Root rot, crown rot, collar rot, and damping-off are all types of plant diseases that may be caused by soil borne pathogens. These diseases impact plant health, causing plant tissues to soften, collapse and rot, leaving them unable to perform regular functions. If left untreated, it can lead to plant death.

There are two main causes of root rot: overwatering and/or the presence of fungal or fungal-like pathogens (water moulds or oomycete) in the soil that attack plant roots. Overwatering depletes the oxygen in the soil, and this causes roots to soften, become ‘mushy’ and die. Overwatering or consistently moist conditions are also favoured by these plant pathogens, which can begin to invade healthy plant tissue, causing rot and dieback. These pathogens can survive in the soil, without the presence of host plants and are also not host specific. Damage usually occurs before symptoms are present on above-ground plant parts.

Armillaria, Phytophthora, and Pythium are all common types of pathogens that cause root rot. They can also affect the collar, crown or stem of plants. Here’s how to identify and treat rot.


Image above: Phytophthora Root Rot of an Avocado tree
(image courtesy of Angie Thomas)

Phytophthora cinnamomi and Phytophthora spp.

What is Phytophthora Root Rot

Phytophthora root rot is a serious and widespread disease of many plants. The water mould, or oomycete, is prevalent in wet conditions and causes healthy plant roots to soften, blacken and die. It can also spread to above-ground plant parts when water carrying spores splash up from the soil. Consequently, this may cause crown rot, collar rot or stem rot. Plants in poorly drained soils or areas prone to flooding are more prone to Phytophthora attack.


Below ground, the roots are blackened and rotting and as a result, this causes yellowing and wilting of foliage, and shoots die from the tips. This may eventually cause plant death. If the disease spreads to above-ground plant parts, stems can become weak, blackened and spindly and the tree may rot after the graft union (collar rot). 

Plants Impacted

  • Avocadoes
  • Citrus
  • Ornamentals
  • Macadamias
  • Stone fruit
  • Rhubarb

How to Control Phytophthora Root Rot

Avoid planting in water-logged spots. Instead, plant in pots and raised beds. If it’s not possible, then improve the soil well before planting by incorporating plenty of gypsum and organic matter like Yates Dynamic Lifter Soil Improver & Plant Fertiliser. Apply a protective spray early in the season or when conditions are favourable (heavy rains and/or heavy clay soils). Avoid overwatering and mulch well, keeping it away from the main trunk.

Yates Products

Yates Anti Rot - Phosacid Systemic Fungicide: for the control of Phytophthora root rot on mature citrus and avocados.

Yates Anti Rot - Phosacid Systemic Fungicide: for the control of phytophthora root rot, collar rot, crown rot on ornamentals (non-edible plants).

Yates Liquid Copper - Fungicide: for the control of crown rot on Rhubarb - apply as a protective dip prior to planting.


Image above: Citrus Collar Rot
(image courtesy of Elise Dando)

Phytophthora citrophthora

What is Citrus Collar Rot

This disease affects the trunk of citrus just above the soil level. It is usually confined to the region just above the graft union (the bump along the trunk, where the scion stock was grafted onto the root stock). Lemons are particularly susceptible to citrus collar rot, but it can affect all citrus, especially after heavy rain events. 


A section of bark around the base of the tree dies back and falls away from the main trunk. Sometimes oozing gum and cracking, around the dead section, occurs. Leaves turn yellow. Tree loss can occur if left unchecked.

Plants impacted

  • Citrus

Image above: oozing gum
(image courtesy of Elise Dando)

How to Control Citrus Root Rot

Cut the bark back to healthy tissue and spray foliage with Yates Anti Rot - Phosacid Systemic Fungicide. A spray of Yates Liquid Copper - Fungicide can also be applied to the affected bark lesion. Do not allow soil or mulch to pile up above the grafting union. Susceptible trees should be given a preventative foliar spray with Yates Anti Rot - Phosacid Systemic Fungicide twice a year.

To help prevent citrus root rot, ensure the graft union is planted well above the soil level. Improve air flow by removing any mulch touching the bark of the tree. Additionally, improve drainage around the tree if water logging occurs frequently or if the ground is often damp. 


Image above: Damping-Off of tomato seedlings

Pythium spp., Rhizoctonia spp. Fusarium spp., Phytophthora spp. and Sclerotium spp.

What is Damping Off

Damping off occurs when seeds or seedlings are attacked by water moulds, causing them to collapse, rot and die – either before or after they have emerged from the soil. Due to their young soft tissues, seeds and seedlings are more prone to attack. The pathogens favour moist, poorly drained soils and survive well on decaying organic matter. They are non-selective and will attack a wide variety of plants.


Seedling stems become soft and water-soaked or mushy and eventually collapse at the base and die. Seeds rot and fail to emerge from the soil.

Plants impacted

  • Seedlings, both ornamental and edible
  • Newly seeded and mature lawns
  • Cuttings

How to Control Damping Off

Remove affected plant material and do not replant into infected soils or potting mix. Plant seeds or seedlings into well-draining or fresh potting mix and do not overcrowd or overwater. If required, apply Yates Mancozeb Plus Garden Fungicide & Miticide to seedlings at first sight or if conditions are favourable for the damping off pathogens.

Yates Product

Yates Mancozeb Plus Garden Fungicide & Miticide - for the control of damping off on seedlings.


Image above: Armillaria Root Rot of a cycad

Armillaria luteobubalina and Armillaria spp.

What is Armillaria Root Rot

Armillaria root rot is a serious disease of trees. The pathogen attacks healthy roots, causing roots to rot and wood to eventually decay. The disease can be hard to detect as the signs of the fungus (fruiting bodies and fungal mycelium) are not always visible until later in the disease cycle. The disease can spread via spores, but it is predominantly spread with the introduction of diseased material into healthy or unaffected areas.


Leaves may yellow, limbs die back, and in worst cases, trees completely die. It can be difficult to identify Armillaria root rot early, as signs of the pathogen often don’t appear until later in the disease cycle. Clusters of honey-coloured mushrooms are found at the base of affected trees and a network of white mycelium is often found underneath bark.

Plants Impacted

  • Trees, both edible and ornamental

How to Treat Armillaria Root Rot

Carefully remove affected plant parts, bag and bin them. The fungus can survive on the smallest piece of plant material, so it’s important to remove as much material as possible and leave the area unplanted for up to 50 days. Diagnosis and treatment can be difficult, so if you suspect Armillaria root rot, consult an arborist for further assistance.

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