Pythium Root Rot

Pythium species


Black Stem Rot of Pelargonium.
Damping Off.



Pale stunted seedlings that may rot at the base, wilt and die. The stem has a wet rot that usually starts in the roots and progresses up the stem soon after emergence or transplanting.


Seedlings may fail to emerge or rot at ground level with the leaves turning orange to red followed by wilting and death. It usually occurs in patches and may follow soil types. It is more common in cold wet conditions or where conditions for germination and early growth ore poor.


Pale stunted seedlings that may rot at the base and die. Reduced tillering in cereals. Roots may be stunted and profuse but with few laterals. Infected roots have a soft, yellow to light brown areas especially near the tips. There may be fewer laterals and fewer root hairs.
Crops may show patches of poor emergence.
More common where cereals are planted on cereal or canola stubbles and in minimum tillage systems or where stubble or trash is retained.
Often associated with dense weed stands that have been sprayed with glyphosate.


A black rot appears at the base of the stem and progresses up the stem. The stem withers and the plant wilts and dies


Pale, round patches up to 1 metre diameter with collapsed or dead plants. Roots may be stunted and brown. and individual seedlings may be distorted with wrinkled leaves.

Species Affected:

Brassicas, Canola, Cereals, Lucerne, Passionfruit, Pelargonium, Strawberries, Wheat and a wide range of other species. Perennial grasses are more sensitive in the seedling stage.


Favoured by cool wet conditions and water-logging.
Soil borne fungus that does not require a specific host.
Spread by infected soil water or on seedlings at transplanting.
Infects many crop and weed species.
May be aggravated by P deficiency.
Favoured by high levels of nitrogen application.

Life Cycle:

Origin and History:


More common in high rainfall areas or wetter parts of the paddock and on acid soils.
Affected plants are usually scattered throughout the crop but may occur as patches in wetter areas.



Generally not a serious disease of conventional crops but may become more prevalent in direct-drilled situations with cold, wet conditions around planting.

Management and Control:

Cereals and grasses.

Avoid planting into cold wet soils.
Avoid direct drilling and stubble retention.
Avoid planting crops soon after knockdown herbicides - especially glyphosate.
Plant crop as shallow as is practical especially in wet soils.
Apply adequate fertilizer to allow better crop recovery.
Avoid heavy applications of nitrogen in the seedling stage and ensure adequate phosphate.
Increase seeding rate to compensate for lost plants.
Seed treatments are reasonably effective and on average give a 5-10% yield increase in minimum tillage systems.
Crop rotations will not control it and most chemical treatments are uneconomic for broadacre use.


Pull out and destroy infected plants.
Take cutting as far from the soil as possible.
Apply fungicides.


Plant runners that are certified as disease free.
Fumigate affected areas before replanting.


Annual Poa, Creeping Bentgrass and Couch are sensitive. Hot humid and wet weather favours disease development especially if it is poorly drained. It often appears in stressed areas such as drainage lines, walkways or compacted areas and around tees near divots. More common when night time temperatures are above 200C and day time temperatures are 30-350C. Fungicides applied as a preventative are generally more effective than applications made after the disease is seen.


Ensure paddocks and seed raising mixtures are well drained. Don't over water.
Avoid planting into cold wet soils.
Avoid planting crops soon after knockdown herbicides - especially glyphosate.
Plant crop as shallow as is practical especially in wet soils.
Apply adequate fertilizer to allow better crop recovery.
Seed treatments with fungicides can provide early protection.
Soil may be treated with fungicide.

Related and Similar Species:

Looks like N deficiency.
In Canola, Fusarium Seedling Rot looks similar and is often associated. Canola Damping Off (Rhizoctonia solani) is also often associated and has red brown to dark brown lesions on the hypocotyl near the soil surface and the cotyledons usually turn red.


(Lamb, 1989)

(McMaugh, 1985)


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