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Ministry of Agriculture, Food and Rural Affairs


Management of diseases of specialty crops requires an understanding of the principles of disease management because specific pest information is often not available. Specialty crop growers will often need to rely on non-chemical disease management options, because few conventional or organic pest control products are registered for many of these crops. It is important to properly diagnose the cause of symptoms on the plant to effectively control disease while avoiding unnecessary control measures. Biotic diseases are caused by fungi, oomycetes (water moulds), bacteria, phytoplasmas, viruses and nematodes. These organisms infect plants, diverting resources from the host to reproduction of the pathogen and living at the expense of their hosts.


Fungi are a group of living organisms that have some similarities to plants, but unlike plants they do not have chlorophyll and so must take their nourishment from living or dead organisms to survive and reproduce. On infected plants, some appear as delicate strands (filamentous mycelium) that grow on or in plant tissue and may not be visible to the naked eye. Most reproduce by spores produced by the millions and spread by air currents, water, soil and insects. Under suitable environmental conditions, and if a suitable host is near, the spores will germinate and infect the plant. They enter through wound sites and natural plant openings (stomates, lenticils) or by forcing their way through the outer layer (epidermis) of plant tissue. Many fungi also produce resting spores that can withstand long periods of unsuitable conditions.

Fungi that infect foliage, flowers and stems are usually spread by air currents or splashing water. Fungi that infect plant roots, crowns or the vascular system of plants (wilts) survive several years in the soil, until suitable germination conditions exist. The damage that they cause includes a breakdown of tissues (soft rot), cell death (necrosis or leaf spots) and the blockage of water conducting tissues.

Fungal diseases are best controlled through the use of resistant varieties, improved airflow through the canopy to reduce humidity and leaf wetness, avoiding overhead irrigation, sanitation, improved drainage, crop rotation and preventative application of pest control products.

Common fungal diseases causing damage to specialty crops include the following:

Powdery Mildew: The first symptoms of this disease are white powdery spots on stems and leaves. If widespread, the entire leaf may become infected. Powdery mildew can be expected after midsummer, when the days are sunny and dry and the nights are cool. This leads to extreme fluctuations in humidity levels, which promotes the development of the disease. Powdery mildew is unsightly, and will reduce the health and vigour of the plants if left untreated. They are one of few fungal pathogens that do not need free water for spores to germinate or infect tissue.

Leaf Spots and Blights: Numerous fungi can cause spots and blights on leaves including Alternaria, Cercospora, Septoria, Colletotrichum (anthracnose), Botrytis, Ascochyta, and Phomopsis. These diseases are often spread by airborne inoculum and are favoured by high humidity and extended periods of leaf wetness. Many fungi that cause leaf blights and spots can survive in dead leaf tissue.

Rusts: Rust diseases are named for the often rust coloured spores that appear in pustules along the leaves and stem of infected plants. Rusts are complex diseases that have up to five different fruiting bodies and spore types, and some require two separate hosts in order to complete their life cycle. Rust diseases are best controlled through the use of resistant varieties because these fungi are often very host-specific. Some rusts can be controlled through eradication of the alternate host.

White Mould: This disease, caused by the Sclerotinia fungus, affects densely growing annual plants during periods of wet weather or frequent watering. The symptoms are rapid browning and rotting of lower stems and leaves, with white cotton-like tufts of mycelium and round, black resting structures - the sclerotia - embedded in the tufts. The sclerotia will remain viable in the soil for long periods of time.

Crown and Root Rots: A wide range of fungi cause rots of the lower stem, crown and roots of most specialty crops. Common rot fungi include Rhizoctonia, Fusarium, Cylindrocarpon, Rhizopus, and Chalara. These fungi are mostly soil-borne and spread by wind-blown soil, movement of soil on machinery and field workers, and infected seeds. They are often favoured by poor drainage, compaction, and dense canopies. Rhizoctonia and Fusarium can also cause damping off of seedlings. These diseases are best controlled through sanitation, crop rotation, and improved soil drainage.

Wilts: Fungi that enter the vascular system of the plant can cause a sudden wilt and collapse of affected plants. The most common wilt fungi are Fusarium and Verticillium. Once symptoms of these diseases appear, it is too late to control the disease. These diseases are best controlled through seed treatments, sanitation of tools and equipment to avoid spread, and crop rotation. Verticillium wilts can infect a wide range of crops and are common on solanaceous crops. Avoid growing susceptible crops after a solanaceous crop.


The oomycetes are a group of fungal-like organisms, often called water moulds, that cause many destructive plant diseases. The symptoms of many oomycete diseases are similar to those caused by fungi, and they are often grouped with the fungi for management purposes. However, these diseases can spread rapidly and are more difficult to control using cultural methods alone. As a result, preventative measures are very important for oomycete diseases. Most oomycete pathogens require significant amounts of wet weather for infection, disease development and spread.

Common oomycete diseases affecting specialty crops include the following:

Downy mildew: Downy mildew is a serious oomycete disease of several specialty crops. Infected leaves develop pale green areas on the upper leaf surface. The lower leaf surface may be covered with a downy, grey-to-purple mould with visible black spores. Downy mildews are very crop-specific. For example, basil downy mildew will not affect plants from other crop families or vice versa. Downy mildew is windborne while others require water splashing and wind to spread the infective propagules. Regardless, all downy mildews are highly infectious. Many can destroy a crop in less than 1 week. Downy mildew is favoured by cool, wet and humid weather conditions.

Phytophthora: Phytophthora are soil-borne or debris-borne water moulds (oomycete) that can rot the root system and lead to complete plant death. They are one of the most destructive of all of the plant pathogens. Some can spread through the soil affecting neighbouring plants and are favoured by wet soil conditions, which allows their swimming spores to travel more rapidly through saturated soil. Phytophthoras produce rain-splashed spore sacks (sporangia) that can land on leaves and either infect directly or burst open to release 8-30 swimming zoospores that begin a foliar phase of the disease. Diseases caused by Phytophthoras can spread as rapidly as downy mildew. Zoospores or spore sacks of some Phytophthora diseases wash off of the leaves into the soil causing additional root rot. Most Phytophthora pathogens can produce a persistent sexual resting spore (oospore) that can persist in soil and/or debris for many years. The disease can be controlled through the use of resistant varieties, if available, improved drainage including raised beds, and preventative sprays of specific pest control products.

Damping-Off: Damping-off disease is caused by various soil fungi and some water moulds (oomycetes) that infect seeds or seedlings, but the most common cause is the water mould (oomycete) Pythium. Failure of plants to emerge can be a sign of damping-off. Seedlings that do emerge rot, often at the base of the stem near the soil, and collapse soon after emergence, Sometimes the roots rot away, leaving stunted dying plants above the soil. The disease rarely attacks all plants in a row or flat, but rather patches or part rows often in lower parts of the field or in a flat that has been over-watered. Excessive soil moisture, dense seeding, and cool soil temperature promote damping-off development.


Phytoplasmas are specialized bacteria-like organisms that cause several diseases of economic importance to specialty crop growers. The most common phytoplasma disease in Ontario is aster yellows. However, there are several other phytoplasma diseases of specialty crops including several types of witch's-broom. Phytoplasma diseases are generally characterized by chlorosis (yellowing) of leaves, stunting, and a proliferation of leaves or branches resulting in a thick clump of vegetative tissue. They also result in excessive production of lateral roots in root crops such as carrots. Like viruses, spread of these pathogens requires a vector, most often sucking insects like leafhoppers. Aster yellows is spread by the aster leafhopper, and control of this disease requires effective control of the leafhopper vector. Weed control outside the field in ditches and road sides where the pathogen can over winter can also help reduce the incidence of aster yellows. It should be noted that in some years when there are many aster leafhoppers, there is very little aster yellows while in other years there are few leafhoppers and lots of aster yellows.


Bacteria are microscopic single-celled organisms that reproduce rapidly inside the plant under favourable conditions. Bacteria enter plants through wounds, pruning cuts and the pores (stomates) of leaves. They can also be spread mechanically on hands, clothing and equipment, though splashing water and rain is the most common means of spread. Once inside, they affect most parts of the plant.

Bacteria are often classified as wilts, blights, or soft rots. Wilt-causing bacteria infect the roots and eventually clog up the vascular tissue, inhibiting the flow of water and nutrients. Blights refer to the rapid rotting of succulent tissue such as shoots, leaves and flowers. Soft rots develop on fleshy tissues in wounded areas of the plant that remain wet for long periods.

Symptoms of wilt disease appear primarily on the leaves, and include large V shaped areas of dead tissue, yellowing, and a wilted appearance. Grey or black streaking may be apparent on leaves and stems. Under warm, humid conditions, plants collapse very quickly. Sometimes an ooze or milky droplet containing millions of bacteria seeps out of infected stems and leaves.

Blights may first appear as black spotting on leaves and stems that rapidly expand. With many woody crops, flower buds, young leaves, and shoots may turn completely black and die. Infection occurs in early spring during extended periods of wet weather.

Soft rots often develop on fruits or vegetables when water sits on them for long periods. This usually occurs where a wound already exists on the plant or where plant material lays on the soil. Bacterial soft rots usually have a foul odour and appear wet and slimy.


Viruses of protein and nucleic acids and are only visible with electron microscopy. They reproduce only in the cells of a living host. The most common viral diseases are classified by their symptoms: mosaics, yellows, stunts, mottles and streaks.

Viral diseases exhibit a variety of symptoms. The most common is the uneven yellowing of the leaf, which gives rise to a mosaic pattern of yellow and green. With some systemic viruses, the areas adjacent to the veins turn yellow. Still other viruses can cause ring spots, stunting, distortions of leaves and flowers, and premature death. Many viruses will cause necrotic spots similar to other disease causing agents.

Many viruses are carried from infected to healthy plants by certain insects such as white flies and aphids. Some viruses are transmitted on the sucking mouth parts of insects, do not require an incubation period within the insect body, and are only transmitted once (non-persistent viruses); while other viruses must undergo an incubation period within the insect, stay with the insect their entire life and can be transmitted by the same insect many times (persistent virus). Some viruses can be transmitted mechanically and can be spread by humans when handling plants, taking cuttings or pruning, or even rubbing against plants with contaminated clothing. Many viruses are carried over from season to season in tubers, bulbs, corms, weeds and occasionally in seed.


Nematodes are microscopic worms that attack plant roots to obtain food. Leaves may also be attacked, though this is rare. In some cases, the roots become stubby, with swollen knots or growths (e.g. root knot nematode). (Do not confuse the nitrogen fixing nodules on leguminous plants with damage from nematode infestation.) Some plant parasitic nematodes cause small scratch-like lesions that allow soil-borne fungal pathogens to enter and cause root rots or wilt diseases. Small lesions are often also visible. As the disease progresses, root rot due to invasion by other organisms usually occurs. The plant gradually loses vigour, showing symptoms of drought, stress, nutrient deficiencies, and stunted growth. Most root infecting plant parasitic nematodes thrive best in sandy soils, but some parasitic nematodes such as the stem and bulb nematode prefer heavy clay soils. Nematodes have limited mobility in the soil, moving slowly by swimming through free water around soil particles. They can spread larger distances by movement of soil by erosion, machinery or on boots. They can also spread by splashing and movement of surface water, or by planting infested propagation materials.