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Organic Crop Production Disease Management

Managing Diseases in Organic Crops

The idea of "disease control" is somewhat misleading. It suggests we can find a solution to a disease and then the problem will no longer exist. The reality is that any recommendations can only reduce losses caused by disease. They do not eliminate disease altogether.

The term "disease management” more accurately conveys the impression of an ongoing process to reduce disease to acceptable levels. Disease management involves making conscious decisions related to numerous agronomic factors over which growers have some controls.

Plant diseases are caused by microorganisms such as fungi, bacteria, viruses and nematodes. A simple model called the disease triangle describes the conditions that govern disease severity.

In order for disease to develop, three factors must be present: a suitable host plant, an infectious pathogen (microorganism that causes the disease), and a suitable environment. Disease control measures aim to reduce or eliminate one of the corners of the disease triangle. Since the three factors (host, pathogen and environment) interact, it’s important to consider each one and incorporate a variety of management approaches.

Crop Rotation

Rotation of susceptible and resistant crops is one of the oldest practices used to control disease. It remains an important practice against many diseases, where a specific control, such as host resistance, is not available. Rotation is particularly effective in controlling soil- and stubble-borne diseases. The success of rotation in disease reduction depends upon many factors, which include the ability of a pathogen to survive in the absence of its host and the host range of the pathogen. Those that have a wide range of hosts will be controlled less successfully. For example, sclerotinia stem rot of canola (Sclerotinia sclerotiorum) has been recorded on about 400 different plant species worldwide. In Saskatchewan, it is known to occur on 13 field crops. Pathogens that live indefinitely in the soil are less likely to be curtailed by rotation than those that can survive only brief periods apart from their hosts.

Transmission of pathogens via seed, the presence of susceptible volunteer crops and weeds that harbour the pathogens, and the distribution of pathogens by wind and other means will reduce the benefit derived from a crop rotation. For instance, rotations are ineffective in controlling rusts in small grain cereals because the rust fungi do not overwinter in western Canada. Inoculum from the south is disseminated by wind in summer. In a similar fashion, diseases such as barley yellow dwarf and aster yellows depend largely on the northward movement of insect vectors, often over several hundred kilometres.

Crop rotation should be used in conjunction with other cultural practices to maximize its benefit. In establishing a rotation, select crops that are as diverse as possible. In general, a disease may infect closely related species, but will not injure those that are unrelated to the natural host (e.g. net blotch in barley).

Cereal Grains

Crop rotation is recommended to control a number of leaf blights of small grain cereals. Leaf diseases such as net blotch (Pyrenophora teres), scald (Rhynchosporium secalis), and speckled leaf blotch (Septoria passerinii) of barley, and tan spot (Pyrenophora tritici-repentis) and septoria blotches (Septoria spp.) of wheat are generally not carried long distances by wind. The pathogens overwinter in crop debris and on the seed. A break of two - three years between susceptible crops will markedly reduce or control these diseases. This rotation break will allow previously infected crop residue to decay in the soil. Sanitation to eliminate volunteer host plants and the use of clean seed is important.

Soil-borne diseases such as take-all (Gaeumannomyces graminis) may be controlled when wheat follows non-susceptible crops, such as oat, pea, flax, sweetclover, sunflower, or fallow. Barley is less susceptible than wheat, but is still affected by the disease. Including barley as a break crop in the rotation should not be considered as it maintains the disease for future susceptible wheat crops. Unlike take-all, common root rot of cereals is caused by several fungi which are both seed and soil-borne. The control of this disease is more difficult to achieve through rotation, particularly in areas where mainly cereals are grown. Non-host crops for common root rot include canola, flax and legumes. However, lentil can be infected by a specific rot root organism (Fusarium avenaceum) which also infects cereal crops.

Ergot occurs on a wide range of cereal plants and grasses. It is most prevalent on rye and triticale but also attacks durum wheat, common wheat and barley, in decreasing order of susceptibility. A rotation allowing one year between successive crops of rye, triticale, wheat or barley will significantly reduce or control this disease. If native or forage grasses border a cereal crop, mowing the grasses at heading will reduce ergot in the adjacent cereal crop.

Oilseed Crops

Canola acreage is now limited in organic agriculture; however, the two major diseases that affect this crop are blackleg (Leptosphaeria maculans) and sclerotinia stem rot. For blackleg control, a rotation to non-susceptible crops for a period of three to four years is vital. Blackleg survives in canola stubble which generally takes a long time to decompose. Mustards (brown, oriental and yellow), cereals, and legume crops are resistant to this disease and can be safely used in a rotation.

At one time, sclerotinia was thought to be controlled moderately well by crop rotation. Research has indicated that little difference exists among crops in two, three or four year rotations. Rotations of four years or longer may offer some control. This length of rotation may not be practical in canola growing areas. Sclerotinia also attacks pulse crops, sunflower, mustard, sweetclover and flax. This further limits the crops that can be used in a rotation to manage the disease.

Other diseases such as white rust and staghead can be a problem on polish canola. Since both of these are stubble-borne, crop rotation is an effective method of control.

Pulse Crops

Ascochyta blight can infect numerous pulse crops such as field pea, lentil and fababean. Each crop has a specific ascochyta blight fungus. Thus, one does not have to worry about ascochyta from one pulse crop infecting another in a rotation.

With lentil, follow at least a three year rotation (i.e. two year break) involving a cereal, oilseed or other pulse crop. This should be longer (up to four years) if the pulse crop residue is resistant to breakdown (e.g. fababean). Stubble residue is the main source of inoculum for this disease. In field pea, mycosphaerella blight (Mycosphaerella pinodes) can also be introduced as airborne inoculum.

Powdery mildew (Erysiphe polygoni) is specific to field pea. Crop rotation will help, depending on climatic conditions. Dew formation, and lack of rainfall, favours the development of the disease. Inoculum is spread by wind and, once established, powdery mildew increases very rapidly. Field isolation may assist in reducing infection which occurs by wind movement.

Root rot diseases can be a problem on pulse crops. Since the pathogens involved do not usually infect cereals, they can be reduced in severity by including a cereal crop or flax in a rotation. Unfortunately, control is complicated by the wide range of alternate non-crop host plants which these pathogens can infect.


Flax is a crop with a limited range of disease problems at present. Serious diseases such as rust and wilt are controlled by disease resistant cultivars. Pasmo (Septoria linicola), seed decay and seedling blights that are specific to flax can be controlled by using rotations with several years away from flax. Careful harvesting and handling to prevent seed coat cracking can reduce seed decay and seedling blight.

Forage Legumes

Forage legumes such as alfalfa, sweetclover and red clover have numerous disease problems that affect both leaf and root tissue. Almost all major diseases of forage crops are amenable to control through crop rotation. The wilts (verticillium and bacterial), crown and root rots and foliar diseases all survive on dead plant material. When a forage crop is plowed down and another crop is planted, there is a period after which the disease inoculum is reduced and dies out. This time period will vary, depending on the time needed for the forage residue to decompose.

Resistant Cultivars

The use of cultivars resistant to the prevalent diseases in the growing region is the most efficient and cost effective means of disease control. There is little additional operating expense and no hazard to the producer or the environment. Equally important is the fact that crop residue of resistant cultivars constitutes less of a disease inoculum problem for future crops.

The use of resistant cultivars in conjunction with other crop management factors, such as field sanitation and crop rotation, can prevent many serious diseases from occurring.

The use of resistant varieties is particularly beneficial where crop rotation is of limited use. This is the case when the disease organism has any of the following properties:

  • The pathogen has a wide range of hosts (common root rots, seedling blights)
  • The pathogen has a long lived resting stage or persists in the soil for a long period of time (fusarium wilt in flax)
  • The pathogen has airborne spores (cereal grain rusts), or is carried by insects (yellow dwarf, aster yellows), that are spread over long distances
  • The pathogen has a very high rate of spread (powdery mildew)
  • The pathogen is seed-borne (cereal smuts, ascochyta blight of lentil, pasmo)
  • The use of the term "resistant" cultivar may be misleading. In the case of ascochyta blight in field pea, the difference in resistance ranges only from very poor to fair. With blackleg in canola, the level of "resistance" ranges from very poor to very good. Growing these "better" varieties does not mean that producers can forget about using rotations or any other management technique that will reduce the level of infection. Such variation in level of resistance within a crop, between varieties, occurs for a number of diseases.

Sanitation Field

The importance of managing disease-infected straw and chaff cannot be overemphasized. For all crops and numerous diseases of these crops, straw is the primary source of future inoculum. Incorporating this residue into the soil by tillage hastens the destruction of the pathogen by beneficial fungi and bacteria. In addition, diseased plant material which is buried under the soil surface prevents future movement of the spores by wind.

Equally important is the value of maintaining this residue on or near the soil surface for conservation and soil improvement. The balance between soil conservation and disease control will vary depending on geographical location, soil type and disease prevalence.

On lighter textured soils or in regions where soils are prone to water and wind erosion, stubble should be left standing over winter, with tillage postponed until spring. With spring-seeded crops, the incorporation of crop residues into the soil, if desirable or necessary, should be done just prior to seeding. Only in exceptional circumstances, such as alfalfa trash heavily infested with leaf pathogens, should stubble burning be considered.

Alternate disease hosts include volunteer plants growing within a crop or weeds along field margins and fence lines. They should be controlled. Left uncontrolled, these types of plants can transmit disease to healthy crop plants. In many cases, the unsatisfactory control of diseases within a rotation (break crop) may be attributed to inadequate control of volunteers.

In the case of ergot in cereal crops, tillage prior to seeding can have a useful function. Cultivation of the soil surface will bury the resting bodies (ergot), preventing them from germinating and infecting succeeding crops.


Seed should be uncontaminated with sclerotia, ergot bodies, smut or bunt balls and free of infected or infested kernels. Many pathogens are seed-borne, such as ascochyta blight in lentil, smuts, barley stripe mosaic (a virus), leaf stripe of barley, pasmo and numerous others. Seed supplies may be analyzed for various diseases by forwarding samples to a seed testing laboratory. It should be noted, however, that relatively few diseases are exclusively seed-borne. It is more common for pathogens to be transmitted in soil or on stubble as well as with the seed. Ascochyta blight of lentil is transmitted on seed and stubble. The beneficial effect of a good crop rotation may be lost or reduced if high inoculum levels are reintroduced into the field by contaminated seed. Seed quality is therefore important and one more factor to incorporate into an effective disease management program.

Sound seed is also important, particularly in crops such as flax, rye and pulses, where cracks in the seed coat may serve as entry points for soil-borne microorganisms that rot the seed after it is planted.

Planting Dates and Rates

Susceptible cultivars of some crops may escape significant damage from disease by planting at a time which avoids exposure to inoculum and thus severe infection. Diseases such as barley yellow dwarf can be controlled by early seeding. The aphids that transmit this disease do not arrive in significant numbers until early summer. Younger plants, which would have been seeded later, are more attractive as food to aphids.

Field peas are readily infected by powdery mildew. The severity of this disease can be reduced by planting early, as soon as soil can be prepared. If pasmo becomes a problem, early seeding, following the risk of frost, will help escape infection. If lentil seed is infected with ascochyta, planting should be delayed until soil temperatures are higher. This practice will reduce the disease severity.

For fall-seeded crops such as winter wheat, later seeding, following the maturation of spring cereals, breaks the life cycle of the mite which carries the wheat streak mosaic virus.

The density of plants and leaf area in a field is determined by seeding rate, plant architecture and growth habit of the crop, as well as climatic conditions. Dense foliage can increase the chance of leaf diseases by providing a larger surface leaf area for infection to occur. In addition a dense leaf canopy can create a moist soil surface, favourable to a pathogen such as Sclerotinia.

Reduced seeding rates may decrease take-all severity in spring wheat. Plant and leaf density and the ability to control it, as well as the disease potential because of it, should be considered. Note, however, that a reduction in the leaf canopy will create an opportunity for invasion by weeds. This may negatively affect overall crop productivity, depending on the particular situation.

Always consider optimum seeding depth. Deep seeding in cold soils can result in seedling blights and damping-off. This is particularly true in pulses or other small-seeded crops such as canola. Semi-dwarf cereals should not be sown deeper than four centimetres. Deeper seeding encourages root disease.

Soil Fertility

Soil Nutrient Levels

Soil fertility levels, or applications of fertilizers which create nutrient imbalances in soil, can have a marked influence on the crop's susceptibility to disease. Judicious applications in both amount and proportions of nutrients should be based on a sound soil testing program. Excessive levels of nitrogen can result in lush leaf tissue which creates an ideal environment for leaf pathogens or the vectors of viral diseases. In contrast, inadequate soil phosphorus can predispose wheat to browning root rot (Pythium spp.). Few diseases respond as dramatically to nutrition as take-all in cereals. Losses from this particular root disease are generally severe when plants are deficient in any of the essential elements.

Twelve of the 13 principal mineral nutrients are reported to affect take-all, either individually or collectively. A deficiency of nitrogen and/or phosphorus can result in a marked increase in take-all. The use of phosphorus in sufficient amounts to stimulate crop growth has a positive effect in reducing losses from take-all. A large single application of phosphorus may decrease take-all more effectively than small applications, providing other nutrients are not deficient and the phosphorous application is not so large that it inhibits the uptake of copper and zinc. The beneficial effects from phosphorus in reducing take-all are a reflection of stimulated root development and increased host resistance.

A shortage of micronutrients, such as zinc or copper, can cause "disease" in the form of deficiency symptoms in cereal, pulse and oilseed crops. The level of micronutrients required for sufficiency may be very low. However, deficiency in micronutrients can have serious consequences. An over-application of certain micronutrients, such as boron, can cause severe toxicity. Plant tissue analysis is the most accurate method for diagnosing problems of this nature.


The addition of livestock manure to improve soil and crop productivity also stimulates higher populations of soil microorganisms which compete with or destroy soil pathogens. Nutrients released from the decomposing residue may also stimulate the activity of some pathogens but, having no host to attack, they die. This positive process occurs with many root-invading pathogens of cereal, oilseed and pulse crops.

The soil incorporation of green manure cover crops such as certain cereal crops (barley and rye), field pea, sweetclover and lentil (cv. Indian Head) can be used effectively to reduce or control root rot pathogens and other diseases. Legumes, especially alfalfa following breaking, are very effective in suppressing disease organisms. Plant residues of this nature stimulate the growth of soil microorganisms which are antagonistic to plant pathogens, thus offering a measure of disease control.

With the addition of manure, it is possible to create an imbalance of nutrients in the soil. The quality of organic material and quantity of nutrients present in manure varies depending on the type, the method of storage prior to application, and even the application method. Following regular applications of manure, one should pay attention to monitoring the levels of nitrogen, phosphorus, sulphur and, in certain cases, micronutrients present in the soil. This should be done by soil testing on a regular basis.

Integration of Disease Management Practices

Disease organisms and their parasites, host crops, associated vegetation, soil and meteorological conditions are all elements of a linked interdependent system.

Since crop plants are subject to more than one disease, methods for the control of each disease must be woven together. In addition, most diseases are transmitted in more than one fashion. This will require integration of several control and management strategies at more than one level. Disease control strategies, in turn, need to be combined with methods for weed, insect and other production concerns. For example, clean cultivation, achieved by burying infected crop residue in the soil, is a highly effective way of controlling many diseases. However, it may be an unacceptable production practice because of its effect on soil erosion and water conservation. Attempts to increase yields by applying higher rates of nutrients, such as nitrogen, can lead to increased leaf disease problems. Manure incorporated into the soil can reduce the level of numerous pathogens. An over-application, however, may create nutrient or chemical imbalances resulting in micronutrient deficiencies.

Integration of disease control and crop production practices must be done carefully and suit the producer, location and type of cropping system. Disease management systems must be devised to utilize control technology that works harmoniously within the cropping system while maintaining the pathogen population below economically damaging levels.

This factsheet was written by Kerry Foster through funding obtained from the Canada-Saskatchewan Agricultural Green Plan Agreement and the assistance of Agriculture Development and Diversification (ADD) Board #34. It has been approved by the Saskatchewan Organic Development Council Research Committee. 

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