Assessment of Dickeya and Pectobacterium spp. on vegetables and ornamentals (Soft rot)
Wolf, J.M. van der; Bergsma-Vlami, M. ; Saddler, G. ; Hélias, V. ; Tsror, L. ; Yedida, Iris ; Pirhonen, M. ; Degefu, Yeshtila ; Tuomisto, J.T. ; Lojkowska, Ewa ; Li, Sean - \ 2020
Zenodo - 109 p.
Euphresco - Plant health - Dickeya - Pectobacterium - soft rot - vegetables - ornamentals - diagnostics - surveys - epidemiology - management
Dickeya and Pectobacterium belonging to the group of soft rot Pectobacteriaceae (SRP) are causing emerging problems in a wide range of vegetable and ornamental crops in Europe, including potato, carrot, cabbage, Chinese cabbage, celery, leek, pepper, parsley, Zantedeschia, hyacinth, Dahlia, Chrysanthemum, Philodendron, Freesia, Saintpaulia, Iris, Aglaonema, Crocus, Campanula and Phalaenopsis. The phytopathogens in both genera are genetically and phenotypically highly diverse. Disease problems in the different hosts are associated with the introduction of new variants or by spread of groups already present in Europe. Within this Euphresco project we aimed to identify and assess the risks of these new variants, and to develop management strategies, including reliable diagnostic methods to prevent introductions and further spread of SRP. To reach our goals, meetings were organized and collaborations were established with specialists worldwide. All information on meetings, protocols and activities of the Euphresco group are published on the Dickeya/Pectobacterium website, conveyed by the James Hutton Institute in Invergowrie (Scotland) (https://engage.hutton.ac.uk, contact person Dr I. Toth/Dr J. Fairly).
During the project, 1.5 days meetings were held in 2015 in Gdansk (Poland), in 2016 in Helsinki (Finland), in 2017 in Edinburgh (Scotland) and in 2018 in Emmeloord (The Netherlands). Meetings were attended by an average of 30 participants from organizations in EU member states, North- and Latin America, Africa, Asia and Australia.
One project’s objective was to develop methods for the detection and identification of Pectobacterium and Dickeya species in different matrices. For this, a panel of reference strains has been compiled for Dickeya and Pectobacterium species. Most strains have been deposited in international collections. For most strains also whole genome sequence data are available. During the course of this project, several diagnostic tests were developed and evaluated, often based on the TaqMan technology.
In several countries, surveys in potato and ornamental crops were conducted, but also in other matrices of the potato ecosystem, including water used for irrigation. In addition, new taxonomic groups that have been identified, are now new species including: P. versatile, P. aquaticum, P. fontis and P. polonicum. In potato, P. brasiliense became dominant as blackleg causing organism and has largely outcompeted D. solani in the last five years. In surface water in Europe, D. zeae was found to be the dominant SRP. In other continents, serious outbreaks of potato blackleg with other SRP has been reported, such as D. dianthicola in the USA and Australia. Various new SRP have been described, namely P. punjabense, P. peruviense, P. polaris, D. lacustris and D. zantedeschia. For the first time, D. fangzhongdai was described in Phalaenopsis. Not all species can cause potato blackleg.
Studies on various virulence factors were conducted for SRP, such as on chemoreceptors, small phenolic plant compounds interacting with signal molecules of Pectobacterium involved in the quorum sensing mechanism of the pathogen. A Tn-seq approach was developed and used to identify new virulence factors.
Information was exchanged on disease management strategies which include cultivation practices, resistance breeding, hygiene and the use of (bio-) control agents. A strict hygiene and an intensive monitoring of seed lots was found to be associated with a significant reduction of infections with blackleg causing SRP. A phage therapy has been developed to protect (seed) potato tubers against soft rot during storage. Various bacteriophages and bacterial antagonists were characterized and some evaluated for control of potato soft rot and/or blackleg. Steam treatments for seed tubers were found to decrease the blackleg incidence. Cold plasma treatment was found to kill SRP grown in vitro. Similarly, stabilized silver nanostructures killed SRP. It was found that seed potato lots can differ in suppressiveness against D. solani. Indications were found that the microbiome in tuber tissue plays a role in this.
Salicylic acid can reduce infection symptoms caused by Dickeya solani in tissue culture grown potato (Solanum tuberosum L.) plants
Czajkowski, Robert ; Wolf, Jan M. van der; Krolicka, Aleksandra ; Ozymko, Zofia ; Narajczyk, Magdalena ; Kaczynska, Natalia ; Lojkowska, Ewa - \ 2015
European Journal of Plant Pathology 141 (2015)3. - ISSN 0929-1873 - p. 545 - 558.
Biological control - Blackleg - Dose effect - Elicitation - Erwinia chrysanthemi - Induced resistance - SAR
The potential for control of Dickeya solani infections in potato by elicitation of in vitro grown potato plants with salicylic acid (SA) was investigated by selective plating and confocal laser scanning macroscopy (CLSM). In replicated experiments potato plants grown on medium supplemented with 25 or 50 μM of SA were evaluated for the phytotoxic effects. Potato plants grown on medium supplemented with SA and inoculated with GFP-tagged D. solani were investigated for blackleg development and colonization of potato plants by the bacteria. Three days after inoculation, colonization of roots by D. solani was observed in 100 % control plants grown on medium without SA but not in plants grown on medium supplemented with 50 μM SA. After 14 days, 100 % of control plants showed severe disease symptoms, whereas plants grown on medium supplemented with 50 μM SA and inoculated with bacteria did not express any symptoms. After 14 days bacteria were found inside 100 % stems of control plants in densities of ca. 103–104 cfu g−1 and inside ca. 10–15 % stems of plants treated with 50 μM SA in densities similar to these in the control plants. The GFP-tagged bacteria were macroscopically detected on the surface of the roots of control plants but not on the surface of the plants treated with 50 μM SA 14 days after inoculation. The implications of SA treatments on plant fitness and disease development are discussed.
Detection, identification and differentiation of Pectobacterium and Dickeya species causing potato blackleg and tuber soft rot: a review
Czajkowski, R.L. ; Pérombelon, M.C.M. ; Jafra, S. ; Lojkowska, E. ; Potrykus, M. ; Wolf, J.M. van der; Sledz, W. - \ 2015
Annals of Applied Biology 166 (2015)1. - ISSN 0003-4746 - p. 18 - 38.
carotovora subsp atroseptica - fragment-length-polymorphism - plant-pathogenic bacteria - erwinia-chrysanthemi strains - polymerase-chain-reaction - 16s ribosomal-rna - monoclonal-antibodies - genetic diversity - ssp-carotovorum - peel extracts
The soft rot Enterobacteriaceae (SRE) Pectobacterium and Dickeya species (formerly classified as pectinolytic Erwinia spp.) cause important diseases on potato and other arable and horticultural crops. They may affect the growing potato plant causing blackleg and are responsible for tuber soft rot in storage thereby reducing yield and quality. Efficient and cost-effective detection and identification methods are essential to investigate the ecology and pathogenesis of the SRE as well as in seed certification programmes. The aim of this review was to collect all existing information on methods available for SRE detection. The review reports on the sampling and preparation of plant material for testing and on over thirty methods to detect, identify and differentiate the soft rot and blackleg causing bacteria to species and subspecies level. These include methods based on biochemical characters, serology, molecular techniques which rely on DNA sequence amplification as well as several less-investigated ones.
Dickeya solani sp. nov., a pectinolytic plant pathogenic bacterium isolated from potato (Solanum tuberosum)
Wolf, J.M. van der; Nijhuis, E.H. ; Kowalewska, M.J. ; Saddler, G.S. ; Parkinson, N. ; Elphinstone, J.G. ; Pritchard, L. ; Toth, I.K. ; Lojkowska, E. ; Potrykus, M. ; Waleron, M. ; Vos, P. de; Cleenwerck, I. ; Pirhonen, M. ; Garlant, L. ; Hélias, V. ; Pothier, J.F. ; Pflüger, V. ; Duffy, B. ; Tsror, L. ; Manulis, S. - \ 2014
International Journal of Systematic and Evolutionary Microbiology 64 (2014)Pt. 3. - ISSN 1466-5026 - p. 768 - 774.
strains - identification - pseudomallei - chrysanthemi - relatedness - clonality - mallei - clade - genus
Pectinolytic bacteria were recently isolated from diseased potato plants exhibiting blackleg and slow wilt symptoms found in a number of European countries and Israel. These Gram-negative, motile, rods were identified as belonging to the genus Dickeya, previously the Pectobacterium chrysanthemi complex (Erwinia chrysanthemi), on the basis of a positive PCR reaction with pelADE primers, 16S rDNA sequence analyis, fatty acid methyl esterase analysis, the production of phosphatases and the ability to produce indole and acids from a-methyl glucoside. Differential physiological assays used previously to differentiate between strains of E. chrysanthemi, showed that these isolates belonged to biovar 3. Eight of the isolates, seven from potato and one from hyacinth, were analysed together with 21 reference strains representing all currently recognised taxa within the genus Dickeya. The new isolates formed a distinct genetic clade in multilocus sequence analysis (MLSA) using concatenated sequences of the intergenic spacer (IGS), as well as genes dnaX, recA, dnaN, fusA, gapA, purA, rplB, rpoS and gyrA. Characterization by whole-cell MALDI-TOF mass spectrometry, pulsed field gel electrophoresis after digestion of whole genome DNA with rare cutting restriction enzymes, average nucleotide identity analysis and DNA-DNA hybridization studies, showed that although related to D. dadantii, these isolates represent a novel species within the genus Dickeya, for which the name Dickeya solani sp. nov. (type strain IPO 2222T =LMG25993T =NCPPB4479T) is proposed
Multiplex detection and identification of bacterial pathogens causing potato blackleg and soft rot in Europe, using padlock probes
Slawiak, M. ; Doorn, R. van; Szemes, M. ; Speksnijder, A.G.C.L. ; Waleron, M. ; Wolf, J.M. van der; Lojkowska, E. ; Schoen, C.D. - \ 2013
Annals of Applied Biology 163 (2013)3. - ISSN 0003-4746 - p. 378 - 393.
fragment-length-polymorphism - carotovora ssp-atroseptica - erwinia-carotovora - pectobacterium-carotovorum - sp-nov. - oligonucleotide-microarray - dickeya-chrysanthemi - genetic diversity - pectin lyase - new-zealand
The objective of this study was to develop a multiplex detection and identification protocol for bacterial soft rot coliforms, namely Pectobacterium wasabiae (Pw), Pectobacterium atrosepticum (Pba) and Dickeya spp., responsible for potato blackleg and tuber soft rot. The procedures were derived from the phylogenetic relationships of these and other Enterobacteriaceae based on recA sequences. The group of Pw strains was highly homogeneous and could be distinguished from the other species. A ligation-based method for detection of Pw was developed. Five padlock probes (PLPs) were designed, targeting recA sequences to identify the Pw, Pba or Dickeya spp., whereas a sixth probe recognised recA sequences of all soft rot coliforms including Pectobacterium carotovorum subsp. carotovorum (Pcc). Two PLP-based applications were developed: one using real-time PCR and one using universal microarrays. Assay sensitivity and specificity were demonstrated using 71 strains of Pw, Pcc, Pba and Dickeya spp. Both multiplex methods can be potentially used for seed testing and in ecological studies, but further validation is required
Dickeya species: an emerging problem for potato production in Europe
Toth, I.K. ; Wolf, J.M. van der; Saddler, G. ; Lojkowska, E. ; Hélias, V. ; Pirhonen, M. ; Tsror, L. ; Elphinstone, J.G. - \ 2011
Plant Pathology 60 (2011)3. - ISSN 0032-0862 - p. 385 - 399.
soft-rot erwinias - carotovora subsp atroseptica - polymerase-chain-reaction - biovar 3 - temperature tolerances - rapid identification - chrysanthemi strains - pectate medium - 1st report - pcr
Dickeya species (formerly Erwinia chrysanthemi) cause diseases on numerous crop and ornamental plants world-wide. Dickeya spp. (probably D. dianthicola) were first reported on potato in the Netherlands in the 1970s and have since been detected in many other European countries. However, since 2004–5 a new pathogen, with the proposed name ‘D. solani’, has been spreading across Europe via trade in seed tubers and is causing increasing economic losses. Although disease symptoms are often indistinguishable from those of the more established blackleg pathogen Pectobacterium spp., Dickeya spp. can initiate disease from lower inoculum levels, have a greater ability to spread through the plant’s vascular tissue, are considerably more aggressive, and have higher optimal temperatures for disease development (the latter potentially leading to increased disease problems as Europe’s climate warms). However, they also appear to be less hardy than Pectobacterium spp. in soil and other environments outside the plant. Scotland is currently the only country in Europe to enforce zero tolerance for Dickeya spp. in its potato crop in an attempt to keep its seed tuber industry free from disease. However, there are a number of other ways to control the disease, including seed tuber certification, on-farm methods and the use of diagnostics. For diagnostics, new genomics-based approaches are now being employed to develop D. dianthicola- and ‘D. solani’-specific PCR-based tests for rapid detection and identification. It is hoped that these diagnostics, together with other aspects of ongoing research, will provide invaluable tools and information for controlling this serious threat to potato production