New approaches for the early detection of tree health pests and pathogens

Lead Research Organisation: University of Worcester
Department Name: National Pollen and Aerobiology Res Unit


The UK's forests, woods and trees are under threat from a growing number of pests and diseases. Many of these threats are alien; historically not present in the UK and having been introduced from overseas. Some of these threats may reach the UK naturally i.e. as wind-borne spores from continental Europe; potentially one pathway for introduction of the disease ash die-back. The alternative and probably more common pathway of introduction is via human activity, especially trade; for example moving infected plants (another pathway identified for ash die-back) or through the shipping of goods associated with infested timber (as was the case with the recent introduction of the Asian long-horn beetle into Kent in packaging crates for stone). These cases clearly demonstrate that we need to do more to improve our nation's biosecurity and protect our plants and trees; both cultivated and in the wider environment.
In order to do this we need better methods for detecting these pests and diseases that allow us to find them earlier and with greater efficiency. By detecting these threats earlier you can minimize the damage they cause, by either preventing an outbreak occurring in the first place or by finding it early and then stopping it from establishing and spreading further. At present we rely on trained inspectors to find these alien pests and pathogens, mainly via visual inspections of imported plants and plant-based products e.g. timber. However, given the volume of inspections required, the finite amount of resource available and the huge practical challenges associated with these inspections, this task is extremely difficult and the efficiency of detection is low.
This project is designed to change that situation by providing better methods for detecting tree pests and pathogens; both moving in trade and in the environment. It will look at new technologies for the detecting changes in infected plants; using either 'sniffer' technology to identify differences in the volatile chemicals given off by diseased and healthy plants or imaging techniques that can detect changes beyond the range of human vision. It will also look at developing and designing novel traps for capturing insects and DNA-based detection approaches that look for air- and water-borne pathogens. This will include better approaches for trapping spores and then applying high-throughput sequencing methods that will allow the identification of not only known pathogens but also new ones too.
However, developing these new technologies is only part of the challenge. It is also necessary to make sure these new methods are fit-for-purpose and that they work in a way that meets the needs of those enforcing tree health regulations (e.g. government), those upon who those regulation impact (e.g. woodland owners and industry) and the end-users who would be expected to use these new tools (e.g. inspectors in the field). We will also examine what type of end-users could be involved; this could be trained government inspectors (the traditional approach) or alternatives such as those working in the industry, volunteers or even the general public. So looking to see if a so-called 'citizen science' approach could be used for any of these new approaches.
It is also important to ensure that these new approaches can be deployed effectively, for example at locations that pose the greatest risk, and in a way that offers the best cost-benefit (i.e. the best balance between cost of using the technology and the improvements it can offer in terms of better pest and disease detection). In order to do this, we will take an interdisciplinary approach; getting experts from many different fields e.g. biology, mathematics, chemistry, engineering, physics, economics and social science, to work together to come up with the best overall solution that works technically, economically and socially.

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.

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.


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Description Firstly. We have developed an automatic approach, global applicable, for mapping of trees using satellites: Trees that are host for pathogens and sources to aeroallergens. This approach is generic an may be applied to other ecosystems than woodlands. The apporach has been tested on the newest generation of satellites: Sentinel.

Secondly. We have demonstrated how you can use eDNA approaches the detect the biodiversity of spores in the air: both near and far away from specific sources, here including trees infested by ash dieback (H.fraxinea). We find, not surprisingly, that the biodiversity of the atmospheric mycobiome (the spores) reflect nearby sources. We also find small amounts of spores from the H.fraxinea or genetically closely relates spores in the air, in areas where we know that there are infested trees in the local environment and during the period when the spores are being released. This suggest that our sampling approach may be used to detect infestation level within a region and potentially as a way of identifying the most infested areas using atmospheric footprint modelling
Exploitation Route The method for tree mapping is published and public available. There has already been requests to use the source code for for this. The method also have a follow-up paper which demonstrates how the method can be applied on large scale. The study demonstrating the detection of the atmospheric mycobiome is almost ready for submission into a leading journal and part of this publication involves making the data public available.
Sectors Agriculture, Food and Drink,Environment,Healthcare,Government, Democracy and Justice

Description Current findings from the research supports a next generation of forecasting systems for bioaerosols in relation human health and plant health. Most important aspects are the species specific forecasts that may affect human health. We have also found new ways to detect fungal spores in relation to human health and global food security. Finally we have developed an approach for automatic mapping of specific ecosystems using satellites. Besides the scientific study this also involves specific model code, which has been requested and provided to other, as far away as India.
First Year Of Impact 2019
Sector Agriculture, Food and Drink,Digital/Communication/Information Technologies (including Software),Environment,Healthcare
Impact Types Societal,Economic

Description COST Action ADOPT, CA18226:|Name:overview
Amount € 714,000 (EUR)
Organisation European Cooperation in Science and Technology (COST) 
Sector Public
Country Belgium
Start 11/2019 
End 10/2023
Description PhD funding
Amount £40,000 (GBP)
Organisation University of Worcester 
Sector Academic/University
Country United Kingdom
Start 10/2017 
End 09/2020
Title Atmospheric concentrations of selected ascospores at the species level 
Description Temporal variations of spore concentrations in the air obtained with two sets of detection devices explaining variations in atmospheric transport and coupled with fruiting body phenology 
Type Of Material Database/Collection of data 
Provided To Others? No  
Impact Data are still being analysed for publication in 2017 
Title Components for WRF-Biochem 
Description A next generation atmospheric transport and transformation model for bioaerosols (BIO), chemistry (CHEM) and integrated weather and weather forecast (WRF). 
Type Of Material Computer model/algorithm 
Provided To Others? No  
Impact Still under development 
Description Final THPBI dissemination event, London, February 2018 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Presentation outlining progress of Early Detection project at BBSRC organised dissemination workshop, held in London in February 2018. Featured wide range of tree health stakeholders including funders, policy makers, researchers, industry and practitioners
Year(s) Of Engagement Activity 2018
Description LWEC TH&PBI projects mid term review workshop, October 2015 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other audiences
Results and Impact Engagement with workshop including all the LWEC TH&PBI projects, funders and stakeholders e.g. Defra PH policy, FC tree health. Gave two presentations about the 'New approaches for the early detection of tree health pests and pathogens' - an update on progress and future planning
Year(s) Of Engagement Activity 2015
Description lecturer on the Basic Aerobiological Course 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Dr. Skjoth participated as a lecturer on the Basic Aerobiological Course, Rzeszow 2016 by contributing on the modelling with HYSPLIT focusing on explaining detection of invasive species using airborne detection of pollen and spores.
Year(s) Of Engagement Activity 2015