Damping off of tomato and chilli seedlings: symptoms and control in the nursery

Photo at the top: Damping off by Pythium in a pot of basil seedlings: most seedlings have collapsed and dried, only a few still stand. Tomato and chilli nurseries look the same. Photo: Roswitha Ulrich, Pflanzenschutzdienst, CC BY-SA 4.0

Quick answer

Damping off of tomato is a nursery disease caused by soil fungi, mainly Pythium and Rhizoctonia. Seeds rot before they come up, or young seedlings get a soft, water-soaked stem at soil level and fall over. It also hits chilli, brinjal and soybean. Prevent it with raised, well-drained beds, thin sowing, light watering and seed treatment.

Damping off of tomato symptoms: how to identify it

Damping off is called ardra galan in Hindi and naru kullu tegulu in Telugu. It is a disease of the seed bed and the nursery tray. It kills seeds and very young seedlings, mostly in the first two to three weeks after sowing. Tomato, chilli and brinjal nurseries are all at risk. The disease shows up in two phases.

• Before the seedlings come up (pre-emergence): the seed or the tiny shoot rots inside the soil. You see gaps in the rows and poor germination, even with good seed. Dig at a gap and you find a soft, brown, rotten seed.
• After the seedlings come up (post-emergence): the stem at the soil line (the collar) turns soft and water-soaked, like it has been boiled. It then becomes thin and shrivelled. The seedling bends over at that point and falls flat, while its leaves are still green.
• Patches: the dead seedlings are not spread evenly. They die in round patches that grow bigger every day, often where water stands or where the seedlings are thick.
• Older seedlings: seedlings with a hard stem may survive, but they stay weak, with a thin, brown, rotten root.

Pythium or Rhizoctonia: how to tell them apart

You do not need to know which fungus it is to start control, but the signs help.

• Pythium (a water mould): soft, wet, water-soaked rot at the base of the stem. It is worst in wet, cool, cloudy weather and in beds where water stands. In the morning you may see fine white threads on the soil around dead seedlings.
• Rhizoctonia solani: a dry, brown to reddish-brown, sunken patch at the soil line. The stem becomes thin and hard, like a wire, before the seedling falls.

Look-alikes

• Cutworm: the seedling is cut clean at the soil line, as if by a blade, and the top often lies on the ground. Dig around the plant in the morning and you may find a grey, greasy caterpillar. See how to identify and control cutworm.
• Fusarium wilt: it comes later, on bigger plants after transplanting. Lower leaves turn yellow, the plant wilts, and when you cut the stem the inside is brown. Read our Fusarium wilt guide for tomato and other crops.
• Bacterial wilt: a bigger, green plant wilts suddenly without yellowing. A cut stem put in a glass of clean water gives a milky stream. See the bacterial wilt guide.
• Heat or dry soil: seedlings wilt in the afternoon but stand up again by evening after watering, and the stem at the soil line stays firm.

Damping off of tomato disease cycle

The fungi that cause damping off live in the soil. TNAU (Tamil Nadu Agricultural University) notes that Pythium survives in soil, seed and water, and spreads through infected plant debris. Pythium forms thick-walled resting spores (oospores) that can stay alive in the soil for a long time. In wet soil it releases small swimming spores that move in water films towards the seeds and roots. Rhizoctonia lives in the soil as fungal threads and small dark resting bodies on old crop debris.

When a seed starts to germinate, it leaks sugars into the soil. These draw the fungus, which enters the soft seed, root or stem at the soil line. The young tissue rots, and the seedling falls. The fungus then grows on the dead seedling and moves to the next one, which is why the patches grow.

Weather that favours it: TNAU lists high humidity, high soil moisture, cloudy days and temperatures below 24 °C for a few days. For chilli nurseries, TNAU notes very high humidity (90% and above), moist soil with poor drainage and a soil temperature of about 20 °C. Crowded seedlings, heavy rain and poor drainage add to the risk.

When it attacks: in Telangana and Andhra Pradesh, kharif nurseries raised during the monsoon face the highest risk, because of rain, cloudy days and wet beds. Nurseries in cool, misty weather in winter can also be hit when beds are watered too much. The danger period is from sowing until the seedling stem turns firm and woody, usually in the first three weeks.

Crops it attacks

Tomato: TNAU names Pythium aphanidermatum as the cause in tomato. It rots seed in the bed and makes young seedlings topple. A nursery can lose a large share of its seedlings in a few days of wet, cloudy weather.

Chilli: one of the most common nursery problems in chilli. Germination drops, and seedlings that come up lodge (fall over) because of a weak, light brown stem.

Brinjal: TNAU lists several soil fungi behind damping off in brinjal, including Pythium, Phytophthora, Rhizoctonia solani and Sclerotium rolfsii. Seedlings in the seed bed suddenly collapse at the collar.

Soybean: soybean is sown straight in the field, so the disease shows as seed rot and seedling blight in the first weeks after sowing, mostly in waterlogged or heavy soils. Product labels call these Pythium seedling blight and Rhizoctonia seedling blight.

When to act (threshold)

There is no spray threshold for damping off. We could not find a published economic threshold from a recognised public source, so we do not give one. Once seedlings fall, they cannot be saved. So damping off in nursery beds is managed by prevention: clean, well-drained beds and seed treatment before sowing. If you see the first patch of fallen seedlings, act on the same day: remove the dead seedlings with the soil around them, stop watering for a day or two, and protect the rest of the bed.

Damping off in nursery: control without chemicals

• Raised beds: TNAU advises raised nursery beds about 15 cm high, so extra water drains away. Never let water stand in the bed.
• Light, careful watering: water with a rose can, not by flooding. Keep the soil moist, not wet. TNAU advises against flood-type watering in the nursery.
• Sunny site: do not raise the nursery in shade. Choose an open place with good air flow.
• Thin sowing: use the recommended seed rate. Thick sowing keeps the soil wet and lets the fungus jump from seedling to seedling.
• Clean soil: do not use soil from a field or bed that had damping off before. Many growers raise seedlings in pro-trays (plastic trays with small cells) filled with fresh cocopeat. Fresh, clean media carry far fewer soil fungi.
• Heat the soil in summer: covering the moist nursery bed with a clear plastic sheet for a few weeks in hot summer weather heats the topsoil. This is called soil solarisation, and it reduces soil fungi before you sow.
• Good seed: sow clean, healthy seed from a reliable source.
• Helpful microbes: TNAU advises treating seed 24 hours before sowing with Trichoderma asperellum at 4 g per kg of seed, or Pseudomonas fluorescens at 10 g per kg of seed. These are friendly fungi and bacteria that guard the seed against the disease fungi. For tomato, TNAU also lists Bacillus subtilis at 10 g per kg of seed.
• Remove sick seedlings: pull out fallen seedlings with the soil around them and throw them away from the nursery. Do not drop them in the compost pit near the bed.
• Healthy seedlings for the field: transplant only firm, healthy seedlings. Throw away any with a thin, brown collar.

Chemical control, crop by crop

Only the products below have that crop and damping off (or Pythium and Rhizoctonia seedling blight) on their official label. Use one product at a time. Do not mix products in one tank.

Tomato and brinjal

None of the products in our store lists damping off on tomato or brinjal on its label, so we cannot suggest one for these crops. Follow the steps in the section above. For a chemical product, ask your local agriculture officer or KVK (Krishi Vigyan Kendra) for one labelled for your crop.

Chilli

Product	Contains	How to use (label)	Wait before harvest
Indofil M45 Fungicide	Mancozeb 75% WP	Soil drench, dose as per label: 3 g in 1 litre of water	10 days

A soil drench means you pour the mixed solution on the soil of the nursery bed so it soaks the root zone, instead of spraying it on the leaves. Our label record gives the strength (3 g per litre) but not how many litres to pour per square metre of bed, so follow the pack leaflet or ask your dealer.

Soybean

Product	Contains	How to use (label)	Wait before harvest
Electron Insecticide+ Fungicide	Azoxystrobin 2.5% + Thiophanate Methyl 11.25% + Thiamethoxam 25% FS	Seed treatment only: 100 ml per 10 kg of seed (10 ml per kg of seed)	Not applicable (seed treatment)

Electron is a ready-mixed product, approved on its label, with two fungicides and one insecticide in one pack. It is for seed treatment only, not for spraying. Its label lists Rhizoctonia seedling blight and Pythium seedling blight on soybean. Treat the seed one day before sowing or on the day of sowing. Put the seed in a polythene bag, pour the product on the seed, and shake until all seeds are evenly coated. Dry the seed in shade and sow. The label allows one application.

Rotate to avoid resistance

Fungicides are grouped by how they work, using the FRAC code (FRAC is the international Fungicide Resistance Action Committee). Using the same group again and again can make the fungus resistant. Some groups carry a high risk of resistance, and some a low risk.

FRAC group	Active ingredient	Resistance risk	Product in this article
M 03 (works at many sites)	Mancozeb	Low	Indofil M45
11 (QoI, strobilurins)	Azoxystrobin	High	One part of Electron
1 (MBC, benzimidazoles)	Thiophanate methyl	High	One part of Electron

The third part of Electron, thiamethoxam, is an insecticide (IRAC group 4A), not a fungicide. If your soybean seed was treated with Electron, avoid using a group 11 or group 1 fungicide again and again in later field sprays on the same crop. Change the group from one spray to the next, and keep to the number of applications each label allows.

Safety and waiting period

• The waiting period before harvest (PHI, pre-harvest interval) for Indofil M45 on chilli is 10 days, as given in the table above. For Electron, the waiting period is not applicable because it is used only on seed.
• Wear gloves, a mask and full-sleeve clothes when you mix a drench or treat seed. Do not eat, drink or smoke while you work. Wash your hands and face well afterwards.
• Treat seed in a shaded, open place, not inside the house or near the kitchen.
• Seed treated with Electron turns pink-red. Never feed treated seed to birds, poultry or animals, and never use it as food. Store it away from food grain.
• The Electron leaflet says it is highly toxic to bees, fish and other water life. Keep treated seed, empty packs and washings away from ponds, canals and wells.
• Read the label and leaflet before use.

Frequently asked questions

What are the symptoms of damping off of tomato?

Seeds rot in the soil and do not come up, so you see gaps in the rows. Seedlings that do come up get a soft, water-soaked stem at the soil line. They bend at that point and fall over in round patches, often while the leaves are still green.

Which fungicide should I use for damping off in a tomato nursery?

None of the products in our store lists damping off on tomato on its label, so we cannot suggest one. Use raised beds, light watering, thin sowing and seed treatment with Trichoderma as TNAU advises. Ask your local agriculture officer or KVK for a fungicide labelled for tomato.

Can seedlings that have fallen over be saved?

No. Once the stem has rotted at the soil line, the seedling will not stand up again. Remove the fallen seedlings with the soil around them, cut down watering for a day or two, and protect the healthy seedlings around the patch.

Why does damping off come back in the same nursery every year?

The fungi survive in the soil and in old plant debris, and Pythium can stay alive in the soil for a long time. If you sow in the same spot with the same soil, the disease waits there for the next crop. Move the nursery, use fresh soil or cocopeat, heat the bed with a plastic sheet in summer, and treat the seed.

Does damping off affect plants after transplanting?

Damping off mostly kills seeds and seedlings in the first few weeks, while the stem is soft. Bigger plants that wilt in the field usually have another problem, such as Fusarium wilt, bacterial wilt or root knot nematode.

Related reading

• Early blight of tomato and potato: symptoms and control
• Fusarium wilt: symptoms and control
• Root knot nematode in tomato, chilli, brinjal and okra: signs and control
• Cutworm: how to identify and control it
• Products for tomato
• Products for chilli
• All fungicides

Sources

• Tamil Nadu Agricultural University, TNAU Agritech Portal: Damping off of tomato
• Tamil Nadu Agricultural University, TNAU Agritech Portal: Damping off of chilli
• Tamil Nadu Agricultural University, TNAU Agritech Portal: Damping off of brinjal
• Fungicide Resistance Action Committee (FRAC): FRAC Code List 2026
• Product labels and leaflets of the products listed above.