Isolation, Detection and Characterization of Pectobacterium and Dickeya Species

Wolf, J.M. van der; Cahill, Greig; Gijsegem, Frédérique Van; Hélias, Valerie; Humphris, Sonia; Li, Xiang; Łojkowska, Ewa; Pritchard, Leighton

doi:10.1007/978-3-030-61459-1_5

Cited by 10 publications

(10 citation statements)

References 101 publications

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“…Several species-specific tools were developed for identifying and quantifying Dickeya and Pectobacterium pathogen species in plant samples, as well as for characterizing the collected bacterial isolates [ 11 ]. In this work, we mainly used a unique marker gapA for characterizing all the collected isolates from blackleg lesions.…”

Section: Discussionmentioning

confidence: 99%

“…From this knowledge in taxonomy and genomics, different molecular tools have been developed for pathogen diagnosis, hence for identifying and discarding the contaminated plant materials from the production process of certified seed potato tubers [ 11 ]. For instance, in France, a quality scheme was set up along production of tuber seeds from the in vitro propagation of potato varieties until tuber harvest in the field.…”

Section: Introductionmentioning

confidence: 99%

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Efficacy of Soft-Rot Disease Biocontrol Agents in the Inhibition of Production Field Pathogen Isolates

Cigna¹,

Robic

Dewaegeneire³

et al. 2023

Microorganisms

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The Dickeya and Pectobacterium bacterial species cause blackleg and soft-rot diseases on potato plants and tubers. Prophylactic actions are essential to conserve a high quality of seed potato tubers. Biocontrol approaches are emerging, but we need to know how efficient biocontrol agents are when facing the natural diversity of pathogens. In this work, we sampled 16 production fields, which were excluded from the seed tuber certification scheme, as well as seven experimental parcels, which were planted with seed tubers from those production fields. We collected and characterized 669 Dickeya and Pectobacterium isolates, all characterized using nucleotide sequence of the gapA gene. This deep sampling effort highlighted eleven Dickeya and Pectobacterium species, including four dominant species namely D. solani, D. dianthicola, P. atrosepticum and P. parmentieri. Variations in the relative abundance of pathogens revealed different diversity patterns at a field or parcel level. The Dickeya-enriched patterns were maintained in parcels planted with rejected seed tubers, suggesting a vertical transmission of the pathogen consortium. Then, we retained 41 isolates representing the observed species diversity of pathogens and we tested each of them against six biocontrol agents. From this work, we confirmed the importance of prophylactic actions to discard contaminated seed tubers. We also identified a couple of biocontrol agents of the Pseudomonas genus that were efficient against a wide range of pathogen species.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Efficacy of Soft-Rot Disease Biocontrol Agents in the Inhibition of Production Field Pathogen Isolates

Cigna¹,

Robic

Dewaegeneire³

et al. 2023

Microorganisms

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“…The practice of rogueing (the removal of diseased plants) of seed potatoes by farmers is recommended by the seed certification procedures as a key component in maintaining the health status of the crop. However, according to Van der Wolf et al (2021b), the efficacy of this method in controlling the spread of SRP bacteria is controversial since it does not always ensure sanitization of the entire crop (Bonde 1950;Pérombelon and Hyman 1992) as the tubers of the diseased plant will not be removed and still maintain an infection source. Boomsma et al (2013) tested the efficacy of rogueing experimentally in the Netherlands without conclusive results.…”

Section: Discussionmentioning

confidence: 99%

“…There are no potato cultivars available which are resistant to SRP, and no control agents are registered for treatment of plant material. Disease management in the European Union is predominantly based on the obligatory use of seed potatoes in which the disease is absent or only present in a low incidence (Van der Wolf et al 2021b). Currently, seed testing and certification is solely based on field inspections.…”

Section: Introductionmentioning

confidence: 99%

Determining the Spatial Pattern of Blackleg Diseased Potato Plants in the Field and Simulated Post-Harvest Tuber Infections in Potato Crates

2021

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Experiments were carried out in 2012 and 2013 to answer two basic questions in the testing of potato blackleg causing agents before and after harvest. Firstly, what is the spatial distribution of symptomatic plants in the field. Secondly, what is the distribution of infected tubers over the crates and the resulting detection probability using the standard method of collecting 200 tubers from the top crates in storage. In both years, ten farmers were equipped with a global positioning system (Garmin GPSMAP 62) and asked to register the position of blackleg diseased plants every time they scouted their potato lot for diseases. To answer the second question, potatoes marked with four nails (only visible internally after harvest) and potatoes with a different skin colour were added to one-hectare (ha) fields of seed potatoes in different patterns of aggregation ranging from random, to aggregated distribution, up to one big hotspot prior to harvest. The invisibly marked tubers were used for the unbiased collection of twenty 200-tuber samples from the storage crates, while the coloured skin tubers were used to ascertain, when the potatoes were graded, the distribution of ‘infected’ potatoes over the storage crates. The experiment was carried out with 0.05 and 0.1% disease incidence, in 2012 and 2013, respectively. Twenty two out of 26 fields proved to have a random pattern of diseased plants at harvest, which indicates that the blackleg diseased plants came into the field as infected seed potatoes. Two of the four aggregated patterns detected, started out as random distributions but became aggregated later in time, indicating spread in the field. A random spatial pattern in the field at harvest proved to result in a uniform distribution of infected tubers in the crates and, consequently, sampling of only the top crates for the 200-tuber sample does not introduce any bias. Fifty percent of the infected farmer lots were detected by the Nederlandse Algemene Keuringsdienst inspectors performing their official field surveys, which was a better performance than the 18% detection obtained by the standard 200-tuber sampling method. Only 6 out of 80 samples from the ‘infected’ lots with 0.05% disease incidence level, and 22 out of 80 samples at the 0.1% disease incidence level were detected by the latter method. It was concluded that intensifying the field survey would be cheaper and more successful than enlarging the tuber sample size to increase the probability for detection of infected seed lots.

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“…Many PCR-based methods have already been developed for generalised and species-specific detection of SRP (reviewed in [ 16 , 17 ]). The accumulation of data on bacterial genomics and taxonomic redistributions has encouraged the design of an updated method for the specific diagnosis of newly established SRP species, particularly Ppa.…”

Section: Introductionmentioning

confidence: 99%

Quantitative Real-Time PCR Assay for the Detection of Pectobacterium parmentieri, a Causal Agent of Potato Soft Rot

Lukianova

Evseev

Stakheev

et al. 2021

Plants

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Pectobacterium parmentieri is a plant-pathogenic bacterium, recently attributed as a separate species, which infects potatoes, causing soft rot in tubers. The distribution of P. parmentieri seems to be global, although the bacterium tends to be accommodated to moderate climates. Fast and accurate detection systems for this pathogen are needed to study its biology and to identify latent infection in potatoes and other plant hosts. The current paper reports on the development of a specific and sensitive detection protocol based on a real-time PCR with a TaqMan probe for P. parmentieri, and its evaluation. In sensitivity assays, the detection threshold of this protocol was 102 cfu/mL on pure bacterial cultures and 102–103 cfu/mL on plant material. The specificity of the protocol was evaluated against P. parmentieri and more than 100 strains of potato-associated species of Pectobacterium and Dickeya. No cross-reaction with the non-target bacterial species, or loss of sensitivity, was observed. This specific and sensitive diagnostic tool may reveal a wider distribution and host range for P. parmentieri and will expand knowledge of the life cycle and environmental preferences of this pathogen.

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Isolation, Detection and Characterization of Pectobacterium and Dickeya Species

Cited by 10 publications

References 101 publications

Efficacy of Soft-Rot Disease Biocontrol Agents in the Inhibition of Production Field Pathogen Isolates

Efficacy of Soft-Rot Disease Biocontrol Agents in the Inhibition of Production Field Pathogen Isolates

Determining the Spatial Pattern of Blackleg Diseased Potato Plants in the Field and Simulated Post-Harvest Tuber Infections in Potato Crates

Quantitative Real-Time PCR Assay for the Detection of Pectobacterium parmentieri, a Causal Agent of Potato Soft Rot

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