Assessment of Dickeya and Pectobacterium spp. on vegetables and ornamentals (Soft rot)
Bibliographic record
Abstract
<em>Dickeya</em> and<em> Pectobacterium</em> belonging to the group of soft rot <em>Pectobacteriaceae</em> (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, <em>Zantedeschia, </em>hyacinth, <em>Dahlia</em>, <em>Chrysanthemum, Philodendron, Freesia, Saintpaulia, Iris, Aglaonema, Crocus, Campanula</em> and <em>Phalaenopsis</em>. 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 <em>Pectobacterium</em> and <em>Dickeya </em>species in different matrices. For this, a panel of reference strains has been compiled for <em>Dickeya </em>and <em>Pectobacterium</em> 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:<em> P. versatile, P. aquaticum, P. fontis </em>and <em>P. polonicum</em>. In potato, <em>P. brasiliense</em> became dominant as blackleg causing organism and has largely outcompeted <em>D. solani</em> in the last five years. In surface water in Europe, <em>D. zeae </em>was found to be the dominant SRP. In other continents, serious outbreaks of potato blackleg with other SRP has been reported, such as <em>D. dianthicola</em> in the USA and Australia. Various new SRP have been described, namely <em>P. punjabense</em>, <em>P. peruviense</em>, <em>P. polaris</em>, <em>D. lacustris</em> and <em>D. zantedeschia</em>. For the first time, <em>D. fangzhongdai</em> 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 <em>Pectobacterium</em> 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 <em>in vitro</em>. Similarly, stabilized silver nanostructures killed SRP. It was found that seed potato lots can differ in suppressiveness against <em>D. solani</em>. Indications were found that the microbiome in tuber tissue plays a role in this.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.001 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one teacher head, not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".