Tomato production: How to keep fungus at bay

In this article, we focus on the fungal infections every tomato producer should guard against.

In wet weather it is advisable to place a handful of grass under any fruit that is in direct contact with the soil. Pruning tomato plants is not recommended as this usually results in a lower yield and more cracked fruit.


For indeterminate (strong-growing) cultivars that are drip irrigated, it’s good practice to remove the leaves from the main stem when the first cluster of tomatoes starts showing colour. If the leaves under the cluster are removed, greater circulation of air between plants will help prevent fungal infection.

The most serious fungal diseases found on tomatoes are:

  • Bacterial canker
  • Bacterial wilt
  • Fusarium wilt
  • Verticillium wilt
  • Early blight
  • Late blight
  • Botrytis rot
  • Tomato spotted wilt virus
  • Tobacco mosaic virus
  • Tomato yellow leaf curl virus


Bacterial canker. Photo: Paul Bachi, University of Kentucky Research and Education Center, on
  • This common disease can be devastating in both field and greenhouse plants.
  • Plants show progressive wilting, and older leaves die (but remain attached to the plant), and there is browning around the leaf edges and in the internal stem tissues.
  • Bacterial canker is primarily spread through infected seed and seedlings.
  • Systemically infected seedlings show no disease symptoms, which makes detection of the disease difficult in nurseries.

Control measures:

  • Plant disease-free seedlings
  • Use resistant cultivars
  • Apply strict sanitation in and around plantings
  • Practise crop rotation


Bacterial wilt and canker. Photo: Gerald Holmes, California Polytechnic State University at San Luis Obispo, on
  • This disease can be a serious problem in warm sub-tropical areas.
  • Initially young leaves show wilting, after which plants wilt quickly and die.
  • There is no browning or yellowing of leaves or stems.
  • If the lower stem of a badly wilted plant is cut across and placed in water, a white milky stream of bacteria flowing
  • out of the cut end is often visible within a few minutes.
  • Stems show a mild internal browning of tissues when cut open lengthways.
  • Bacterial wilt attacks a wide range of plants, some of which are economically important crops.
  • It is spread by infected seedlings, infected water and the movement of infected soil and ground water to healthy production areas.

Control measures:

  • Plant disease-free seedlings
  • Plant resistant cultivars
  • Apply strict sanitation practices
  • Implement crop rotation
  • Control weeds and nematodes
  • Avoid over-irrigation


Bacterial speck. Photo: Gerald Holmes, California Polytechnic State University at San Luis Obispo,
  • Bacterial speck and black stem are both caused by the same bacterial pathogen Pseudomonas syringae pv. tomato.
  • Bacterial speck is common, occurring as small brown spots on leaves, stems and fruit.
  • Leaves could die, and infected fruit is downgraded.
  • Nursery plants are often the primary source of infection.
  • Bacterial speck is frequently found with bacterial spot.
  • Black stem causes a blackening of stems and leaf stalks.
  • Although the blackening is fairly superficial, the plant is harmed.
  • This disease is primarily a problem of tomatoes under protection and seldom occurs in the field.
  • High humidity in greenhouses/tunnels is conducive to the spreading of this disease.

Control measures:

  • Practise crop rotation
  • Implement strict sanitation practices
  • Avoid over-irrigation
  • Reduce humidity in the greenhouse/tunnel
  • Plant disease-free seedlings
  • Apply chemical control


Early blight on tomato leaves. Photo: Dwight Sipler on
  • This widespread disease occurs in humid, moderately hot, or in semi-arid, areas that regularly experience dew.
  • The pathogen attacks leaves, stems and fruit.
  • Lesions start as small brown spots on older leaves and stems, and grow rapidly into large brown/black spots with concentric rings that are often visible in the lesion.
  • The fruit is attacked at the stem end where water accumulates.
  • Leaf and fruit drop usually result.

Control measures:

  • Plant resistant cultivars
  • Use only disease-free seedlings
  • Apply chemical control
  • Eradicate weeds and volunteer tomato plants
  • Provide a well-balanced fertilisation programme
  • Do not use an overhead irrigation system
  • Apply crop sanitation


Late blight on tomato leaves. Photo: Dwight Sipler on
  • This disease is also common and can be very destructive under prolonged wet, cool conditions.
  • All parts of the plant above the ground can be attacked.
  • Leaves initially show light green blighted areas, which quickly turn black, with a whitish/grey fungal growth often visible underneath the lesions when conditions are very humid.
  • Stems show extensive black lesions.
  • Leaves and stems are quickly killed during the spreading of the pathogen.
  • Infected fruit show diffuse blackening with a greasy appearance and deteriorate rapidly. Under optimal conditions, late blight can cause total crop loss within a week.

Control measures:

  • Apply chemical control
  • Do not use overhead irrigation systems
  • Maintain crop sanitation practices


Powdery mildew. Photo: S. Loewen on
  • This widespread disease is a serious problem in hotter areas.
  • The disease favours hot periods when humidity is low.
  • Initially, pale green/yellow spots with a diffuse margin occur on the upper leaf surface.
  • Later spots enlarge and develop into large necrotic (brown) lesions.
  • If lesions are viewed from below (under the leaf), a whitish fungal growth is sometimes just visible.
  • Badly infected leaves die, but seldom drop, and fruit gets sunburnt.
  • Plants grown under drip irrigation are more susceptible to powdery mildew than plants under overhead irrigation.

Control measures:
Apply chemical control, weed control and crop rotation with non-susceptible crops.


Grey mould. Photo: Paul Bachi, University of Kentucky Research and Education Center, on
  • Grey mould leads to fruit rot.
  • It could be a problem when tomatoes are grown at moderate temperatures and under high humidity or prolonged leaf wetness (dew).
  • All above-ground parts of the plant could be attacked.
  • The pathogen invades the plant through wounds (eg. pruning wounds, growth cracks), or through dead/dying tissue (old flowers, dead leaves).
  • Light brown lesions are formed, and the fungus is often clearly visible as a grey/brown growth within the lesion.
  • The disease occurs in both field (F) and greenhouse (GH) tomatoes, but is more common in greenhouses where high humidity frequently occurs.

Control measures:

  • In the case of GH tomatoes, reduce humidity levels by venting.
  • Remove infected plants/plant debris from the production area
  • Optimise ventilation between plants.
  • In the case of F tomatoes, plough in crop residues.
  • And in the case of GH and F tomatoes, apply chemical control.


Tomato spotted wilt virus. Photo:
  • TSWV occurs on various host plants.
  • Young leaves curl downwards and can show rings.
  • Older leaves are bronzed or show a mosaic pattern.
  • Stems and leaves may show a necrotic (browning) pattern, and infected fruit display characteristic concentric rings.
  • Infected plants are stunted.
  • TSWV is spread primarily by the western flower thrips and the onion thrips.
  • The larval stage of the thrips acquires the virus when feeding on the plant, but the virus is transmitted to healthy plants during feeding by the adult thrips. TSWV is not transmitted by seed.

Control measures:

  • Apply chemicals for the control of thrips
  • Plant resistant varieties
  • Apply crop sanitation and weed control


Potato virus y. Photo:
  • PVY also attacks potato and pepper plants.
  • Infected leaves initially show yellow or transparent veins, later developing a mosaic pattern and sometimes necrotic (brown) spots.
  • Occasionally, infected plants are symptomless.
  • PVY is spread by aphids.
  • This makes a preventative control programme of aphids essential.

Control measures:

  • Control aphids chemically
  • Avoid planting near other susceptible crops
  • Plant resistant cultivars
  • Practise crop sanitation and weed control


Stringlike foliage on a tomato plant caused by tobacco mosaic virus. Photo: M. A. Hansen, VPISU, on
  • First reported on tobacco, TMV attacks a wide range of host plants.
  • Leaves show abnormal growth (malformation, stunting) and a green or yellow mosaic pattern.
  • Necrosis (browning) occurs on leaves, stems and fruit.
  • Fruit ripens unevenly, is small and shows browning of the fruit wall when sliced open.
  • TMV is spread mechanically.
  • Examples of how it can be spread are by tobacco products, workers (hands, clothes), implements or infected water.
  • TMV is transmitted by seed, pollen or roots.

Control measures:

  • Apply strict sanitation in the production area
  • Plant resistant cultivars
  • Control weeds
  • Ban the use of tobacco products in and around plantings


Blossom end rot. Photo: Mike Munster on

Hard brown spots occur on the tomato’s blossom end.

Control measures:

  • Mulching
  • Avoiding root pruning
  • Regular irrigation
  • Calcium fertilisation (calcium nitrate, gypsum and lime)
  • Avoiding high nitrogen fertilisation


  • This article was written by Erika van den Heever, Reinette Gouws and Alistair Thompson, attached to South Africa’s Agricultural Research Council, and first appeared in Farming SA.

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