Everybody talks about collaboration in plant health
Communication, communication, communication… was the key focus of Euphresco’s priorities for 2018. Euphresco was invited to contribute to discussions on a number of initiatives, including the organisation of a Global Surveillance System on emerging pests (GSS, led by the International Center for Tropical Agriculture) and on the development of a global plant health research roadmap to guide international collaboration (led by the International Bioeconomy Forum - IBF). The CPM13 side session ‘Collaboration with research organisations’ held at FAO Headquarters was an important landmark to advertise the benefits of international collaboration and to discuss global phytosanitary research coordination. While Euphresco is involved in strategic discussions, we do not forget communication at a more operational level with the scientific community and the policy makers that use research evidence. In 2019, Euphresco will continue to engage with all plant health research stakeholders, and research data will be at the centre of discussions.
Research that supports policy and policy that shapes research
Since its inception, Euphresco was shaped as a tool to support small and medium size research projects intended to produce knowledge and evidence to support policy. The modernization of the European regulatory approach to plant health will be an exceptional opportunity to build strong links between research and policy and to engage from the beginning with all the European and international stakeholders working on plant health. An article has recently been published in the EPPO Bulletin that provides an opinion on how Euphresco (research) activities could support the implementation of the new EU Plant Health Regulation.
Reliable and rapid diagnostic processes are essential to support official activities and to apply phytosanitary measures. It is then logical that diagnostics is an important component of Euphresco activities. The article ‘From transnational research collaboration to regional standards’ published in the BASE journal, describes the work undertaken on three important pests for the Mediterranean basin.
Transnational research collaboration to start soon
Each year, Euphresco members identify research priorities to be tackled by transnational collaboration. Nine research projects will start in the next months on the following topics:
2018-A-271: Rapid identification of plant-health related bacteria by MALDI-TOF mass spectrometry. Matrix assisted laser desorption/ionization - time of flight mass spectrometry (MALDI-TOF MS) has been a useful tool for rapid microbial identification in clinical microbiology. The potential of the technique has not been fully exploited in plant health, as reference spectra of bacteria are missing from commercial databases, thus limiting the application of this technology in plant pathology. The project aims to characterize, through MS, a number of plant-pathogenic bacteria, to produce reference spectra to support pest identification and to organise an interlaboratory comparison.
2018-A-275: Use of new diagnostic tools for the detection of Pantoea stewartii subsp. stewartii from plant and seeds.Pantoea stewartii subsp. stewartii and Pantoea stewartii subsp. indologenes are phylogenetically closely related bacteria and the molecular tools currently available cannot distinguish them. This is a problem for maize, where Pantoea stewartii subsp. stewartii causes the development of water-soaked lesions, while Pantoea stewartii subsp. indologenes is not virulent. Moreover, the available tests do not allow distinction between strains of Pantoea stewartii subsp. stewartii and therefore do not allow their geographic origin to be traced. The project aims to organise a test performance study for a selection of molecular tests on pure cultures and seeds.
2018-A-281: Sensitive detection of Diplocarpon mali in apple orchards via the combination of spore sampling and real-time PCR. The introduction and spread of D. mali in orchards may be unnoticed due to similarities with symptoms from infection by Alternaria, Phyllosticta or Venturia species. Surveys for this pest are difficult and detection methods are not very reliable, which is why the status of this organism in many countries is unknown. The project intends to develop and validate a protocol based on spore capture and real-time PCR that would allow fast and reliable detection of Diplocarpon mali.
2018-A-289: Plant Health Bioinformatics Network. The advances that High-Throughput Sequencing (HTS) technologies brings to genomics are closely linked to the developments in computational biology or bioinformatics, essential to the analysis and interpretation of the large amounts of genetic data generated. One of the main bottlenecks for the plant health sector to fully benefit from HTS is the lack of expertise on data analysis. The project aims to set the foundation for a network of plant health bioinformaticians and computational biologists in order to facilitate communication and knowledge sharing. Training material will be developed, and a proficiency test will be organized on (partially artificial) reference datasets suited for validation of data analysis pipelines.
2018-A-293: Phytosanitary risks of newly introduced crops. In recent years, a tendency towards cultivation of novel crops has been shown. Many of the ‘new’ crops have a long history of cultivation outside of Europe. Of particular interest are the tuber-forming crops that are of American origin. Although they are not part of the Solanaceae family, these tuber-forming plants share the same geographical origin as potato, and they might harbour known potato viruses or new viruses that might pose a phytosanitary risk to potato or other crops. The project aims to improve knowledge on the variety, origin and distribution of the newly introduced crops and to analyse plant propagation material for the presence of pests. This knowledge will support pest risk assessment.
2018-C-285: Tree health in urban environments: occurrence of organisms harmful to plants in urban greenery and the risk they represent to forestry, horticulture and agriculture. Urban greenery is an important part of city environment. However, from a plant health perspective, it is often a very fragile ecosystem, created by the introduction of new species or native plants of foreign origin into a very stressful environment. Urban greenery can represent an important entry point for invasive alien pests. The project aims to validate diagnostic tests and monitoring protocols and to collect data on the occurrence of pests associated with wood decay and necrosis in urban trees, using generic and pest-specific methods. A symposium will be organised to exchange knowledge across different disciplines including diagnostics and management.
2018-E-294: High Throughput Sequencing (HTS) (also called Next Generation Sequencing (NGS)) standards and best practices for regulatory applications. Advances in HTS technologies offer great potential for identification and characterization of pests and vectors. The complexity of this technology, combined with the need for exhaustive reference databases and high computing power to effectively analyze data for decision making purposes, strongly point toward the necessity for NPPOs to work collaboratively to define priorities, improve protocols and procedures where necessary, and define standard best practices. Benefiting from and in collaboration with other initiatives such as the COST Action DIVAS, the Euphresco project NGS-detect, the EU-funded project VALITEST, this project will contribute to define Standard Operating Procedures (SOPs) and best practices for the use of HTS using small RNAs, dsRNAs and ribosomal RNA depleted total RNA approaches for the diagnosis of viruses and viroids in a single test.
2018-E-274: Corythucha arcuata: Evaluation of the pest status in Central Europe and development of strategies to slow the spread. Since the first detection of the oak lace bug, Corythucha arcuata in Italy in 2000, this invasive Hemipteran pest has now spread to nearly a dozen other European countries. A recent pest risk assessment carried out in Croatia concludes that the infestation will reduce vigour of oaks and make them more prone to other pests and major economic damage is possible. The project aims to develop a better understanding of the impacts of C. arcuata in forest and urban settings. This will include the identification of the pathways for spread and the assessment of how well adults overwinter under bark.
2018-F-304: Spodoptera frugiperda: spread, establishment, damage potential and control measures for the EU. Native to the tropical and subtropical regions of the Americas, Spodoptera frugiperda (fall armyworm) geographical distribution has changed considerably in the last years with its introduction in the African continent. The moth is a strong flyer and it has been shown to regularly migrate to cooler region in the summer, so it can threaten the EPPO region. The project aims to make a review of the lessons learnt on the use of different control measures in various (African) countries in order to identify the most suitable (for the EPPO region) approaches. The cold hardiness ability and climate limit of S. frugiperda will be assessed.
Collaboration is possible for organisations proposing activities that fit within the Euphresco research framework and which will support their own participation in the projects. In-kind contributions and alignment of existing research activities allows organisations to join the Euphresco consortia without committing monetary funds. Any request for participation in the above-mentioned projects should be sent to the Euphresco coordinator.
National research priorities currently under discussion
Euphresco projects start as ideas, based on national priorities and proposed by each Euphresco member. Through discussions, exchange and networking, the suggestions become projects. New suggestions for 2019 have been submitted by Belgium, France, Italy, Mexico, the Netherlands, Slovenia and the United Kingdom. The list is available from the Euphresco website and expressions of interest can be sent to the Euphresco coordinator.
Open science
The funds through which all Euphresco activities are organised are public (national funds) and as such Euphresco has adopted from the beginning an open science approach, i.e. the most important research outputs are publicly accessible.
The Euphresco project ‘Use of barcoding from theory to practice’ (PRACTIBAR) was initiated in May 2017 to raise awareness on barcoding as a generic method for pest identification and to train experts of competent organisations. Given the success of the four interactive (theoretical and practical) trainings organised in Paris and Wageningen (NL), video-tutorials were posted on youtube and are available to anybody interested to know more about the method.
Recently, some interesting projects ended and final reports with recommendations for the policy makers were published on Zenodo.
Project 2016-F-186 Inventory of living collections of cyst and root knot nematodes in Europe and their maintenance techniques
Project 2016-I-226 The applications of remote sensing in plant health
Project 2016-G-228 Assessment and prioritisation of pathways
More open science: the Digital Research Object Portal
Governmental funding agencies require that publicly funded research is accessible (open access) and transparent (open data) to every citizen. The amount of (research) data that is made open is increasing and with it the number of specialised or multi-purpose databases to store the data and make it accessible for use and re-use. The higher the number of infrastructures, the more difficult is to track all data made open. The Digital Research Object Portal (DROP) has been developed, that works as a node, a unique entry point for user to retrieve open access documents (such as scientific articles, protocols, guidelines and international Standards) and research data in plant health that are stored in various infrastructures worldwide. The task is gigantic, this is why it was decided to tackle the problem by developing a pilot on a very important plant pest, Xylella fastidiosa. The prototype will be fed with data and documents produced in the framework of the EU-funded projects XF-ACTORS and POnTE. We are happy to collaborate with scientists (in addition to those in XF-ACTORS and POnTE) that are interested to have their research products referenced in the Portal. Opening data and making data re-usable improves the visibility of the scientist’s work and increases the number of citations. For any enquiry, please contact the DROP manager. If successful, the Portal will be maintained after the end of the XF-ACTORS project by Euphresco and its scope will gradually expand to cover all regulated and emerging pests.
Scientific Colloquium 'Plant Health at the Age of Metagenomics'
The advent of new technologies has changed views on microbial diversity. From a tool in the hands of a few academic wizards, metagenomics has evolved to provide answers to practical challenges in all sectors of human society, including agriculture. Metagenomic analyses provide one type of data: genomic sequences, and a lot of them. In fields such as virology, the number and diversity of viral sequences identified in metagenomic data far exceeds that of experimentally characterized virus isolates (Simmonds et al., 2017). Questions are raised on how to interpret and use findings, from the taxonomy of metagenomic-revealed new viruses to their biological significance. Looking closer into metagenomic data may provide (part of) the answer. The scientific colloquium ‘Plant Health at the Age of Metagenomics’, organised by EPPO and Euphresco on the 26th of September 2019, is an opportunity for research funders, policy makers and scientists to be informed about methodologies that have been used to infer important phenotypic properties from metagenomic plant health data. How easy is to mine the metagenome, looking for information to instruct phytosanitary measures? What tools are available? What other data is needed and is worth sharing in order to build a new framework for pest risk assessment, diagnostics and management? A preliminary agenda of the event can be found on the Euphresco website. There is no registration fee for the Colloquium. Pre-registration is possible by clicking here. More information can be obtained from the Euphresco coordinator.
Knowing more about Euphresco
Anybody interested in receiving information on the Euphresco activities can subscribe to the newsletter by completing the form on the Euphresco website. Those interested in participating in Euphresco projects can contact the Euphresco coordinator.
