New approaches for the early detection of tree health pests and pathogens
Lead Research Organisation:
Science and Technology Facilities Council
Department Name: RAL Space
Abstract
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Technical Summary
This project has 6 work packages (WP), each based around a different combination of skills and expertise. For WP2-6 there will be a focus on a particular detection technology, while WP1 will provide the technical oversight needed for effective deployment of these different technologies, as summarised:
WP1:a participatory interdisciplinary approach will be used to evaluate the needs of stakeholders and to ensure that the technologies meet these. It will also focus on the requirements of effective technology deployment, using mathematical modeling to develop sampling strategies, to create network-based risk maps and economic assessments of cost-effectiveness. Further aspects of deployment will be analysed using social science approaches including end-user acceptability and the potential for using citizen science.
WP2:analytical chemistry approaches will be used to identify diagnostic volatile organic compounds produced by pests, pathogens and diseased hosts and to translate these onto commercial-available portable platforms for use by inspectors in the field.
WP3:multispectral imaging will be used to identify markers for the early detection of biotic/abiotic stress in plants. A prototype bioimaging camera will be constructed that can be used to validate this approach in the field.
WP4:will develop mathematical models of spore movement and investigate metagenomics for broad-spectrum surveillance utilizing existing monitoring networks e.g. pollen traps. In addition, a novel integrated cyclone-based trapping and molecular detection system will be developed and evaluated.
WP5:novel semiochemical attractants will be identified for a range of wood-boring beetle pests, incorporated into traps designed for efficient detection and then deployed in a risk-based network.
WP6:methods for sampling and rapid screening water for Phytopthora spp., including 'unknowns' will be developed and validated. This will combine high-throughput sequencing with a rapid bioinformatic.
WP1:a participatory interdisciplinary approach will be used to evaluate the needs of stakeholders and to ensure that the technologies meet these. It will also focus on the requirements of effective technology deployment, using mathematical modeling to develop sampling strategies, to create network-based risk maps and economic assessments of cost-effectiveness. Further aspects of deployment will be analysed using social science approaches including end-user acceptability and the potential for using citizen science.
WP2:analytical chemistry approaches will be used to identify diagnostic volatile organic compounds produced by pests, pathogens and diseased hosts and to translate these onto commercial-available portable platforms for use by inspectors in the field.
WP3:multispectral imaging will be used to identify markers for the early detection of biotic/abiotic stress in plants. A prototype bioimaging camera will be constructed that can be used to validate this approach in the field.
WP4:will develop mathematical models of spore movement and investigate metagenomics for broad-spectrum surveillance utilizing existing monitoring networks e.g. pollen traps. In addition, a novel integrated cyclone-based trapping and molecular detection system will be developed and evaluated.
WP5:novel semiochemical attractants will be identified for a range of wood-boring beetle pests, incorporated into traps designed for efficient detection and then deployed in a risk-based network.
WP6:methods for sampling and rapid screening water for Phytopthora spp., including 'unknowns' will be developed and validated. This will combine high-throughput sequencing with a rapid bioinformatic.
Planned Impact
The interdisciplinary design of this proposal will ensure maximum ongoing impact. Central to this is stakeholder engagement and our proposal has adopted a novel approach to facilliate this. Traditional approaches to developing new detection or diagnostic technologies have assumed the 'build it and they will come' approach; where the focus is on the technical aspects of the novel methodology, rather than the needs of end-users and the specifics of how it will be effectively deployed. This proposal reverses that by taking an inclusive view of what is required to achieve a successful outcome i.e. the deployment of a new technology that improves our biosecurity, and then co-designs technologies which fit that purpose. It achieves this by embracing an interdisciplinary approach and through establishing early engagement with stakeholders and end-users. Critical to this is the creation of a Learning Platform (Work package 1) which sits at the core of the project and cuts across the other technology-driven work packages (WPs 2-6). This platform will create communication channels, facilitate collaboration and knowledge sharing across work packages and stakeholder groups, actively disseminating project outcomes and enabling the pathways to impact. This will be delivered as a series of workshops; both cross-cutting (looking at the broader issues associated with detection and its successful deployment) and more focused (looking at specific issues associated with a particular technology and the contexts for its use). In addition to interacting with stakeholders (e.g. policy-makers, inspectors, NGOs, industry), this approach will use the breadth of expertise established within the consortium and assembled from across a wide-range of disciplines. This brings together 'technology-owners' (natural and physical scientists) with 'technology-evaluators' (mathematical and social sciences) to ensure that the best technological approaches are married with suitable sampling and risk-based deployment strategies, that they have stakeholder acceptability and offer genuine cost-efficiency benefits to public and private stakeholders alike.
In addition to the novel approach built into the project design, the effective delivery of impact will also benefit from a consortium which has an extremely strong track record of delivering translation science, to policy and industry alike. As government science agencies, the major remit for both Fera and Forest Research is to take science and technology and to translate it into policy-focused tools and evidence. This is a role they provide routinely for Defra and Forestry Commission, and their associated inspectors on the frontline in the field (e.g. Fera PHSI and FC Inspectors). In terms of delivery of technologies to end-users including industry, there is also a strong track record across the consortium in a whole range of contexts e.g. Worcester (horticulture industry diagnostics), JHI (potato industry diagnostics), Greenwich (pest trap deployment) and Fera (field diagnostics deployment). The integration of a number of SMEs within the consortium is another pathway to impact; providing a route for new technologies to be made freely available beyond the end of the project. Finally as plant and tree health sits within a European regulatory framework, the ability to engage with international partners and stakeholders is important. The consortium has a wealth of experience and contacts in this area, in particular through its central role in a range of related EU-funded projects e.g. Q-Detect (Fera-led), ISEFOR (Aberdeen-led) and PERMIT (FR-led). It will also build upon existing systems for knowledge exchange within our region, especially through the use of the European Plant Protection Organization (EPPO). By working with EPPO, using activities such as its workshops and conferences, we will be able to reach out to tree health practitioners across Europe; in many cases the real frontline for UK biosecurity.
In addition to the novel approach built into the project design, the effective delivery of impact will also benefit from a consortium which has an extremely strong track record of delivering translation science, to policy and industry alike. As government science agencies, the major remit for both Fera and Forest Research is to take science and technology and to translate it into policy-focused tools and evidence. This is a role they provide routinely for Defra and Forestry Commission, and their associated inspectors on the frontline in the field (e.g. Fera PHSI and FC Inspectors). In terms of delivery of technologies to end-users including industry, there is also a strong track record across the consortium in a whole range of contexts e.g. Worcester (horticulture industry diagnostics), JHI (potato industry diagnostics), Greenwich (pest trap deployment) and Fera (field diagnostics deployment). The integration of a number of SMEs within the consortium is another pathway to impact; providing a route for new technologies to be made freely available beyond the end of the project. Finally as plant and tree health sits within a European regulatory framework, the ability to engage with international partners and stakeholders is important. The consortium has a wealth of experience and contacts in this area, in particular through its central role in a range of related EU-funded projects e.g. Q-Detect (Fera-led), ISEFOR (Aberdeen-led) and PERMIT (FR-led). It will also build upon existing systems for knowledge exchange within our region, especially through the use of the European Plant Protection Organization (EPPO). By working with EPPO, using activities such as its workshops and conferences, we will be able to reach out to tree health practitioners across Europe; in many cases the real frontline for UK biosecurity.
Organisations
- Science and Technology Facilities Council (Lead Research Organisation)
- Economic and Social Research Council (Co-funder)
- Forestry Commission Scotland (Co-funder)
- Scottish Government (Co-funder)
- Department for Environment Food and Rural Affairs (Co-funder)
- Natural Environment Research Council (Co-funder)
- UNIVERSITY OF OXFORD (Collaboration)
- XMOS (Collaboration)
Description | We have developed a hyperspectral imaging camera system for the spectral analysis and the generation of a spectral library of disease dothistroma in Scots pine. We have developed a data set of key spectral features in artificially inoculated and naturally infected samples to determine stressor associated due to biotic or abiotic factors. These have been combined into a complete handheld system for in field analysis |
Exploitation Route | From this reserch we have been successful in two further research projects - ST/N006801/1 with Newcastle university and ST/P007066/1 |
Sectors | Aerospace Defence and Marine Agriculture Food and Drink Environment Manufacturing including Industrial Biotechology Culture Heritage Museums and Collections Security and Diplomacy |
Title | hyperspectral imaging camera |
Description | direct spectral imaging for the analysis of biotic and abiotic stresses in plants and leaf samples |
Type Of Material | Biological samples |
Provided To Others? | No |
Impact | The technology is under development |
Title | Controlled growth study |
Description | Collection of spectral data from needles collected from Pine saplings grown in a controlled environment. Some of the saplings were infected with Dothistroma, while others were left uninfected as controls. Data set can be used to see the changes with time as the disease progresses. The disease status of the needles was confirmed with PCR genetic testing. |
Type Of Material | Database/Collection of data |
Year Produced | 2016 |
Provided To Others? | No |
Impact | We have used this dataset to simulate hyperspectral data and to build models to predict the disease status of a Pine sapling. Also to get an idea of when spectral methods can be used to detect Dothistroma in a sample. |
Description | Detector manufacturer Ximea |
Organisation | XMOS |
Country | United Kingdom |
Sector | Private |
PI Contribution | We are jointly development of the control software and analysis of data from the detectors that we are using |
Collaborator Contribution | Iterative software and firmware upgrades based on our input to their detectors |
Impact | Knowledge exchange |
Start Year | 2015 |
Description | Development of Statistical Analysis Techniques |
Organisation | University of Oxford |
Department | Department of Statistics |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | We have been able to provide spectral and hyperspectral data from healthy and diseased trees under controlled conditions. As well as time to carry out statistical analyses to refine and develop robust statistical models |
Collaborator Contribution | Dr Dan Lund from Department of Statistics, University of Oxford has been able to provide his expert opinion on the best way to analyse our data to develop the robust models to predict tree health |
Impact | development of statistical models for the detection of tree health. Multi-disciplinary collaboration between statistics and chemistry/physics |
Start Year | 2015 |
Title | Hyperspectral imaging software |
Description | collecting and processing hyperspectral images from Ximea cameras using Labview |
Type Of Technology | Software |
Year Produced | 2017 |
Impact | we are able to collect and process the images from our Ximea hyperspectral cameras without having to use proprietary software |
Description | Interview with jouralist |
Form Of Engagement Activity | A magazine, newsletter or online publication |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Interview with jounalist from Imaging & Machine Vision Europe An article titled: How healthy are our woodlands? was published in Imaging & Machine Vision Europe in their December 2021/January 2022 issue. |
Year(s) Of Engagement Activity | 2021 |
URL | https://www.imveurope.com/feature/how-healthy-are-our-woodlands |
Description | Learning Labs |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Industry/Business |
Results and Impact | Visiting potential end stakeholders for which our research with hyperspectral cameras could be useful, gave us opportunities to discuss their problems and our research techniques |
Year(s) Of Engagement Activity | 2015 |
Description | User engagement meeting was set up and attended by the water companies that would use the final instrument |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Industry/Business |
Results and Impact | A meeting was set up between the project partners and water industries. |
Year(s) Of Engagement Activity | 2014,2015 |