Symptoms

The first step to identifying possible solutions to a plant health problem is understanding the problem correctly. CABI’s PestSmart Diagnostic Field Guide supports diagnostic decisions by showing relationships between common symptoms on plants and the various possible causes.

This page on PlantVillage reproduces  CABI’s PestSmart Diagnostic Field Guide document,  which provides images and descriptions of many typical symptoms associated with biotic and abiotic factors that harm plant health. Among the biotic factors, the major pest groups are represented. Throughout the Field Guide, the term ‘pests’ will refer to all animals, microorganisms and weeds that damage plants. The most common abiotic factors of plant health decline are also highlighted. This book does not attempt to show all possible plant/disorder combinations; therefore, it is important to understand the different types of symptoms caused by each factor and to use that knowledge to make a field diagnosis.

Wilt is a very common symptom of plants in distress. Plants rely on the water in leaves and stems to hold them up; without the water the plants will wilt, i.e. the green parts of the plant
will hang down limply. Unless water is restored to a wilted plant it will die. The roots or stems or base of the stem may be the affected area of the plant although the symptom will mostly be seen in the leaves. Sometimes it can be just one region of the plant that is affected (indicating a problem in the stem) but more usually the whole plant will wilt. Wilts can be temporary whereby the plant will recover at night but wilt again the next day, this can be normal if the sun is strong and the ground dry but it may also indicate a problem.

FUNGI: Fungi commonly produce wilts in plants by preventing water from flowing up the tubes (xylem) in the stems, resulting in the leaves becoming starved of water. Wilt-inducing fungi are mostly soil borne pathogens and they attack the roots and the base of the stem. There is often discolouration of the xylem. The main fungal groups that produce wilts are Fusarium and Verticillium. Whereas Fusarium can produce a pink colouration inside the stem, Verticillium produces dark streaks. Cut the stem open and look for discolouration, making sure you compare it to a healthy plant.

WATER MOLDS: Wilt is associated with damping off of seedlings and root-attacking phytopthoras. Damping off occurs where the base of the seedling rots quickly and the plant wilts and dies. It can be caused by a variety of true fungi but Pythium (water mould) is often involved as well. Downy mildews and foliar-attacking phytophthoras do not generally wilt plants unless the attack is extremely severe.

BACTERIA: Bacteria are a common cause of wilting in plants. Unlike in the case of fungi (where the cause is usually localised in the base of the stem) bacteria occur throughout the stem and the prevention of water moving up the plant is due to the presence of the huge numbers of bacteria (and the gums they produce) in the water-carrying tubes. If you cut open a bacteria-infected stem, as you pull apart the cut ends it is sometimes possible to see strands of gum stretching between the two sides. It is also possible to put the cut stem into still water and observe bacterial streaming (see below). As for fungi they too can produce discolouration within the stem. Bacteria commonly associated with wilting are Pseudomonas, Ralstonia and Xanthomonas.

VIRUS: It is extremely unusual for viruses to cause wilting. There are exceptions, the most common one being Tomato spotted wilt virus. Often the virus will produce other symptoms in addition to wilting.

PHYTOPLASMA: This is not a symptom that is usually associated with phytoplasma infection but there is an exception: phytoplasmas reach such high numbers in coconut (Coconut lethal yellowing) that the water-carrying tubes become blocked, causing wilt in much the same way as bacteria do in other hosts. Witches’ broom and little leaves are much more typical of this group of pathogens.

NEMATODE: Root loss due to nematode feeding causes the plant to be more susceptible to water stress as they are simply unable to take up enough water to replace that lost through the leaves. Nematodes eat the fine root hairs which are responsible for the uptake of water so, even if the roots seem to be mostly intact, the water uptake part of the root system may be missing. Nematodes can be extremely damaging but produce only general symptoms above ground and unless the roots are examined it will be almost impossible to diagnose nematode infection.

INSECTS: Wilt induced by insects is common. It is often the larval stages that cause this symptom, and they may be present in the soil or in the stem. Consider which part of the plant is wilting – is it the whole plant or just a part of it? Split the stem open and look for stem borers. The insect may be providing access for pathogens which rot the plant so when you see a rot, consider whether it is associated with insect damage.

PHYSICAL: Both a shortage of water and too much water (waterlogging) are abiotic causes of wilting. If the wilt is over a large area then consider whether this may be the cause. If wilted plants are close to healthy ones in well watered soil then there is probably a biotic cause.

The whole of this bean seedling is wilting due to the beanfly maggots attacking the base of the stem.

Lepidoptera larvae: the damage caused is an access point for pathogens. Stem borers often have reduced legs and prolegs and may superficially appear like a fly larva (maggot).

Coconut lethal yellowing, a phytoplasma disease of palm

Cassava shoot fly, the tip of the plant has wilted due to the feeding of the larva within the stem.

Phytophthora attacking the roots and base of this squash plant has caused the plant to wilt

Images of Wilt

Tomato spotted wilt virus symptoms on fruit.

Phytopthora infestans attacking the upper stem of tomato. Notice that that the plant is not wilting despite extensive damage to the stem.

Phytopthora capsici attacking the roots of capsicum pepper, the plant is severely wilted due to the damage to the roots.

Internal staining is commonly associated with fungal pathogens that cause wilts. In this cinchona stem the Internal staining is apparent once the outer bark has been removed.

Base of oil seed rape seedlings having damped off after attack by Pythium.

Fusarium oxysporum f.sp. cucumerinum on cucumber. Leaves are severely short of water. The leaves will soon turn yellow and then brown as the plant cannot survive in such conditions.

Leaves are exposed to a great range of potentially damaging agents. Once a leaf is damaged a mark of some sort will always remain, not all of these marks are considered leaf spots. A true leaf spot is the site of an infection by a pathogen. It will start small and enlarge with time. It is an extremely common symptom and experience is required to identify the cause. In this section other spots on leaves are included as leaf spots.

FUNGI: The leaf spot is a classic symptom of many groups of fungi. The leaf is generally unaffected except for the area of the leaf spot and immediate surrounding area. The margins of the leaf spot may be a different colour to the inside. Bacteria and water moulds (see below) can produce similar symptoms. Leaf spots on grasses often turn into streaks because of the geometry of the leaf, i.e. the leaf veins direct the pathogen along the length of the leaf. Fungal lesions will spread but will generally not consume the whole leaf. They appear to reach a certain size and then stop growing; this is not the case for some foliar pathogens, especially Phytophthora (a water mould) and bacteria, which can spread aggressively across the whole leaf. An indication that the leaf spots are caused by a true fungus is that they are all of similar size (or go on to grow to a similar size) and the older ones may have fungal fruiting bodies within them (see below). Visible fruiting bodies are not produced by bacteria or water moulds (although water moulds may produce fluffy spores). The fungal fruiting bodies are not always present (even in fungal infections) and are difficult to see with the naked eye but are often visible with a hand lens.

The leaf spot is a classic symptom of many groups of fungi. The leaf is generally unaffected except for the area of the leaf spot and immediate surrounding area. The margins of the leaf spot may be a different colour to the inside. Bacteria and water moulds (see below) can produce similar symptoms. Leaf spots on grasses often turn into streaks because of the geometry of the leaf, i.e. the leaf veins direct the pathogen along the length of the leaf. Fungal lesions will spread but will generally not consume the whole leaf. They appear to reach a certain size and then stop growing; this is not the case for some foliar pathogens, especially Phytophthora (a water mould) and bacteria, which can spread aggressively across the whole leaf. An indication that the leaf spots are caused by a true fungus is that they are all of similar size (or go on to grow to a similar size) and the older ones may have fungal fruiting bodies within them (see below). Visible fruiting bodies are not produced by bacteria or water moulds (although water moulds may produce fluffy spores). The fungal fruiting bodies are not always present (even in fungal infections) and are difficult to see with the naked eye but are often visible with a hand lens.

Pictures of fungal fruiting bodies in leaf spots. The presence of the fruiting bodies is a sure indication that the pathogen is a fungus, but if they cannot be found then this does not mean that it is not a fungus causing the problem. In the top pair of photographs only the two spots arrowed (right) contain fruiting bodies (left). Some fungi do not produce fruiting bodies in this form. All of these photographs were taken with a compact camera and a hand lens, so the magnification is no greater than that achievable in the field.

WATER MOULD: Leaf spots caused by water moulds are often rapidly spreading (especially in wet weather) and may not have a clearly defined border. They are usually not limited by the leaf veins and may have a water-soaked region around the spot, which may have fluffy white material (spores) on the surface.

BACTERIA: Bacteria cannot penetrate a leaf in the same way as fungi and so bacterial leaf spots (in the early stages of attack) are often associated with the edge of the leaf or minor damage. As the bacterial numbers increase you will see the spots spread across the leaf. Bacterial leaf spots are more likely to be limited by the leaf veins in the initial stages but when the infection is growing rapidly, the expanding numbers of bacteria will push the infection past leaf veins. The edges of a bacterial leaf spot are often water-soaked, the plant tissue leaks material and the bacterial gums fill up the air spaces that are usually within the leaf. You will never see structures within a bacterial leaf spot as bacteria do not produce fruiting bodies which are characteristic of fungi. Bacteria often colonise stressed plants and the leaf spots will carry on spreading, especially if the leaf is under stress or is old.

VIRUS: Viruses can produce a type of leaf spot on some occasions but they are usually in a ring or crescent pattern. Remember that viruses generally do not often cause the plant tissue to die, so a viral leaf spot will not usually have much dead tissue associated with it, but it will be a different colour (almost always yellow) from the remainder of the leaf.

INSECTS: Feeding damage by insects that have sucking mouthparts can leave marks that look like fungal or bacterial spots and damage by biting insects that do not perforate the leaf can look similar.

NUTRIENT DEFICIENCY: A severe deficiency of any mineral will lead to poor growth but it is unusual for a plant to suffer such extreme shortage that would lead to cell death. The main exception is rapidly expanding tissue, such as the ends of tomatoes or courgettes. If calcium is in short supply the ends of the fruits will break down and appear like a fungal or bacterial rot (not ‘leaf spot’ but something similar on a fruit).

PHYSICAL AND HERBICIDE: Bright sunshine can produce patches of dead tissue on leaves and fruit which may appear as spots. Wilted leaves exposed to bright sunshine and succulent fruits that are undergoing a period of rapid growth are the most susceptible. Shaded portions of wilted leaves exposed to the sun generally recover at night. Any type of stress that causes wilting will make plants more susceptible to sunscald. Paraquat and diquat (and other less common herbicides) can cause what appear to be leaf spots: the otherwise healthy leaf is covered in small tan-coloured spots within which the tissue is dead. These symptoms are produced rapidly following herbicide application.

Strong sunlight can cause burnt patches on fruit (marrow).

Paraquat damage on cassava. Notice how the areas of damage are next to areas of healthy leaf with little transition between the two.

Strong sunlight can cause burnt patches on leaves (cucumber).

Insect feeding can produce damage that looks like bacterial or fungal infection. This may be due to the physical action of feeding or due to toxins injected into the plant. Mirid damage on cacao.

Zinc deficiency in wheat: a pale grey spot on the middle of the leaf.

Blossom end rot on tomato: this disorder is common on tomato and is seen when the fruits are rapidly expanding. It looks like a bacterial or fungal rot but is due to a shortage of calcium.

These water soaked patches are a very unusual symptom of a virus, these symptoms are more associated with a bacterial infection.

Coconut plant bug damage on cashew.

Potassium deficiency in lucerne: the marginal yellowing is associated with scattered white necrotic spots.

These rings and crescent shapes have a viral cause but spots with rings within them are more typically produced by fungal pathogens

Bacterial infection of cabbage (left) and bean (right). Notice how in both cases the spots usually begin at the leaf edge.

The presence of the fruiting bodies is a sure indication that the pathogen is a fungus, but if they cannot be found then this does not mean that it is not a fungus causing the problem. In the top pair of photographs only the two spots arrowed (right) contain fruiting bodies (left).

What appeared to be fungal fruiting bodies (left) were removed by wiping with a wet thumb (right) indicating that they were insect frass and not of fungal origin.

Leaf spot caused by Phytophthora colocasiae on Taro. The leafspot is spreading rapidly, there is some water soaking around the edges of the lesion. The tan dots are not fungal fruiting bodies (this is a water mould) but dried droplets of exudate that had oozed from the leaf.

Leaf spot caused by Phytophthora infestans on tomato. Note the zone of lighter coloured leaf around the darker necrotic area: this is the area where spore production may be taking place.

Ensure that the ‘fruiting bodies’ are not natural features of the leaf (left) or some artefact like insect frass (right). Older lesions may have been colonised by secondary microorganisms. These secondary invaders may produce fruiting bodies that could be mistaken for those of the disease-causing pathogen. When looking for fruiting bodies, try to find them in the younger lesions.

Fungal fruiting bodies in leaf spots

Fungal fruiting bodies in leaf spots

Leaf spots of Venturia inaequalis on apple in Nepal.

In this condition, a biotic or abiotic factor causes the plant to lose control of the correct growth pattern and it grows in an uncontrolled way. The pathogen is either producing (or causing the plant to produce) the wrong balance of chemicals that regulate its growth. The clustered growth of many branches all emerging from a central point is not an especially common symptom: it usually occurs on woody plants and is often associated with ‘little leaf’.

FUNGI: Common. In woody plants only, not so in herbaceous plants.

PHYTOPLASMA: This is a classic symptom of phytoplasma. The dormancy of the side buds is broken and the cluster of tiny shoots all competing with each other is the result.

MITES: Mites can get into the growing point of the plant and cause witches’ broom symptoms. The constant feeding on the material at the very tip of the plant causes it to produce multiple shoots. It is not possible to see the mites at the tip as the kind of mites that cause this symptom are too small to be seen, even with a hand lens.

PHYSICAL AND HERBICIDE: Glyphosate can produce witches’ brooms in many plants. If you spray with glyphosate, much of the upper parts of the plant will appear dead, however sometimes, a while later, the lateral buds will break dormancy and small witches’ brooms will develop.

Doses of glyphosate that do not kill the plant can induce unusual growth habit. Note the reduced leaf size and clustered internodes. Nettle (left) and annual mercury (right) showing regrowth following glyphosate treatment.

Witches’ broom caused by a phytoplasma on pigeon pea.

Fungal witches’ broom on silver birch. Extreme proliferation of branches from a single point creates a witches’ broom.