C1 – Damping-off Diseases and Root Rots


Damping-off (seedling death prior to, or soon after emergence) is most commonly caused by Pythium species, Rhizoctonia solani, and occasionally Phytophthora species or Botrytis cinerea. A wide range of herbs can be affected by damping-off, under all production systems. The same fungi can cause root, crown and stem-base rots on mature herb plants, particularly affecting soil-grown herbs (e.g. parsley crown and root rot caused by Phytophthora primulae). Root rots caused by Pythium and Phytophthora species can also occur where re-circulating irrigation systems are used for herb production. Pythium and Phytophthora species are closely related fungal-like micro-organisms, with both being favoured by abundant moisture and similar in their sensitivity to fungicides. Some Pythium and Phytophthora species have a wide host-range, while others are restricted to a limited number of hosts. R. solani has a wide host range and commonly causes damping-off and wire-stem of seedlings, and stem base damage to cuttings and young plants. Information provided in this guideline is adapted from HDC Factsheets 16/04 and 17/04.

Occasional diseases on field-grown herb crops such as violet root rot (Helicobasidium brebissonii) and liquorice rot (Mycocentrospora acerina) on parsley, and white rot (Sclerotium cepivorum) on chives, could also affect soil-grown herb crops under protection but are not widely reported.


It is often difficult to differentiate damping-off and root rot symptoms caused by Pythium species, Phytophthora species and Rhizoctonia solani; accurate diagnosis is important to ensure appropriate disease management.

A common symptom of damping-off is poor seedling emergence. Where seedlings are grown in pots or trays, areas of affected plants enlarge leaving bare patches (Figure 1). Damping-off is less common in module or plug trays where there is reduced chance for disease spread between seedlings. Pythium species are the most common cause of damping-off, resulting in seedling stem collapse, with the affected area having a water-soaked appearance that enlarges and turns brown/black, often becoming constricted. Damping-off caused by Pythium species usually develops from the root tips upwards and seedlings often collapse all in one direction. In contrast, R. solani usually progresses from the soil or compost surface downwards, with seedling collapse in all directions.

Root, crown and stem-base rots
The effect of Pythium root rot is often first seen on above-ground parts, as poor growth, yellowing, wilting and plant death (Figure 2). Affected roots appear water-soaked, grey or brown and shrivelled (Figure 3). The outer cortex of the root sometimes falls away easily, leaving just the central vascular strand. Pot coriander grown under all year round production systems can be particularly susceptible to Pythium root rot.


[]Figure 1.
Patchy emergence of Euphorbia seedlings due to damping-off caused by a Pythium species


[]Figure 2.
Coriander seedlings infected with Pythium root rot


[]Figure 3.
Coriander roots affected with a Pythium species (top) showing stem base constriction, discolouration and reduced root growth, compared with healthy roots (bottom)

Phytophthora species more commonly attack mature plants rather than seedlings. Above ground and root rot symptoms are similar to those caused by Pythium root rot. One difference, is the ability of Phytophthora species to progress from the roots to invade the stem base and cause a visible rot, more frequently than Pythium species. Parsley root and crown rot (Phytophthora primulae) is the most common Phytophthora disease of herbs. In soil-grown crops, patches of stunted plants with yellowing foliage may be the first indication of a crown rot problem (Figure 4). When the roots and crown are cut open, brown discolouration is visible, which becomes darker as the infection progresses (Figure 5). The outer cortex of the root may easily slough away. Severe infection results in foliage collapse and eventual plant death.


[]Figure 4.
Yellowing of parsley foliage and withered roots due to Phytophthora crown and root rot


[]Figure 5.
Parsley root discoloured (upper) due to infection by Phytophthora primulae, compared with a healthy root (lower)

Infection by R. solani on older seedlings can lead to red-brown discolouration and constriction of the stem base (‘wire-stem’) (Figure 6). Seedling leaves in contact with infested soil/growing media may be rapidly invaded by R. solani, and become water-soaked and rotten. On mature plants, R. solani can cause crown rot, stem base rot (brown discolouration; Figure 7) or stem base canker, the latter typified by longitudinal cracking and a dry appearance. Root rots caused by R. solani typically develop as discrete brown lesions along the root length with rotting of the cortical tissue. Under warm, humid conditions, the fungal strands of R. solani may be seen growing over the compost surface and as webbing over leaves.


[]Figure 6.
Typical wire-stem symptom on a seedling, caused by Rhizoctonia solani


[]Figure 7.
Stem base rot and root lesions on basil due to Rhizoctonia solani

Disease sources and spread

For Pythium and Phytophthora species, infested crop debris, contaminated soil and growing media, capillary matting, non-mains water supplies, water-holding tanks, dirty tools and unsterilised pots and trays, are the main sources of disease. Neither pathogens are seed-borne but they may be introduced to a nursery via infected cuttings or plug plants. Both pathogens produce resting spores (oospores) that are capable of long-term survival (several years) in the absence of a host. Resting spores are stimulated to germinate by exudates from host plant roots. Once germinated, swimming spores are produced that are readily dispersed by water splash, water movement in soil/growing media, and in the irrigation water where production is on ebb and flood benches. Pythium species can also be transmitted by adult shore flies and sciarid flies. Air-borne transmission rarely occurs.

R. solani can originate from many of the same sources as Pythium and Phytophthora species, although water supplies are not usually an infection source. R. solani can survive between growing seasons in crop debris and soil, either as survival structures (sclerotia) or thickened fungal strands. Under favourable conditions, R. solani can rapidly colonise growing media by extensive hyphal growth and may spread between plants by growth of hyphae between touching leaves and stems. Spread of R. solani by air and water is limited as the fungus very rarely produces spores.

Conditions for infection

For Pythium and Phytophthora root rots, infection and spread are favoured by high moisture levels in the growing medium or soil. In general, infection can occur over a wide temperature range as long as free water is present, although temperature optima vary with species (e.g. 15-20°C for P. primulae on parsley). Neither Pythium nor Phytophthora species are strong competitors in soil, although they may rapidly colonise sterilised soil where there is less competition from other micro-organisms. Rapid germination of resting spores and fast growth rate in response to plant exudates enable these fungi to be successful invaders of plant roots. Any cultural factors that adversely affect plant growth (e.g. over watering or high fertilisation rates) can predispose plants to infection.

R. solani can grow and cause infection under a wide range of environmental conditions, although it generally grows best over the surface of growing media or soil that is evenly moist and warm. Factors that delay plant establishment (e.g. sub-optimal temperatures or incorrect pH) may facilitate infection by R. solani.

Integrated disease management

Cultural control

Planting material
Planting material (seedlings, plugs and cuttings) introduced from other nurseries should be inspected carefully for signs of diseases, and rejected if symptoms are observed. When seedlings are being transplanted, avoid using seedlings from trays with poor emergence or other signs of damping-off.

Glasshouse and crop hygiene
Diseased plants and associated growing media should be removed and discarded into a covered skip. This is particularly important with sub-irrigation systems. Regularly clean and disinfect benches, matting, tools and propagation areas (also see Section A – Principles of IPM). Rhizoctonia species can colonise polystyrene trays and these should be thoroughly treated by steaming if re-used. Disinfectants with activity against Pythium and Phytophthora species include Jet 5 (containing peroxyacetic acid) and sodium hypochlorite. The latter also has activity against R. solani. Note that there is a risk of phytotoxicity to plants by root uptake if hypochlorite residue remains on a treated surface where new plants are placed. Train staff to implement good crop hygiene, paying particular attention to footwear as Pythium species can be transferred on the soles of shoes.

Regularly clean and disinfect water storage tanks and irrigation lines (e.g. with sodium hypochlorite or Jet 5). Tanks should be covered to prevent contamination. Water samples can be sent for laboratory testing to determine the presence of Pythium or Phytophthora species. In addition, on-site testing for Pythium, Phytophthora and Rhizoctonia species can be done using baiting techniques and lateral flow device (LFD) kits from for example, Forsite Diagnostics Ltd (www.forsitediagnostics.com). HDC Project HNS / PO 188 is currently developing guidelines for growers, to enable more effective use of baits and LFDs for on-site water testing. Where there is a known higher risk of pathogen contamination (e.g. where water is collected and re-cycled), measures to treat water may need to be implemented. Possibilities include the use of UV-light, chlorine or ozone treatment, or slow sand-filtration (see Further Information).

Crop management

Regular inspection of plant roots may enable early detection of root rot problems. Avoid rapid changes in environmental conditions that may check plant growth, particularly for young plants. Good growing conditions, including correct growing medium, nutrient levels and pH, will minimise the development of root rot diseases. The growing medium should be well drained and irrigation should be applied only as needed, to avoid prolonged periods of saturation (e.g. using well managed trickle or sub-irrigation).

Since shore flies and sciarid flies are potential vectors of Pythium species, occurrence of these insects should be kept to a minimum. Refer to Sections B.2 and B.3 for details on the management of shore flies and sciarid flies.

If root rot occurs in a soil-grown crop, do not re-use the same area for subsequent crops without attention to soil drainage and possible use of an appropriate fungicide drench treatment. Extending the interval between one crop and the next may reduce disease risk but Pythium, Phytophthora and R. solani are all capable of long-term survival in soil.

Biological control

Prestop and Prestop Mix both containing the fungus Gliocladium catenulatum are approved for use on all edible crops, with moderate efficacy against damping-off and root rots caused by Pythium, Phytophthora, Rhizoctonia and Fusarium species. Products may be applied by drip irrigation, growing media incorporation, drench treatment or foliar spray.

Chemical control (protected herbs)

Where there is a significant disease risk, use a preventative fungicide programme. For Pythium and Phytophthora root rots, this is best achieved using a drench or a ground spray treatment (according to label or EAMU directions) with one of the products listed in Table 1. In addition, Apron XL (metalaxyl-M) can be used as a seed treatment for herb seed, for control of Pythium root rot. For soil-grown herbs, avoid repeated use of products containing metalaxyl-M on the same land in successive years, as over time this can result in reduced fungicide efficacy due to a process known as enhanced microbial degradation. There is also a risk of Pythium and Phytophthora species developing resistance if this active ingredient is used frequently. Metalaxyl-M as SL 567A can only be used between April and October.

There are no conventional products approved as drenches for control of Rhizoctonia stem base and root rots on protected herbs, although Amistar (azoxystrobin) and Rovral WG (iprodione) may be applied as foliar sprays. Young plants are particularly susceptible to attack by R. solani so early preventative treatment is likely to be most effective. Be aware that for Amistar, the harvest interval is 28 days for crops harvested in November to April and 14 days for crops harvested in May to October.

Before selecting products to use for root rot control on protected herbs, test treat a small batch of plants before widespread application if using a product for the first time, to ensure crop safety.

Growers using fungicides containing azoxystrobin, metalaxyl-M or CAA fungicides (e.g. dimethomorph and mandipropamid) should be aware of the need to use strategies to minimise the risk of selecting resistant strains; for further details, see Section A – Principles of IPM.

Table 1. Fungicides with activity against damping-off and root rots caused by Pythium and Phytophthora species and permitted on protected herbs (March 2013)

Fungicide group and active ingredient(s) Example products Compatibility with pest biological control
1. CAA


Safe to Phytoseiulus persimilis, moderately harmful to Orius
Not yet known
2. Dithiocarbamate + phenylamide
Mancozeb + metalaxyl-M
Fubol Gold
Moderately harmful*
3. Microbial
Gliocladium catenulatum
Prestop Mix
4. Phenyl-amide
Apron XL (seed treatment only)
Safe to many biocontrols; moderately harmful to Aphidoletes and Amblyseius swirskii
5. Phosphonate + carbamate
Fosetyl-aluminium + propamocarb hydrochloride
Previcur Energy
Safe to many biocontrols; moderately harmful to Aphidoletes and Amblyseius swirskii

*Adverse effects on certain biological agents

  • Full details for the use of biological control agents and compatibility of pesticides are available from biological control suppliers or consultants.
  • Pesticide approval information in this guideline is current at 31 March 2013.
  • Regular changes occur in the approval status of pesticides arising from changes in pesticide legislation or from other reasons. For the most up to date information, please check with a professional supplier or the CRD website http://www.pesticides.gov.uk/.  General enquiries on pesticides and detergents are now being handled by the Defra Helpline (as of April 2013): Tel: 08459 33 55 77.
  • Always follow label recommendations or statutory conditions for use on Extension of Authorisation for minor use (EAMU, previously SOLA) notices of approval.
  • Always follow instructions for Pesticide Resistance Management guidelines given on the label or EAMU.
  • Growers must hold a paper or electronic copy of the current EAMU before using any product under the EAMU arrangements. Any use of a pesticide with an EAMU is at grower’s own risk. Relevant EAMUs are sent to HDC members by HDC, or are available from CRD (see above) or from consultants.
  • Use pesticides safely.

Further information

HDC Factsheet 16/04. Control of Phytophthora, Pythium and Rhizoctonia in container-grown hardy ornamentals.

HDC Factsheet 17/04. Control of Pythium, Phytophthora and Rhizoctonia in pot and bedding plants.

HDC. 2005. Slow Sand Filtration. A flexible, economic biofiltration method for cleaning irrigation water. A Grower Guide. 30 pp.