysporum f.sp. radicis-lycopersici




Sources of resistance not as common as for Fusarium wilt.

Grafting on resistant rootstock may control disease.

Fusarium wilt

Fusarium oxysporum f.sp. lycopersici


Yes; race specific


Three races of the pathogen.

Grafting on resistant rootstock may control disease. 

Gray mold

Botrytis cinerea

Crop debris



More common in greenhouses.

Late blight

Phytophthora infestans

Crop debris



Usually does not overwinter in Midwestern states.

Leaf mold

Passalora fulva

Crop debris



More common in greenhouses and high tunnels

Powdery mildew

Pseudoidium neolycopersici

Crop debris



More common in greenhouses.

Root-knot nematode

Meloidogyne spp.




Host resistance may not be effective for Meloidogyne enterolobi.

Septoria leaf spot

Septoria lycopersici

Crop debris



Disease is common in mild climates.

Southern blight

Sclerotium rolfsii




Disease is more common in warmer climates.


Tobacco mosaic virus, Tomato mosaic virus

Crop debris



Sanitation is critical.


Tomato spotted wilt virus




Transmitted by thrips.

Verticillium wilt

Verticillium spp.




Host resistance is only effective against race 1. Disease is common in cooler climates.

White mold (timber rot)

Sclerotinia sclerotiorum




White rot affects many hosts.

a Crop debris=Pathogen survives as long as crop debris intact. Soil=Pathogen survives in soil in the absence of host for indefinite periods. Insect=Pathogen survives in and is transmitted by insect.
b Host resistance commercially available. Yes=Disease symptoms are not observed. Incomplete=Disease symptoms are present at lowered severity.
c Seed transmission of disease is common method of pathogen movement.

Scouting and Disease Diagnosis

It is difficult to prevent any disease from occurring in a tomato field, regardless of the grower's vigilance. Scouting regularly in the field, greenhouse, or high tunnel will allow the grower to implement management strategies earlier and to prevent further damage. Ideally, scouting once a week is recommended, given how quickly problems can arise. If the field is small, look at every plant. If not, make a zigzag pattern through the field, varying the pattern each time.

To differentiate lesions caused by infectious versus non-infectious disorders, remember that disease lesions enlarge from a single infection point and change in appearance as they progress. Disease lesions often have subtle color differences between the inside and outside of the lesion. They also may have ridges or rings. Infectious diseases often cause a chlorotic area around the lesion due to phytotoxins or other metabolites produced by the pathogen. The pattern in the field can help differentiate. Diseases typically, but not always, tend to have “hot spots” in a field, and will spread from plant to plant over time.

Figure 4 septoria leaf spot

Figure 4. Lesions of Septoria leaf spot on a tomato leaf. Hints that the lesions are caused by an infectious disease include the varied shades of color of the lesions from interior to exterior, the chlorotic halos, and the random distribution of the lesions on the leaf. Photo credit: Dan Egel, Purdue University.

Not all disorders are caused by an infectious agent. Abiotic disorders—those caused by non-living factors such as inadequate moisture, pH, or fertility, spray damage, or wind damage, etc.—will likely appear suddenly (within 1-3 days) and generally do not progress.

Such processes often produce lesions of only one color. Nutrient imbalances may produce chlorotic areas or even necrotic areas between the veins. For example, nitrogen deficiency shows up as lighter green or yellow on older leaves.

It is important to have disorders or diseases diagnosed immediately to effectively implement management strategies and prevent the issue in the future. Knowing what diseases have occurred in a field also allows the grower to better manage crop rotations. Contact your local extension agent or agronomist to help in quick diagnoses, or to help with sending samples to an expert at a clinic. It is not necessary each time you see something wrong, but until you become familiar with disease symptoms in your tomatoes, it makes sense to have an expert provide a diagnosis, which most clinics provide at a nominal cost. When sending a sample to a clinic, be sure to include the symptoms you found, when they first appeared, and where in the field the problem occurs. Include the variety and anything else unusual that you observed.

Publications or websites with color photos can be a good resource to help diagnose diseases of tomato. They are more helpful if you are already familiar with diseases and other problems. Resources from university or government agencies are the most reputable sources. Examples include Vegetable MD Online from Cornell University, the Long Island Research & Extension Center website, Tomato leaf and fruit diseases and disorders from Kansas State University and Tomato disease management in greenhouses from Purdue University. More resources are listed in the references.

Figure 5. A combination of scouting and accurate diagnosis can differentiate between gray mold (left) and blossom-end rot (right) of tomato—two common problems with very different management options. Gray mold is caused by a fungus, while blossom-end rot is a nutritional disorder. Photo credit: Dan Egel, Purdue University.

Approved Organic Products for Tomato Disease Management

Organic products can be broken into several categories:

  • Inorganic
  • Peroxide-based
  • Bicarbonate
  • Botanicals
  • Biological control

IMPORTANT: Before using any pest control product in your organic farming system:

  1. Read the label to be sure that the product is labeled for the crop and pest you intend to control, and make sure it is legal to use in the state, county, or other location where it will be applied.
  2. Read and understand the safety precautions and application restrictions.
  3. Make sure that the brand name product is listed in your Organic System Plan and approved by your USDA-approved certifier. If you are trying to deal with an unanticipated pest problem, get approval from your certifier before using a product that is not listed in your plan—doing otherwise may put your certification at risk.

Note that, although OMRI and WSDA lists are good places to identify potentially useful products, all products that you use must be approved by your certifier. For more information on how to determine whether a pest control product can be used on your farm, see the related article, Can I Use This Input On My Organic Farm?


Perhaps the oldest disease control treatments consist of applying inorganic elements in some form. One example is copper. Copper sulphate and slaked lime—Cu(OH)2, known as the Bordeaux mix—was used in that region of France in the 1800's to deter grape thieves and was subsequently found to help manage downy mildew. Copper can be found in many forms in numerous products: copper hydroxide, copper sulfate, copper oxychloride, and copper salts of fatty acids, among others. Copper can effectively reduce the severity of a number of diseases, including bacterial spot and speck, early blight, and Septoria leaf spot.

Copper products have some disadvantages:

  • Some bacterial pathogens have become insensitive (resistant) to copper compounds present at typical levels on the leaf surface.
  • Over-application of copper products may cause stunting or yellowing of tomato plants or speckling of fruit.
  • Because copper is a heavy metal, overuse of copper products can cause the buildup of residues that negatively impact soil and water quality.
  • Most copper products have a 48-hour re-entry period.
  • Since copper is a heavy metal, applicators and workers should avoid contact with the product or the residue.

Sulfur is another inorganic element that can be used in organic agriculture for disease management. The most common formulation of sulfur products is a dust. Sulfur products are effective against powdery mildew and some types of mites. Applications of sulfur at temperatures above 85oF may damage plants. Dry formulations of sulfur may be available, which produce less dust.

Silicon is sometimes used as part of the active ingredient of products. Potassium silicates are a common example.

Mode of action: Inorganic products attack bacterial and fungal pathogens at multiple sites. Products that contain the inorganic elements copper or sulfur discussed here bind to and destroy critical biochemical pathways of bacterial and fungal pathogens. In contrast, the role of silicon as an active ingredient is less clear. Some silicon products may activate plant defenses. Other silicon products claim to enhance plant cell walls or desiccate pathogens.

Specificity: Since copper attacks the pathogen in various ways, many diseases may be managed with products containing copper. The range of diseases sulfur may help manage is limited to powdery mildew. Silicon products may be labeled for many diseases.

Residual: How long copper, sulfur, or silicon lasts on the leaf surface after application depends on the product formulation, among other factors. In general, the residual of such products is fair to good compared to other organically-approved products discussed here.

Examples of OMRI-listed copper products include Badge X2® (copper oxychloride; copper hydroxide); Nordox (cuprous oxide); Champ® WG (copper hydroxide); Kocide® 3000-O (copper hydroxide); Basic copper 53 (basic copper sulfate).

An example of a sulfur dry flowable product is Microthiol Disperss®.

An example of a silicon-based product is Sil-Matrix®.


Fungicide and bactericide products based on the peroxide molecule—the terms hydrogen dioxide and hydrogen peroxide are sometime used interchangeably—use the oxidizing properties of hydrogen peroxide to sanitize plant surfaces of potential pathogens. Hydrogen peroxide may be combined with other active ingredients in pesticides such as sodium carbonate, peroxyhydrate, or peroxyacetic acid. Peroxide-based products may also be combined with active ingredients that may not be permitted in organic production, such as salts of phosphorous acid.

Mode of action: Hydrogen peroxide is an oxidizing agent, which can have detrimental effects on pathogen cells. The plant cuticle minimizes potential phytotoxic effects; however, carefully follow the label to reduce any potential problems.

Specificity: These products are relatively non-specific and can potentially affect any pathogen. In practice, peroxide products seem to be more effective on bacteria than fungi, perhaps because the cell wall in fungi may offer some protection. While the nonspecific nature of peroxide products is a plus in foliar disease management, it also means that beneficial microbes on the plant surface may be affected as well. Take care in applying peroxide-based products when biological control products are also being used (see Biological Control).

Residual: Peroxide-based products are toxic to pathogens on contact. However, once the product dries, there is no residual and no additional control occurs. Therefore, peroxide-based products should be applied frequently, or applied with or alternated with products that have more residual activity. Read the label of peroxide-based products carefully to determine how tank mixes may be made.

An example of a peroxide-based product is Oxidate®.

Bicarbonate Products

Bicarbonate compounds are commonly present in the environment. Concentrated bicarbonate products can be used in disease management. Most products are potassium bicarbonate.

Mode of action: Bicarbonate compounds may cause cell wall collapse in the pathogen.

Specificity: Although nonspecific, bicarbonate products have greatest activity against powdery fungi. However, only the portion of the powdery mildew pathogen outside the plant is affected.

Residual: Moderate—rain can easily wash away bicarbonate products.

Examples of potassium bicarbonate products include Armicarb®, Milstop® and Kaligreen®.


Products in this category are plant-based. A compound (or compounds) extracted from the plant is the active ingredient used to control plant disease; the mode of action varies widely.

For example, Regalia® is an extract of the plant Reynoutria schalinensis. Evidence suggests that the plant produces phenolic compounds in response to Regalia® application that may fight pathogen infection and disease. Regalia® may therefore fall into the category of products meant to elicit plant defense compounds.

The product Trilogy® uses an extract of neem oil to suppress plant pathogens. Neem oil comes from the neem tree (Azadirachta indica) and works on contact with plant pathogens.

The mode of action, specificity, and residual of botanical products depends on the product and the active ingredient. Both examples above are nonspecific; that is, a broad range of pathogens could potentially be affected. Both the contact activity of neem oil and the defense reaction of Regalia® could affect many different pathogens. A defense reaction elicited by Regalia® could last some time. However, a contact product such as neem oil might not adhere to the plant surface for long.

Biological Control

The use of beneficial microbes to manage diseases has great potential. After decades of research, however, biological control still isn't well understood. One reason is that each known instance of biological control differs in particulars. For purposes of this article, biological control active ingredients are broken down into four modes of action:

  • Active ingredients found within microbes or produced by them during fermentation to create a product.
  • Microbes that elicit a defense reaction from the plant.
  • Microbes that compete for space and resources on a leaf with the pathogen.
  • Microbes that parasitize the pathogen.

Some products fall into more than one category. For example, some products produce molecules toxic to pathogens and elicit a defense reaction.

Microbes with cellular active ingredients: Biological control products in this category contain internal molecules that, when released, may help control a plant pathogen. An example is the product Serenade® Opti. The active ingredient is the microbe Bacillus amyloliquefaciens strain QST 713. The lipopeptides produced by B. amyloliquefaciens may directly suppress pathogens. In this sense, the microbes in Serenade® Opti don't necessarily have to be alive for the product to be effective. However, there is also evidence that Serenade® Opti initiates a plant defense response which is described below.

Serenade® Opti is labeled for a number of diseases. In greenhouse experiments, it has been shown to help reduce the severity of early blight.

Serenade® ASO utilizes the same strain of microbe in a different formulation to include soilborne pathogens such as Fusarium and Pythium.

Microbes that elicit a defense reaction: Plants that become diseased or stressed may produce metabolites to fight infection. Some non-pathogenic microorganisms can initiate such reactions and induce resistance in the plant. The biochemical nature of this is complex and not completely understood. However, a successful reaction can suppress disease development.

However, applying an induced resistance product to plants that are already stressed—for example, drought-stressed—may reduce yield or fruit quality. Therefore, labels on some induced resistance products recommend not using them on stressed plants.

A product example is Lifegard® WG with the active ingredient Bacillus mycoides isolate J. B. mycoides has no direct effect on the pathogen, but rather induces a response in the host plant.

Microbes that compete for resources with pathogens: Plant pathogens that land on a leaf surface or a root must survive until an opportunity to enter into the plant arrives. The amount of time it must wait before being able to cause disease depends on the pathogen's biology, the plant host, and weather, among other factors. When a plant pathogen arrives on the surface of a plant, the presence of beneficial microbes already colonized on the leaf or root can inhibit the pathogen from also colonizing that space. Therefore, some products consist of a microbe that thrives on the surface of the plant and outcompetes any pathogen that survives. Such products may lessen the severity of plant diseases.

Because it is critical that such beneficial microbes live on the plant's surface, the grower must be careful about what products are tank-mixed or alternated. For example, a copper product tank-mixed or alternated with a living microbe may reduce the biocontrol product's efficacy by killing the microbe. Similarly, tank-mixing a peroxide product with a living microbe may render the latter ineffective

The biology of biological control microbes applied to the leaf surface or root is not well understood.

Examples of products in this category include Actinovate® AG and Prestop®. Prestop® also may parasitize some plant pathogens. Actinovate® AG and Prestop® are labeled for both foliar and soil applications.

Microbes that parasitize plant pathogens: The microbes that cause plant disease are parasites of plants (plant pathogens). However, some plant pathogens can be parasitized by other microbes. Such microbes are called hyperparasites—parasites of parasites. Where hyperparasites can reduce the populations of plant pathogens, disease symptoms might also be reduced.

Some hyperparasites seem to be relatively nonspecific, such as the active ingredient of Prestop®, Gliocladium catenulatum strain J1446. Evidence suggests this microbe may parasitize pathogens as different as Pythium and Fusarium. Recent data supports the use of Prestop® for the management of early blight of tomato; however, it is not clear if G. catenulatum is acting as a hyperparasite or some other mechanism is active.

The product AgriPhage™ is specific to the pathogen. The active ingredient is a phage, which is a virus that affects only the bacterial plant pathogen that causes bacterial spot of tomato. The phages that are the active ingredients are so specific that each type affects only certain strains of the bacterium that causes bacterial spot of tomato. Manufacturers get around this limitation by tailoring the product for the strains present in your field. The company may ask you to send in a leaf or fruit sample of bacterial spot from your field so it can produce a specific type of phage for your situation. Or the manufacturer may be familiar with the phage types that have worked in your area and provide a product that affects more than one strain of bacterial spot. AgriPhage™ products can be designed to control bacterial spot of both tomato and pepper, bacterial speck of tomato, and bacterial canker of tomato.

As of this writing, AgriPhage™ was listed on the National Organic Program (NOP) accreditation, but does not appear on the OMRI list.


A famous quote from the book The Art of War, (by Sun Tzu in the 5th Century B.C.) is “Know your enemy.” Growers should learn which diseases of tomato are common in their area and on their farm. Growers should also understand which diseases are likely to be transmitted in seed, which are likely to survive in crop residue, and what fungicides are likely to help slow the spread of disease.

Enlist the help of extension agents, agronomists, and plant diagnostic labs to identify diseases. Use information from manufacturers, government agencies, and universities to determine which varieties are resistant to the diseases of interest. Most importantly, scout your field regularly so when the “enemy” does appear, you'll be ready.

References and Citations

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Published October 28, 2019

This is an eOrganic article and was reviewed for compliance with National Organic Program regulations by members of the eOrganic community. Always check with your organic certification agency before adopting new practices or using new materials. For more information, refer to eOrganic's articles on organic certification.