Plant Disease Diagnostics
Plant diagnostics has been part of the Teagasc service to the horticulture industry for over fifty years. It began at Kinsealy in 1962 and became part of Ashtown Food Research Centre in 2012.
Pest and disease infestations often coincide with climatic changes such as irregular rainfall, increased humidity, or drought, which in themselves may lower crop output. Pest outbreaks may have a devastating impact in a given year, but cause only marginal losses in other years (Yudelman, Ratta, and Nygaard 1998).
We are one of the only plant clinics in the country that deal with such a wide range of plant diseases from the:
- Vegetable Sector
- Protected Crop Sector
- Nursery Stock Sector
- Cut Foliage Sector
- Soft Fruit Sector
- Cultivated mushroom industry
The main focus of our work is on fungal pathogens which can cause large crop losses to a farmer. Samples are either submitted through our advisors and specialists, or a site visit arranged directly with the clinic by our clients. On-site visits involve a basic audit of the disease problem and a sample collection for identification and possible further pathogen identification in our purpose built Ashtown horticultural laboratories.
Rapid disease identification is extremely important in order to suitably manage crop diseases. This may involve a chemical treatment schedule, biological treatment or ideally, a more integrated crop pest and disease management approach.
Plant Clinic Update - August 2019
August saw a large amount of mushroom samples for quality check and pathogen diagnosis.
Results are commercially sensitive so not shared here.
We offer a range of services for mushroom growers including growing advice, virus detection, bacterial disease detection and compost quality checks.
Plant Clinic Update - July 2019
July is often a busy month for the clinic. 2019 was no exception. Here are a selection of samples that came in to us.
Submitted for a contamination check by the grower who suspected that the seeds may be carrying a pathogen. In this case, the seeds were very clean with some minor environmental contaminants present, of little concern.
Leaf lesions were infected by a common pathogen known as Alternaria
Lots happening on this sample with small amounts of Ramularia, Alternaria and Cladosporium. The main cause of the issue appeared to be bacterial in nature though.
Characteristic black raised lesions which were identified as a Puccinia sp. commonly associated with the disease Box Rust.
Mushrooms and Mushroom casing
Quality and disease checks. No issues.
This was an unusual case of leaf yellowing. No disease cause was isolated and the tree later recovered and thrived. Possible spray damage.
This plant was heavily infested by Scale insects but the primary disease cause was found to be a common pathogen known as Pestalotiopsis funerea.The majority of Thuja samples I've seen in the last 10 years have been infected by this fungus and it's usually the first thing I look for. Spores are easily visible with a small hand-lens as black masses at the leaf tips.
Routine QA check. No issues.
These plants tested positive for the presence of Phytopthora. This is quite easy to diagnose in strawberries. The strawberry crown can tell you what's wrong with it once it has been sectioned in 2. To be 100% we also use a lateral flow device specific for Phytophthora and visualise structures down the microscope. In the picture below, note the dark discolouration.
This was a bit of a mystery. Leaves were blackening and tested negative for Phytopthora. No other pathogens were present on the leaves given as a sample. A root sample has been requested for clarification. Hopefully this will clear up the mystery. Griselinia is normally quite a hardy plant never giving any issues.
Distinctive blotching on leaves were being casued by an infestation of Gall Mites.
Clinic Update May to June 2019
Pear leaves (Pyrus sp.)
This sample was showing signs of blackening. The grower suspected insect damage but the insect was identified as St.Marks Fly, a beneficial insect and useful polinator. There were no pathogens on the leaves but there had been a recent frost in the area. The trees were also very exposed on a hillside site and it was concluded that frost damage was the most likely primary cause.
Lettuce (Lactucae sp.)
The lettuce as dying back and Fusarium was suspected by the grower. The roots were rotting but the damage was attributed to a Pythium sp. infection after samples were grown on artificial media and viewed by light microscope. No Fusarium was present.
A Viburnum tinus plant was submitted with leaf lesions. These were found to be caused by an Alternaria sp. infection. No Phytophthora present as suspected by the grower.
Leaf spotting was attributed to Stigmina carpophila, a fungus which is known to cause shothol-like symptoms on Prunus spp.
Pumpkin leaves (Cucurbita sp.)
Lesions on leaves were caused by a bacterial infection
An interesting sample which was dying back. It was heavily infected by Scale insects and Two Spotted Spider mites. The main cause was likely to be water issues which was weakening the plant allowing the insect issues to have a greater effect on its vigour.
Peach plant (Prunus persica)
The leaves were severely distorted. The fungal pathogen Taphrina deformans was found to be the cause of the distortion.
Cabbage (Brassica oleraceae)
Leaves submitted by our Veg Advisor were showing severe blistering associated with Albugo candida.
There were no diseases associated with the leaf damage and feeding damage insect pests were concluded to be the most likely cause.
This sample had severe leaf lesions. The fungus Venturia inequalis which causes 'Apple scab' was found on the lesions at very high levels.
This plant had a severe shothole problem. It was found to be caused by the bacteria P.syringae pv syringae.
Ashtown Plant Clinic - April 2019
Mushrooms (Agaricus bisporus)
A busy month for the clinic with a high volume of mushroom samples submitted for testing. A brown or 'chestnut' variety of commercially grown mushroom was exhibiting symptoms of poor growth.
Basil (Ocimum basilicum)
A sample of Basil was submitted for testing exhibiting a root crown rotting type symptom. This was weakening the plant and the stems were breaking off. There were some Sciraid fly larvae present in low numbers and these were discounted as the primary cause. A fungus known as Rhizoctonia was consistently associated with the rotting. Rhizoctonia can be probematic on nurseries due to its persistance in the soil and environment. It is commonly associated with 'damping-off' of seedlings and can be easily diagnosed with a hand lens. The mycelia (strands of fungi) are dark brown and form a lattice pattern on the affected parts as the disease progresses.
Sweet William (Dianthus barbatus)
Several samples of Sweet William were submitted exhibiting a large leaf spotting. The spots themselves were large (<10mm),tan in colour with a dark purple border. On examination by microscope, a high level of a fungal pathogen known to cause problems on Dianthus was observed. These were identified as likely to be Cladosporium echinulatum due to their distinctive shape and size. In the picture below (Fig 1), you can see how the spots take up a significant proportion of the developing leaves, leading to distortion. The plants will often succumb to this disease when it reaches this stage.
Fig 1. Cladosporium leaf spot on Dianthus
Prunus laurocerasus 'rotundafolia' (Laurel)
A common visitor to the clinic due to our involvment in cut foliage research project 'New Leaves'. Shothole disease is one of the biggest problems for Laurel plants when used as a crop for the cut foliage sector or in hedging. The samples sumitted were severely impacted by an infection caused by the fascinating bacteria Pseudomonas syringae pv syringae. We diagnose this disease using a two stage identification. Firstly we grow it on a media (King's B or Pseudomonas agar base) which causes the pathogen to produce fluorescine. Fluorescine glows under uv light, making the candidate bacteria easy to pick out. We then perform a 'PCR' (polymerase chain reaction) on the bacterial DNA. This allows us to confirm that P.syringae is present.
Christmas tree (Nordmann fir)
This sample was just submitted today. It is stunted and is having problems thriving. This sample tested positive for the presence of a Phytopthora sp., although this was possibly a secondary organism taking advantage of plant weakened during the drought in 2018.
If you would like to submit a sample to the clinic for testing, contact your Teagasc Advisor for details on the process.
Compiled by Brian McGuinness, Ashtown Plant Clinic. email@example.com.
Ashtown Plant Clinic - February/March
Sample numbers are increasing as we head for spring. So far we've had a wide range of samples with different issues. Some examples of the type of samples we've recieved in February and March were:
Rhubarb (Rheum rabarbarum)
Nutritional problems leading to leaf discolouration and distortion
Red Claws (Escallonia rubra-macrantha)
Several Escallonia samples came in, all infected with Septoria escalloniae, leasing to a characteristic leaf spot and accompanying defoliation. Septoria is a fungal pathogen and research conducted by Teagasc has shown that fungicides containing Boscalid in combination with Pyraclostrobin can be effective in reducing this disease and helping this beautiful plant to recover. Chlorothalonil can also reduce disease. The Septoria spotting on Escallonia tends to increase from late summer through winter, so treating your plants with a fungicide around August and December might help it recover coming into the Spring. Try to remove excessive leaf debris from under the plant as the fungus more than likely overwinters on fallen leaves. This allows the pathogen to reinfect the plant in the following growing season. Some varieties of Escallonia have a higher apparent resistance to the Septoria leaf spot disease. For further details contact firstname.lastname@example.org
Cabbage (Brassica oleracea)
This sample was a bit of a mystery but there was some damage due to presence of fungal pathogen Alternaria brassicae. This fungus has very distinctive spores and leaf spots making it easily recognisable in the field with a simple hand lens. Spores are large, dark-brown/Black and shaped like a 'club'. The leaf spots tend to be dark as a result and often there is some zonation or 'ring-like' patterns. If you think you have an Alternaria problem, we can confirm its presence and help you treat it usually within a couple of hours after sample receipt.
Daffodils (Narcissus sp.)
This is daffodil season, so no surprises here. We had several varieties into the clinic including 'Mando', Golden ducet', 'Tamara' and 'Red baron'. We found several problems including the Small Narcissus bulb fly (Eumerus sp.) and a Ramularia sp. fungus causing 'white mold' on leaves. Ramularia is a common visitor to the clinic since 2015. (https://www.teagasc.ie/media/website/publications/2015/TodaysFarm_MarApr2015.pdf).
Pea shoots (Pisum sativum)
Not a sample we frequently get, but this sample was affected by a Pennicillium sp. which was enjoying the nice warm damp environment in the pots.
Mushrooms (Agaricus bisporus)
One of the most frequent visitors to the clinic are white button mushrooms (Agaricus bisporus). The mushroom industry is Irelands largest horticultural sector and we regularly recieve samples for testing. Teagasc are one of the world leaders in mushroom research. We have recently opened a state-of-the-art mushroom research facility here in Ashtown Research Centre.
Ashtown Plant Clinic - January 2019
Griselinia littoralis (Gris)
Griselinia is a common feature of many Irish gardens. We've had a recent sample of dieback in a hedgerow which was diagnosed with a Phytophthora sp. root infection. This is an unusual occurence for such a hardy plant but may have been due to a weakened plant or pre-existing root damage, possibly insect/slug related. Soil was fine as were all plants surrounding it.
Brassica oleracea (Cabbage)
Cabbage samples were submitted with suspected 'Light leaf spot' caused by the fungus Pyrenopeziza sp. After examination, the pathogen turned out to be an Alternaria brassicicola infection causing greyish spotting with small black dots (pycnidia) in a 'bullseye' type pattern. Pycnidia are tiny fruiting bodies where the fungus produces its spores. When it rains, the pycnidia burst and spores can be splashed several meters from the plant, particularly when rain is coupled with high winds. Spores land on other plants and under the right conditions (light, moisture, temperature), they germinate and the fungus gains entry to the plant. It can often enter through the stomata or if there is any existing leaf damage.
Samples can be submitted to the clinic through your advisor or by contacting email@example.com.
Take a look at our plant pathology laboratories and see what services we offer.
Xylella fastidiosa information
The Xylella bacterium causes wilting and death of plants. It enter the water-conducting xylem vessels where it multiplies and blocks the transportation of water. As spittle bugs feed on the fluid from the plant xylem they can become infected by the bacteria and pass it on to other plants. The 3 different supspecies of Xylella fastitiosa present in Europe are fastidiosa, pauca and multiplex. The bacteria are very specific in their hosts and may not effect closely related plant species or even some varieties.
The bacterium is a major concern for a few reasons; it is devastating most likely fatal to its host, it has a very wide host range 60 + plant species that show symptoms and more than 240 that can carry the disease without symptoms. Its vectors, spittle bugs, can be found all across Europe so it can easily be spread. To date there is no cure for the bacteria.
The European Commission have published the latest update of host plants susceptible to the bacterium Xylella fastidiosa in the union territory (16/1/2017 https://ec.europa.eu/food/sites/food/files/plant/docs/ph_biosec_legis_emergency_db-host-plants_update08.pdf) .
There are now over 300 known host species susceptible to the bacterium, though not all of these species develop disease, and not all species are affected by all Xylella subspecies (pauca,multiplex,fastidiosa,sandyi ) .
The list of host plants includes many common trees and ornamentals relevant to the Irish horticulture industry including Acer, Aesculus, Brassica, carex, Cornus florida, Fuchsia magellanica, Ginkgo biloba, Hedera helix, Hemerocallis, Hydrangea paniculata, Liquidambar styraciflua, Liriodendron tulipifera, Magnolia grandiflora, Olea europaea, Platanus, Prunus, Quercus, Rosmarinus officinalis, Rubus, Salix, Veronica, Vinca. The full list of susceptible plants is available here: http://eur-lex.europa.eu/legal-content/EN/TXT/PDF/?uri=CELEX:32015D0789&from=EN .
X.fastidiosa was first regulated at EU level as a harmful organism with quarantine status in 1992 (Directive 2000/29/EC) but was not confirmed in Europe until 21st October 2013 when an outbreak of X.fastidiosa subsp. pauca was detected on olive trees in the Apulia region of Italy.
Reaction from the EU commission was swift with emergency measures published on 13th February 2014 which aimed to prevent the spread of X.fastidiosa within the union (Decision 2014/87/EU). This was quickly followed in July 2014 by the publication of more detailed measures to prevent disease introduction and spread within the EU.
Despite the introduction of these emergency measures, further outbreaks were reported in the neighbouring Italian province of Brindisi on the 9th of March 2015, Corsica on the 27th July 2015 (on Polygala myrtifolia) ,and the French mainland in the region of Provence-Alpes-Cote dâ€™azur on 18th September 2015.
Detection and spread
Sap-sucking insects are important potential disease vectors once disease becomes established in an area. The primary risk comes from movement of infected material which means Irish plant importers will have to be vigilant in the sourcing and subsequent monitoring of imported host plant material.
Symptoms on plant material include dieback, stunting and leaf scorch, all of which are symptoms of many other plant pathogens and environmental factors such as frost damage. This makes a laboratory diagnosis necessary and involves identification of the disease at the molecular level by DNA extraction from infected material.
The ability of X.fastidiosa to â€˜hideâ€™ within asymptomatic plant material adds an extra layer of complication to its detection and control.
Suspected cases of this disease should be reported to the Plant Health Division of the Department of Agriculture Food and the Marine (DAFM). DAFM can be contacted as follows:
Horticulture and Plant Health Division,
Department of Agriculture, Food and the Marine,
Backweston Administration Building,
EU territory Latest Developments of Xylella fastidiosa - updated every 15 minutes
Ramularia causing issues for Daffodil growers
A recent diagnosis at the Ashtown plant clinic has confirmed it's Ramularia season for Daffodil growers. On this occasion, the variety 'Standard Value' seems to be badly affected. Ramularia causes a disease commonly known as 'White mould'
White mould. Infects the leaves and stems of daffodils, resulting in foliar lesions, eventually causing leaf death.
Lesions are found on both sides of leaves, starting as small, sunken off-white streaks predominately near the leaf tips. Spots later progress to yellowish spots covered with white mould. Resting spores known as sclerotia are immersed in the leaf, dark brown in colour. The fungus survives in the dead plant material as sclerotia, which then germinate to produce fungal spores. White mould is also spread between plants during wet and windy conditions.
If present, the disease usually develops just after the first leaf emergence (January). Cool, dry weather can reduce disease spread.
The most effective means of control of the disease is removal of the dead material as practicable. It has been suggested that daffodils are not replanted for a year as this is sufficient to kill off the remaining conidia and sclerotia. If this is not possible it is also suggested that replanting with more resistant cultivars can help to reduce the occurrence of the disease.
This species of Ramularia was originally described from northern Italy detected in England less than ten years later and since then has spread through Western Europe and, more recently, has been found in Eastern Europe. It appeared in an outbreak in the western USA in the early 1930s but does not appear to have spread further in North America apart from into the adjacent part of Canada. In the UK, it has been severe in the Channel Islands, Scilly Isles, Cornwall and Devon. It was reported as being common in Scotland in the late 1920s and 1930s but not so much after that although it was generally thought to be confined to Narcissus, although it was recorded on a specimen on Pancratium maritimum from Portugal.
J.C. David, 2004. IMI Descriptions of Fungi No.1609, CABI Bioscience, Egham, Surrey.
Botrytis infection on Paeonies'
High Risk periods
Damp, humid, wet-weather. Periods of prolonged plant-wetness.
Young plants usually begin to rot at soil level when they are 12-20 cm in height. Stems appear water-soaked, and the infection can be mistaken for a bacterial issue. Shoots wilt and fall over in a short period of time. Just above soil level, the stalk will be covered with a greyish fungal growth where conidia (fungal spores) are produced. Conidia are transported by wind, insects (attracted by rotting material), water splash and physical contact by staff to other leaves and buds. This causes further in leaf spotting and bud dieback. Small buds turn black and die. Larger buds turn brown and fail to produce a flower. If a plant is infected, most of the buds will more than likely fail.
Biology and lifecycle
Botrytis spp. are saprophytic (living on dead/decaying plant material) and parasitic (feeding off living material). First signs appear on the base of the stalks and the fungus over-winters on fallen plant debris. In the spring, as temperature increases ( Late March- early April) conidia form and spread to young, soft plant tissues. As the disease progresses, a gray-mold develops. The gray mold is made up of spores that are either wind-blown, splashed or transported by insects or touch by hands or tools onto new plants.
Prevent infection: Plant debris should be removed often destroyed, not composted. Wash hands after contact with infection. Spray tools periodically with a weak bleach solution (2%) or 70% ethanol solution. (Shop-bought bleaches are usually 5% in strength (check label), so dilute 1:2.5 i.e. 1 liter 5% sodium hypochlorite plus 1.5 liters water = 2.5 liters of 2% sodium hypochlorite)
Soil drainage: Peonies in well-drained soil have a reduced risk of botrytis formation. Do not overwater.
Location: Increased air circulation reduces disease risk. Space plants as widely as possible (2-3 feet is optimal but may not be practical in some situations). If possible, remove aging leaves from plants.
Use disease-free roots: If propagating, only take divisions only from healthy, disease-free plants.
Fungicide: Stem and bud Botrytis is the main disease issue and a programme for control will have to be implemented from emergence in the spring. The programme should be maintained throughout the growing season through harvest and should extend out to early Autumn. Rovral WG and Switch are systemic fungicides which have full label recommendations and can be used in a programme with protectants such as Amistar and Signum which have off label approval. Fungicides must be applied in advance of the disease as a protectant.
Quick video of disease check on Parlsey
Septoria on Parsley (mp4 video)