Global threats from Phytophthora spp.; understanding drivers of emergence and opportunities for mitigation through nursery best practice
Lead Research Organisation:
Forest Research
Department Name: Centre for Ecosystems Soc and Biosecur
Abstract
This project will address the risks to UK tree species from Phytophthora introduction and spread by; i) examining the current distribution and diversity of Phytophthoras in UK plant nursery systems, ii) providing the evidence base to refine nursery 'best practice' criteria for a UK-wide voluntary nursery accreditation scheme, iii) identifying those Phytophthora species not currently present in the UK but which pose the greatest threat to our ecosystems based on their biological traits and environmental profiles, iv) identifying key international pathways for Phytophthora spread and national points for biosecurity focus and v) understanding better the risk of genetic interaction occurring when Phytophthoras meet, resulting in new aggressive types.
To achieve these objectives, the distribution and diversity of Phytophthora species in water and plant samples collected from different UK plant nursery management systems, including those locations considered to be high risk in terms of importing new Phytophthoras, will be studied using state-of-the-art DNA sequencing technology. Water samples from streams and ponds in amenity environments will also be collected to investigate the wider distribution of nursery-associated Phytophthoras. This work will identify nursery practices resulting in the highest density and diversity of Phytophthora pathogens and the highest probability of onward spread into woodland or other natural ecosystems. These data will provide evidence to guide the development of a UK-wide voluntary nursery accreditation scheme. Nurseries signing up to the scheme will adhere to a set of 'best practice' criteria designed to reduce the risks of importation and dissemination of Phytophthoras. Feasibility assessments will involve consultation with nursery managers, consumers and other stakeholders in order to identify economic and social opportunities and barriers, and attitudes towards implementation of such a scheme. We will also explore options to promote the visibility and legitimacy of the accreditation scheme to consumers such that there is an added advantage for nurseries to take part.
Identifying future global Phytophthora threats and potential routes of entry will be essential in refining nursery 'best practice' and other national biosecurity measures. To do this, data on current known global distribution of Phytophthoras infecting woody species and biological characteristics that may affect establishment will be collated from databases and national surveys conducted in a broad range of countries. Models will identify those species occurring in locations resembling the UK's climate and ecosystems and those species that are ecologically similar to Phytophthoras that have established in Europe, strengthening the evidence base for inclusion of pathogens in the UK Plant Health Risk Register. We will also look at the pathways of international trade and tourism and the risks of new Phytophthora introductions via these routes, identifying national focus points for biosecurity based on a raised risk that new Phytophthoras will arrive at these locations. Pathway analyses will be used to inform nursery managers and accreditation scheme criteria of the highest risk trade practices.
Current practices are increasing the diversity of co-existing Phytophthoras in the environment, yet we have little understanding of the potential for new aggressive Phytophthoras to arise through hybridisation or other mechanisms of genetic exchange when new species meet. Whole genome sequences of Phytophthora species will be examined to determine the extent to which genetic exchange has occurred among Phytophthoras and related organisms, and how this might have enabled these pathogens to adapt on to tree species, change virulence or host range. This work will enhance our fundamental understanding of pathogen evolution.
To achieve these objectives, the distribution and diversity of Phytophthora species in water and plant samples collected from different UK plant nursery management systems, including those locations considered to be high risk in terms of importing new Phytophthoras, will be studied using state-of-the-art DNA sequencing technology. Water samples from streams and ponds in amenity environments will also be collected to investigate the wider distribution of nursery-associated Phytophthoras. This work will identify nursery practices resulting in the highest density and diversity of Phytophthora pathogens and the highest probability of onward spread into woodland or other natural ecosystems. These data will provide evidence to guide the development of a UK-wide voluntary nursery accreditation scheme. Nurseries signing up to the scheme will adhere to a set of 'best practice' criteria designed to reduce the risks of importation and dissemination of Phytophthoras. Feasibility assessments will involve consultation with nursery managers, consumers and other stakeholders in order to identify economic and social opportunities and barriers, and attitudes towards implementation of such a scheme. We will also explore options to promote the visibility and legitimacy of the accreditation scheme to consumers such that there is an added advantage for nurseries to take part.
Identifying future global Phytophthora threats and potential routes of entry will be essential in refining nursery 'best practice' and other national biosecurity measures. To do this, data on current known global distribution of Phytophthoras infecting woody species and biological characteristics that may affect establishment will be collated from databases and national surveys conducted in a broad range of countries. Models will identify those species occurring in locations resembling the UK's climate and ecosystems and those species that are ecologically similar to Phytophthoras that have established in Europe, strengthening the evidence base for inclusion of pathogens in the UK Plant Health Risk Register. We will also look at the pathways of international trade and tourism and the risks of new Phytophthora introductions via these routes, identifying national focus points for biosecurity based on a raised risk that new Phytophthoras will arrive at these locations. Pathway analyses will be used to inform nursery managers and accreditation scheme criteria of the highest risk trade practices.
Current practices are increasing the diversity of co-existing Phytophthoras in the environment, yet we have little understanding of the potential for new aggressive Phytophthoras to arise through hybridisation or other mechanisms of genetic exchange when new species meet. Whole genome sequences of Phytophthora species will be examined to determine the extent to which genetic exchange has occurred among Phytophthoras and related organisms, and how this might have enabled these pathogens to adapt on to tree species, change virulence or host range. This work will enhance our fundamental understanding of pathogen evolution.
Technical Summary
This project will address risks of introduction and spread of Phytophthora spp. in trade by examining the distribution of Phytophthoras in water and plant samples collected from different UK plant nursery management systems using metabarcoding techniques. This work will identify nursery practices resulting in the highest density and diversity of Phytophthora pathogens, providing baseline data to facilitate the refinement of nursery 'best practice' protocols. Stakeholder and consumer attitudes to implementation of a UK-wide nursery 'best practice' accreditation scheme and what this should look like will be identified through surveys, interviews and other engagement processes. A cost-benefit analysis of options to change nursery practice and infrastructure required to meet best practice standards will be conducted from different perspectives. To identify future global Phytophthora threats and potential routes of entry into the UK, thus informing nursery best practice and national biosecurity strategies, data will be collated on the distribution, diversity, ecological traits and impacts of Phytophthora species worldwide. Ecological modelling will identify those species most at risk of establishing in UK ecosystems and analyses of trade, unregulated imports and the role of tourism in spreading infested material will identify pathways linking Phytophthora 'source' regions to the UK. To understand better the extent to which hybridisation and other mechan
Planned Impact
WP2 and WP5 provide a very strong framework for dialogue and collaboration between researchers, industry stakeholders, policy makers and consumers throughout the project. Three multi-stakeholder workshops (at project start, middle and end) will aim to build trust and cooperation between industry, Plant Health policy teams and researchers. The project will also add in feedback (twice annually) to the Defra Tree and Plant Health Stakeholder/Policy Group. Two-way public outreach activities will include face-to-face engagement with gardening groups and landscaping companies, consumer attitude surveys, the Opal Network and involving online UK gardening forums. The project's Expert Advisory Panel (EAP) will include policy, regulatory and industry representatives (eg HTA, Woodland Trust), providing further links to relevant initiatives. At the project end, a meeting will be held with members of the UK Tree Health and Plant Biosecurity Expert Taskforce and UK Chief Plant Health Officer on the results of ranking Phytophthora risks, trade pathways and Phytophthora diversity in UK nurseries. Project information will be disseminated at conferences, meetings, seminars and workshops ongoing in each consortium member's active KT programmes, and linking to international projects (e.g. LIFE+ ObservaTREE project and COST Action FP1401). These will reach a broad range of forestry, horticulture and science organisations (including HTA, National Association of Tree Officers, Aboricultural Association, Woodland Trust, IUFRO). A particular strength of this consortium is its ability to fast-track new information into both academic and industry training. Project findings will be published in high quality academic and trade journals (i.e. Plant Pathology and Genomics journals, Horticulture and Nursery Trade magazines). Data will be made available to all relevant stakeholders through open access publication, including a dedicated project wiki/i-share site, CEH Information Gateway, Genbank, Phytophthoradb. In yr3 a collaborative framework for continued development of the accreditation scheme will be established, thus ensuring project impact beyond the three year grant duration.
Organisations
- Forest Research (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)
- Murdoch University (Collaboration)
- Scion (Collaboration)
- Fera Science Limited (Collaboration)
Publications
Barwell LJ
(2021)
Evolutionary trait-based approaches for predicting future global impacts of plant pathogens in the genus Phytophthora.
in The Journal of applied ecology
Dunn M
(2019)
Buying better biosecurity: Plant-buying behaviour and the implications for an accreditation scheme in the horticultural sector
in PLANTS, PEOPLE, PLANET
| Description | The multidisciplinary 'Phyto-threats' project was initiated in 2016 to address the increasing risks to UK forest and woodland ecosystems from trade-disseminated Phytophthora as implicated in the recent upsurge of Phytophthora diseases in the UK and the establishment and spread of these pathogens in the wider UK environment in diseased propagation material. The project focused on understanding the drivers of emergence of Phytophthora species and opportunities for mitigation by; i) examining the distribution and diversity of Phytophthoras in different UK plant nursery management systems to identify high risk nursery practices, ii) conducting feasibility assessments with nursery managers, consumers and other stakeholders to identify economic and social opportunities and barriers to implementation of best practice, iii) identifying future global Phytophthora threats through modelling biological traits and environmental profiles, and iv) analysing genome sequences of Phytophthora species to gain genetic insights into what makes a species virulent. Diversity of Phytophthora in UK plant nurseries A major component of the Phyto-threats project was to address the risk of Phytophthora spread through nursery practices. Over the last three years, the project team together with Plant Health inspectors collected over 4000 water and root samples from plant nurseries located across Britain. These included fifteen partner nurseries intensively sampled in a 'fine-scale' survey and a further 118 nurseries sampled as part of a 'broad-scale' survey. Samples were tested for the presence of Phytophthora DNA using a state-of-the-art metabarcoding approach. Approximately 50% of all samples were positive for Phytophthora, with 51 Phytophthora species identified so far across all samples including quarantine regulated pathogens and species not previously reported in the UK. Some of the most diverse Phytophthora assemblages were found in river water used to irrigate plants and in open reservoir irrigation sources, as well as in puddles which formed around plant stock, confirming that effective water treatment and good drainage are essential components of Phytophthora management. Phytophthoras were also detected in diseased shelterbelt or landscape trees present at some nurseries, acting as additional inoculum reservoirs. Trees growing in the immediate environment of each nursery should therefore be included in routine Statutory Plant Health inspections. Another issue highlighted by the survey is that, in some cases, native plant stock being raised from seed collected from ecologically sensitive sites and destined for planting back out at these sites were found to be harbouring damaging Phytophthora species. These findings have considerable implications for the proposed massive expansion of UK woodland and have led to discussions on new guidance documentation for woodland restoration. Feasibility of accreditation and introduction of nursery best practice to mitigate disease risks Data on Phytophthora diversity are being related to nursery management practice and this evidence will inform the Plant Health Management Standard being developed as part of the new 'Plant Healthy' accreditation scheme which targets producers and consumers across the UK plant supply chain. Social and economic scientists have generated information on the feasibility of accreditation and what it should look like, based on a survey of 1500 plant buying members of the general public and collated perspectives from nurseries, retailers (including garden centres), landscape architects and designers following 153 survey responses and 37 interviews. One of the key findings was the need for engagement on plant health risks to secure collaboration from all sectors. The public are driven by quality rather than biosecurity practices so quality should be emphasised to promote an accreditation scheme. Many nurseries will have to improve their biosecurity practices to become accredited, however, few nurseries are willing/able to incur substantial cost to become accredited. A requirement for large landscape contracts to use stock from accredited growers would increase demand (and therefore suppliers' interest). Importantly, large retailers are willing to work with science and policy to improve practices and could serve as important players in raising awareness of plant health. A cost-benefit analysis of introducing best practice from a nursery perspective highlighted the difficulties of obtaining good data in order to estimate costs, as the overall number of quantitative responses from nursery managers on costs of implementing best practice and costs of avoiding outbreaks of Phytophthora was too low to enable confidence in the analysis. However, an exploratory cost-benefit analysis indicated that the predicted benefits of introducing nursery best practice need to consider a wider range of pests and diseases (for example, Xylella) than Phytophthora in order to outweigh the costs. Global Phytophthora risks to the UK In order to model Phytophthora risks, a global Phytophthora distribution database containing close to 40,000 country-level records from garden/amenity, forest, nursery and agricultural sectors was collated in addition to a large dataset of UK Phytophthora records. A database listing the biological traits of all 179 described Phytophthora species was also developed. These databases have been made available to researchers and other end-users. Applying ecological modelling approaches to these data, global Phytophthora introductions were found to be strongly correlated with the level of connectivity to source regions by the live plant trade, with cold-adapted Phytophthora species better able to exploit trade pathways than others. The extent to which a species can disperse geographically was also linked to cold tolerance, the ability to infect roots and the ability to cause foliar symptoms. Wider host ranges were strongly linked to optimum growth rate, thick resting-spore walls (facilitating long-term survival) and ability to cause both root and foliar symptoms. In summary, thermal traits and cold tolerance are strongly linked to invasion success. These factors could be used in horizon scanning when looking to predict the potential impact of newly discovered species. Tools to help policy and practice were developed from this study. These included a Phytophthora importation tool which focusses on potential trade pathways; users can visualise the Phytophthora diversity in exporting countries and the volume of imports from those locations to assess risk. An interactive database of Phytophthora pathogens and associated hosts was also developed, which is searchable by host and by pathogen and links to risk maps of UK suitability for the pathogens. A third tool allows users to interact with maps of Phytophthora disease records in the UK. The maps show which species are predominantly nursery-associated and which are common in the wider environment. Predicting risk via analysis of Phytophthora genome content A better understanding is required of what makes a particular Phytophthora species more virulent than others. This knowledge gap was addressed by identifying genetic differences between closely related highly damaging and less-damaging Phytophthora species, the rationale being that by comparing the genes present in less damaging species with those of highly damaging species, it might be possible to find genes linked to virulence. To do this, targeted genome sequencing was carried out for three Phytophthora species not known to be damaging but which are closely related to aggressive pathogens. Using the latest sequencing and assembly technology, this project produced three of the most complete Phytophthora genomes currently available for a Phytophthora species (at this time 30 Phytophthora species have had their genomes sequenced). Each of the three genomes sequenced in this project have ~19,500 predicted genes and the analyses looked at how many genes are shared and how many are unique to each group of species. Initial findings revealed 40 genes present in highly damaging species which are not present in the less damaging species and which might be linked to virulence. The next steps are to analyse the function of these genes in order to start to unravel what makes a Phytophthora virulent. Gene content can then be used to predict which newly discovered Phytophthora species have the potential to be most damaging. |
| Exploitation Route | As the project progressed there was evidence of partner nurseries improving practice based on advice delivered by the science team as a result of Phytophthora findings, for example raising plants off the ground, improving drainage and taking decisions not to trade in high-risk hosts. Nurseries also started asking questions of growing media suppliers - what are the processes of sterilisation and can they guarantee pathogen-free components?, and seed suppliers - has this seed come from disease-free orchards? In relation to raising from locally collected seed native plant stock destined for restoration planting at ecologically vulnerable sites, one nursery manager is now considering offering dedicated growing of stock to high biosecurity specification close to each restoration site and well away from the main commercial premises. Another partner nursery has now employed a full time Plant Health specialist to train staff on plant health issues, audit existing plant health processes within the nursery, and to update plant health standards. Parallel to the Phyto-threats project a joint accreditation initiative led by the HTA and industry has been developing. This is the 'Plant Healthy Assurance Scheme' (PHAS) https://planthealthy.org.uk/, which is based around a 'Plant Health Management Standard' (PHMS) currently consisting of a check-list of 23 requirements that demonstrate that a business is operating responsibly. The PHMS is not prescriptive at this early stage in the development of the scheme but rather highlights problem areas on a nursery and offers advice on how this can be resolved. It is expected that as more information on biosecurity risk becomes available, more prescriptive measures will be incorporated. The Phyto-threats science team are liaising with those leading on PHAS to provide the scientific basis for more prescriptive measures around water source and usage, plant disposal, growing media and raising plants off the ground to be referenced in the scheme guidance since the project's main outcomes strongly suggest that a set of priority prescriptive measures will be necessary for accreditation to be effective. Additionally, the project's findings of widespread Phytophthora contamination have led to the recommendation that the PHAS audit process includes a component of targeted testing for pests and pathogens. To this end the various strands of engagement with the Statutory Plant Health teams in England/Wales and Scotland has facilitated a greater awareness of what the metabarcoding technology can offer and generated discussion of its potential for routine nursery testing, as part of regular Statutory surveillance or for incorporation into an accreditation scheme. Other outcomes: One message passed on to Plant Health teams was a recommendation that trees growing in the immediate environment of each nursery should be included in routine Statutory Plant Health inspections. Another issue highlighted by the nursery survey is that, in some cases, native plant stock being raised from seed collected from ecologically sensitive sites and destined for planting back out at these sites were found to be harbouring damaging Phytophthora species. These findings have considerable implications for the proposed massive expansion of UK woodland and have led to discussions on revised guidance documentation for woodland restoration. Social science surveys and interviews to investigate the feasibility of accreditation have delivered the following main findings which will be used to help shape what accreditation should look like and how nursery stakeholder and consumer support can be enhanced; • Accreditation must cover multiple businesses, or at least their stock • Many nurseries will have to improve their biosecurity practices to become accredited • Few nurseries are willing/able to incur substantial cost to become accredited • What accreditation 'looks' like (teeth, costs and benefits) will be influential • More evidence is needed of how regulated pests and diseases could impact growers, and how biosecurity practices avert such risks • Public are driven by quality rather than biosecurity practices. Thus, quality could be emphasised to promote an accreditation scheme • A requirement for large landscape contracts to use stock from accredited growers would increase demand (and therefore suppliers' interest). • Retailers are willing to work with science and policy to improve practices and could serve as an important player in raising awareness of plant health The global Phytophthora databases developed as part of this study have been made available to researchers and other end-users and will be updated as new species are described and information becomes available. A number of model outputs were produced to help influence policy and practice. These included a Phytophthora importation tool which focusses on the role of international trade in the movement of Phytophthoras and allows users to visualise the Phytophthora diversity in exporting countries and the volume of imports from those locations. An interactive database of Phytophthora pathogens and associated hosts was also developed, which is searchable by host and by pathogen and links to risk maps of UK suitability for the pathogens. The hosts include UK woodland and commercial forestry species, which could be used to inform species choices for commercial planting and afforestation. A third tool allows users to interact with maps of Phytophthora disease records in the UK. The maps show which species are predominantly nursery-associated and which are common in the wider environment. Many of the approaches developed in this project are also applicable to the wider field of plant health, including the threat posed by X. fastidiosa. For example, the metabarcoding methodology and publicly available Phytophthora classifier tool developed as part of this project can be applied to the broader detection of pathogens including bacterial pathogens in nurseries, fungal pathogens in spore traps and invertebrate pests in insect traps, and the comparative genomics pipelines will have application in evolutionary analyses of fungi and other organisms. The ecological model frameworks developed are widely transferable to other tree pests or diseases since they account for sparse, clustered recording effort and encompass a wide range of potential pathways and environmental factors that may influence arrival and spread of such species. The project also contributed to the body of knowledge of traits that underpin invasiveness for plant pathogens. DNA samples arising from the nursery and amenity environment surveys will create a substantial resource available for research into other plant pathogens, including bacteria. Improving sanitation practices in plant nurseries and communication and engagement across a wide spectrum of consumers and other stakeholders focussed on the importance and availability of high-health planting material will help to raise the profile of plant health and associated risks across the plant supply chain, thus lessening the impact of a broad range of plant pests and diseases. A new, two-year EUPHRESCO project (Early detection of Phytophthora in nurseries and traded plants of EU and third countries) involving more than eight partner countries will ring test the nursery sampling and metabarcoding method developed as part of Phyto-threats. This project takes core biological and social science elements developed as part of Phyto-threats out into the international sphere to develop a co-ordinated strategy for the early detection of Phytophthora pathogens in plant nurseries and traded plants for planting across EU and third countries. This new project with its much wider geographical focus will inform international best practice, complement phytosanitary regulation and enhance engagement on Plant Health with traders operating in different countries. |
| Sectors | Environment,Other |
| URL | https://www.forestresearch.gov.uk/research/global-threats-from-phytophthora-spp/ |
| Description | The Phyto-threats project team has been actively engaged with fifteen partner plant nurseries across England, Scotland and Wales, representing a range of different business types across the sector (ie from forest tree nurseries and propagators to hardy horticultural plant distributors/traders and retailers), some of whom are major players in the UK nursery trade. The WP1 project team has undertaken 3-4 sampling visits to each of these fifteen nurseries over the three years of the the project and has given feedback on Phytophthora findings in relation to management practice, prompting discussion with nursery managers on how to improve practice in order to reduce Phytophthora infestation, in particular ensuring clean water supply, improved drainage, choosing not to trade in high risk hosts and questioning seed and potting mix suppliers as to their Plant Health practices. One nursery has now employed a full-time Plant Health advisor. Others have made infrastructural changes such as putting in raised benching and disinfectant stations. Two nurseries have made the decision not to trade in Juniper because of the high association with Phytophthora austrocedri. These are just some examples of how the project's findings have been used by our industrial partners. The WP2 team has also been conducting interviews with nursery managers to gain an understanding of their perspectives on accreditation. The results of a consumer survey in which 1500 members of the plant buying public were asked for their views on accreditation - in particular their willingness to travel and pay for accredited stock - are being made available to the nursery sector though the production of a summary report. Similarly a survey of attitudes of nurseries and garden centres towards biosecurity and accreditation has been published as a technical report available online. These findings are being used to inform the development of the Plant Health Assurance Scheme. A demonstrable shift in attitude amongst industry stakeholders towards supporting accreditation occurred between the first project stakeholder workshop held in October 2016 and the second stakeholder workshop held in October 2017. By the third workshop in November 2019 it was clear that there is now a perceived willingness across the industry to support a single, all-encompassing accreditation scheme for the plant trade in the UK. The Phyto-threats project is now working with the Horticultural Trades Association and Defra in developing their pilot plant health assurance scheme. Managers of the scheme are looking to the Phyto-threats project to supply some of the key underlying data to help shape the future of accreditation in the UK. The global Phytophthora databases developed as part of this study have been made available to researchers and other end-users and will be updated as new species are described and information becomes available. A number of model outputs were produced to help influence policy and practice. These included a Phytophthora importation tool which focusses on the role of international trade in the movement of Phytophthoras and allows users to visualise the Phytophthora diversity in exporting countries and the volume of imports from those locations. An interactive database of Phytophthora pathogens and associated hosts was also developed, which is searchable by host and by pathogen and links to risk maps of UK suitability for the pathogens. The hosts include UK woodland and commercial forestry species, which could be used to inform species choices for commercial planting and afforestation. A third tool allows users to interact with maps of Phytophthora disease records in the UK. The maps show which species are predominantly nursery-associated and which are common in the wider environment. |
| Sector | Government, Democracy and Justice,Other |
| Impact Types | Economic,Policy & public services |
| Description | Evidence derived from Phyto-threats submitted to a review of the UK Forestry Standard (UKFS), supporting the recommendation that the UKFS includes biosecurity accreditation for forestry nurseries |
| Geographic Reach | National |
| Policy Influence Type | Participation in a guidance/advisory committee |
| URL | https://forestry.gov.scot/publications/105-the-uk-forestry-standard |
| Description | Provide evidence in the form of an online advisory factsheet to support recognition of nursery best practice by Landscape designers |
| Geographic Reach | National |
| Policy Influence Type | Citation in other policy documents |
| URL | https://www.landscapeinstitute.org/technical/plant-biosecurity-group/ |
| Description | Provide evidence to support the development of prescriptive measures in the Plant Healthy Certification Scheme |
| Geographic Reach | National |
| Policy Influence Type | Citation in other policy documents |
| Impact | Evidence from the Phyto-threats nursery sampling was used to develop a two-sided 'best practice' flier for the nursery industry. This flier was developed in conjunction with those leading the development of the UK Plant Healthy Certification Scheme, and is being used to underpin the development of the audited management standard which certified nurseries must adhere to. The flier is included in the scheme's online general guidance for the horticultural sector. |
| URL | https://planthealthy.org.uk/resource-topics/guidance-for-hort |
| Description | An analysis of Phytophthora diversity in plant nurseries and peat-free growing media |
| Amount | £3,000 (GBP) |
| Organisation | Royal Society of Biology (RSB) |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 06/2021 |
| End | 09/2021 |
| Description | Assessment of large-scale plant biosecurity risks to Scotland from large scale plantings for landscaping and infra-structure projects |
| Amount | £40,000 (GBP) |
| Funding ID | PHC2019_05 |
| Organisation | Government of Scotland |
| Sector | Public |
| Country | United Kingdom |
| Start | 02/2020 |
| End | 09/2020 |
| Description | Assessment of large-scale plant biosecurity risks to Scotland from large scale tree plantings for environmental benefits |
| Amount | £40,000 (GBP) |
| Funding ID | PHC2019_06 |
| Organisation | Government of Scotland |
| Sector | Public |
| Country | United Kingdom |
| Start | 02/2020 |
| End | 09/2020 |
| Description | Assessment of large-scale plant biosecurity risks to Scotland from non-specialist and online horticultural sales |
| Amount | £40,000 (GBP) |
| Funding ID | PHC2019_04 |
| Organisation | Government of Scotland |
| Sector | Public |
| Country | United Kingdom |
| Start | 02/2020 |
| End | 09/2020 |
| Description | Characterising Phytophthora diversity in three Scottish plant nursery waste systems |
| Amount | £300 (GBP) |
| Organisation | University of Edinburgh |
| Sector | Academic/University |
| Country | United Kingdom |
| Start | 01/2022 |
| End | 05/2022 |
| Description | Contract Research Fund |
| Amount | £250,000 (GBP) |
| Organisation | Government of Scotland |
| Sector | Public |
| Country | United Kingdom |
| Start | 08/2016 |
| End | 07/2018 |
| Description | Euphresco topic 2019-A-316 Early Detection of Phytophthora in nurseries and traded plants on EU and third countries |
| Amount | £100,000 (GBP) |
| Organisation | Government of the UK |
| Sector | Public |
| Country | United Kingdom |
| Start | 04/2020 |
| End | 03/2022 |
| Description | Identifying and mitigating future Phytophthora risks to the UK |
| Amount | £117,786 (GBP) |
| Organisation | Department For Environment, Food And Rural Affairs (DEFRA) |
| Sector | Public |
| Country | United Kingdom |
| Start | 04/2022 |
| End | 03/2024 |
| Description | Identifying the plant health risks associated with plant waste disposal and peat-free growing media, and developing best practice guidance for waste disposal and composting across sectors |
| Amount | £49,530 (GBP) |
| Funding ID | PHC2021/02 |
| Organisation | Plant Health Centre |
| Sector | Public |
| Country | United Kingdom |
| Start | 01/2022 |
| End | 08/2022 |
| Description | Learning to adapt to an uncertain future: linking genes, trees, people and processes for more resilient treescapes (newLEAF) |
| Amount | £1,002,489 (GBP) |
| Funding ID | NE/V019813/1 |
| Organisation | Natural Environment Research Council |
| Sector | Public |
| Country | United Kingdom |
| Start | 08/2021 |
| End | 07/2024 |
| Description | Metabarcoding analysis of Phytophthora diversity in spore traps and implications for disease forecasting in the P. ramorum management zone. |
| Amount | £12,000 (GBP) |
| Organisation | Plant Health Centre |
| Sector | Public |
| Country | United Kingdom |
| Start | 12/2019 |
| End | 03/2020 |
| Description | PHC2019_04 Assessment of large-scale plant biosecurity risks to Scotland from non-specialist and online horticulture sales |
| Amount | £40,000 (GBP) |
| Funding ID | PHC2019_04 |
| Organisation | Plant Health Centre |
| Sector | Public |
| Country | United Kingdom |
| Start | 02/2020 |
| End | 03/2021 |
| Description | Plant Health Centre, Scotland |
| Amount | £12,000 (GBP) |
| Organisation | Government of Scotland |
| Sector | Public |
| Country | United Kingdom |
| Start | 11/2018 |
| End | 03/2019 |
| Description | Risks associated with Phytophthora in peat-free growing media in the UK - Extension |
| Amount | £34,600 (GBP) |
| Funding ID | TH12122FR03 (Extension) |
| Organisation | Department For Environment, Food And Rural Affairs (DEFRA) |
| Sector | Public |
| Country | United Kingdom |
| Start | 10/2022 |
| End | 03/2023 |
| Description | Risks associated with phytophthora in peat-free growing media in the UK |
| Amount | £24,935 (GBP) |
| Organisation | Department For Environment, Food And Rural Affairs (DEFRA) |
| Sector | Public |
| Country | United Kingdom |
| Start | 12/2021 |
| End | 03/2022 |
| Description | Statistical analysis and ecological community modelling of Phytophthora data |
| Amount | £20,631 (GBP) |
| Organisation | Department For Environment, Food And Rural Affairs (DEFRA) |
| Sector | Public |
| Country | United Kingdom |
| Start | 12/2021 |
| End | 03/2022 |
| Description | Strategic priorities fund - Bacterial plant diseases programme |
| Amount | £5,500,000 (GBP) |
| Funding ID | CA792 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2018 |
| End | 03/2021 |
| Title | Phytophthora global impacts |
| Description | Data and code to reproduce the analysis in Barwell et al. Evolutionary trait-based approaches for predicting future global impacts of plant pathogens in the genus Phytophthora |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| URL | https://zenodo.org/record/4081473 |
| Title | Phytophthora global impacts |
| Description | Data and code to reproduce the analysis in Barwell et al. Evolutionary trait-based approaches for predicting future global impacts of plant pathogens in the genus Phytophthora |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| URL | https://zenodo.org/record/4081474 |
| Title | THAPBI Phytophthora ITS1 Classifier Tool (PICT) |
| Description | THAPBI PICT is a sequence based diagnostic/profiling tool focused on identifying Phytophthora species present in Illumina sequenced environmental samples. With appropriate primer settings and a custom database, THAPBI PICT can be applied to other organisms and/or barcode marker sequences - not just Phytophthora ITS1. It requires overlapping paired-end Illumina reads which can be merged to cover the full amplicon marker. Longer markers or fragmented amplicons are not supported. The worked examples include oomycetes, fungi, microalgae, and bats, and cover markers in ITS1, ITS2, 18S rRNA and COI and more. The main criteria has been mock communities with known species composition. |
| Type Of Material | Data analysis technique |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| Impact | This bioinformatics tool is being rolled out for use in a new Euphresco project (Early detection of Phytophthora in nurseries and traded plants in EU and third countries) which is using standardised methodology to investigate Phytophthora diversity in traded plants in eleven countries globally. |
| URL | https://doi.org/10.5281/zenodo.4529395 |
| Description | Global traits and impacts of Phytophthoras |
| Organisation | Murdoch University |
| Country | Australia |
| Sector | Academic/University |
| PI Contribution | Forest Research, Centre for Ecology and Hydrology and the James Hutton Institute are collaborating with these international partners on WP3 of the Phytothreats project, to increase the breadth and accuracy of the global database of traits and occurrence of Phytophthora pathogens. This has involved merging trait databases compiled at Forest Research with those compiled at Murdoch University and the joint development of a conceptual framework for how ecological traits of Phytopthoras might linked to invasion success, through each stage of invasion (arrival, establishment, spread and impact). This framework and the traits data lay the foundation for subsequent analyses in WP3 of the links between invasion success and triats using global occurrence data. It is expected that two manuscripts will be jointly submitted with the Australian and New Zealand in 2018, one on the traits database and conceptual framework and one linking traits to global impact metrics of Phytophthoras. |
| Collaborator Contribution | As above: joint formulation of a conceptual framework for how ecological traits of Phytopthoras might linked to invasion success, joint compilation of traits and phylogenetic data for Phytophthoras, joint writing and editing of manuscripts |
| Impact | It is expected that two manuscripts will be jointly submitted with the Australian and New Zealand in 2018, one on the traits database and conceptual framework and one linking traits to global impact metrics of Phytophthoras. |
| Start Year | 2017 |
| Description | Global traits and impacts of Phytophthoras |
| Organisation | Murdoch University |
| Country | Australia |
| Sector | Academic/University |
| PI Contribution | Forest Research, Centre for Ecology and Hydrology and the James Hutton Institute are collaborating with these international partners on WP3 of the Phytothreats project, to increase the breadth and accuracy of the global database of traits and occurrence of Phytophthora pathogens. This has involved merging trait databases compiled at Forest Research with those compiled at Murdoch University and the joint development of a conceptual framework for how ecological traits of Phytopthoras might linked to invasion success, through each stage of invasion (arrival, establishment, spread and impact). This framework and the traits data lay the foundation for subsequent analyses in WP3 of the links between invasion success and triats using global occurrence data. It is expected that two manuscripts will be jointly submitted with the Australian and New Zealand in 2018, one on the traits database and conceptual framework and one linking traits to global impact metrics of Phytophthoras. |
| Collaborator Contribution | As above: joint formulation of a conceptual framework for how ecological traits of Phytopthoras might linked to invasion success, joint compilation of traits and phylogenetic data for Phytophthoras, joint writing and editing of manuscripts |
| Impact | It is expected that two manuscripts will be jointly submitted with the Australian and New Zealand in 2018, one on the traits database and conceptual framework and one linking traits to global impact metrics of Phytophthoras. |
| Start Year | 2017 |
| Description | Global traits and impacts of Phytophthoras |
| Organisation | Scion |
| Country | New Zealand |
| Sector | Public |
| PI Contribution | Forest Research, Centre for Ecology and Hydrology and the James Hutton Institute are collaborating with these international partners on WP3 of the Phytothreats project, to increase the breadth and accuracy of the global database of traits and occurrence of Phytophthora pathogens. This has involved merging trait databases compiled at Forest Research with those compiled at Murdoch University and the joint development of a conceptual framework for how ecological traits of Phytopthoras might linked to invasion success, through each stage of invasion (arrival, establishment, spread and impact). This framework and the traits data lay the foundation for subsequent analyses in WP3 of the links between invasion success and triats using global occurrence data. It is expected that two manuscripts will be jointly submitted with the Australian and New Zealand in 2018, one on the traits database and conceptual framework and one linking traits to global impact metrics of Phytophthoras. |
| Collaborator Contribution | As above: joint formulation of a conceptual framework for how ecological traits of Phytopthoras might linked to invasion success, joint compilation of traits and phylogenetic data for Phytophthoras, joint writing and editing of manuscripts |
| Impact | It is expected that two manuscripts will be jointly submitted with the Australian and New Zealand in 2018, one on the traits database and conceptual framework and one linking traits to global impact metrics of Phytophthoras. |
| Start Year | 2017 |
| Description | Global traits and impacts of Phytophthoras |
| Organisation | Scion |
| Country | New Zealand |
| Sector | Public |
| PI Contribution | Forest Research, Centre for Ecology and Hydrology and the James Hutton Institute are collaborating with these international partners on WP3 of the Phytothreats project, to increase the breadth and accuracy of the global database of traits and occurrence of Phytophthora pathogens. This has involved merging trait databases compiled at Forest Research with those compiled at Murdoch University and the joint development of a conceptual framework for how ecological traits of Phytopthoras might linked to invasion success, through each stage of invasion (arrival, establishment, spread and impact). This framework and the traits data lay the foundation for subsequent analyses in WP3 of the links between invasion success and triats using global occurrence data. It is expected that two manuscripts will be jointly submitted with the Australian and New Zealand in 2018, one on the traits database and conceptual framework and one linking traits to global impact metrics of Phytophthoras. |
| Collaborator Contribution | As above: joint formulation of a conceptual framework for how ecological traits of Phytopthoras might linked to invasion success, joint compilation of traits and phylogenetic data for Phytophthoras, joint writing and editing of manuscripts |
| Impact | It is expected that two manuscripts will be jointly submitted with the Australian and New Zealand in 2018, one on the traits database and conceptual framework and one linking traits to global impact metrics of Phytophthoras. |
| Start Year | 2017 |
| Description | Responsibility and cost-sharing: Assessing barriers towards nursery accreditation |
| Organisation | Fera Science Limited |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | Sharing of findings from interviews with nursery managers to date. Sharing of question frameworks and experiences with data collection from research participants. |
| Collaborator Contribution | Data collection through interviews with plant nursery managers. Subsequent findings are to be shared. |
| Impact | In Progress: collaboration just started in 2018 so no outputs or outcomes yet. |
| Start Year | 2017 |
| Description | 195. Pritchard P, Cock PJA, Thorpe P, Randall R, Green S, Cooke DEL, 2019. Metabarcoding diagnostics of Phytophthora species in environmental samples. Poster at XVIII International Congress on Molecular Plant-Microbe Interactions, July 14-18, 2019 Glasgow, UK. |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Leighton Pritchard presented a poster at an international conference on Molecular Plant Microbe Interactions on the computational elements of pathogen metabarcoding. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.ismpmi.org/Congress/2019/program/Documents/ISMPMI_Program_Final_626.pdf |
| Description | 28th USDA Interagency Research Forum on Invasive Species held in Annapolis, USA |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Sarah Green (Forest Research) attended the 28th USDA Interagency Research Forum on Invasive Species held in Annapolis, Maryland, January 10-13, 2017. She presented a paper entitled 'Tackling emerging forest Phytophthoras in the UK: Mitigating risk of new introductions and managing diseased landscapes for the future' during the session 'Forest Phytophthora: They get around' organized by IUFRO Working Party 7.02.09, Phytophthoras in Forests and Natural Ecosystems. Sarah's presentation included an overview of the LWEC3 Phyto-threats project; rationale and objectives. The talk generated discussion on the overall willingness of nurseries to participate in the project, and the conundrum posed by ever increasing trade flows whilst trying to reduce risks of global spread of pests and diseases. Sarah also took the opportunity to ask for collaborators to assist the Phyto-threats workpackage 3 team, led by Beth Purse, in compiling data on global Phytophthora occurrence. She learned of an ongoing project by Yilmaz Balci from USDA-APHIS who has about 21 new Phytophthora species (as yet undescribed) which he will publish on this year. Twelve of the species were collected during surveys in South and Central America and the rest were collected from eastern USA. These will be added to the Phyto-threats traits database when the data become available. In general there was much enthusiasm for having one central Phytophthora database (listing biological traits and distribution) available globally. This is a big project however and one which would require additional resources to manage beyond the lifetime of Phyto-threats. There were a number of other speakers who gave presentations of particular interest to the Phyto-threats project. Everett Hansen of Oregon State University reported on the high diversity of Phytophthoras found during surveys of Oregon wildlands. Laura Sims, University of California, discussed how plant disease predictions for invasive soilborne Phytophthora species are consistent with host ecology and with genus-level co-evolutionary history. Rebecca Epanchin-Niell of 'Resources for the Future' based in Washington DC described a cost-benefit analysis of the live plant trade during her talk 'Informing efficient strategies to reduce pest risk from live plant imports'. The analysis was done in relation to risks to US forests from introductions of insect pests, but it involved economic estimates of the welfare benefits of the live plant trade, expected damages per forest pest establishment (over time as invasion spreads) and included an assessment of the relatedness of imported plant species to important forest species in the US. This work can be viewed in more detail in; Epanchin-Niell and Liebhold, 2015. Benefits of invasion prevention: Effect of time lags, spread rates, and damage persistence. Ecological Economics 116; 146-153 http://www.sciencedirect.com/science/article/pii/S092180091500172X Also of interest was a talk by Rebecca Ganley of Scion, Rotorua, New Zealand, who described her colleague Peter Scott's work in compiling a list of all Phytophthora species reported in every country globally. They are using modelling approaches to predict the number of Phytophthora species likely to be present in each country in the world. The Phyto-threats workpackage 3 team are now in touch with the NZ group to scope the potential for collaboration/sharing of resources. |
| Year(s) Of Engagement Activity | 2017 |
| Description | All-project team meeting May 4th 2017 |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Study participants or study members |
| Results and Impact | Project team meeting, James Hutton Institute (JHI), Invergowrie, Dundee May 4th 2017 The aim of this meeting was to bring the entire project team and members of the Expert Advisory Panel together to share and discuss research progress over the first year of the project for the three work packages that have started, and to outline and receive feedback on future research plans. Following the talks and discussion sessions participants were given a short tour of the JHI pathology and sequencing labs. The meeting started with a welcome by Sarah Green (Forest Research, FR) and brief introductions of everyone present including their affiliations. 09.30-11.00: WP1 Phytophthora distribution, diversity and management in UK nursery systems - David Cooke (JHI) and Pete Thorpe (JHI) David Cooke introduced the WP1 team, which consists of David Cooke, Leighton Pritchard Peter Thorpe, Eva Randall, Beatrix Clark (all JHI), Sarah Green (FR), Debbie Frederickson-Matika (FR), Tim Pettitt (Uni of Worcs), Alexander Schlenzig (SASA) and Jane Barbrook (APHA). Nursery sampling For context, David provided a snapshot of the distribution of P. infestans clones in Europe from 2013-2016 based on 5000 isolates from the Euroblight project, showing how an airborne pathogen can rapidly change its distribution. David then gave an overview of WP1 objectives and methods for the nursery sampling, including some practical issues such as range of plant species sampled, which varies among nurseries according to what stock they hold. Generally, the sampled plants are a mix of known and unknown hosts for Phytophthora, and may be symptomatic or asymptomatic at the time of sampling. Mostly root samples are taken, except in a few instances where foliage/stem samples have been taken from symptomatic plants. Water supply is sampled at source and run-off. In general, sampling effort at each nursery is a balance of time available and the need for detail, focusing on working through the hazard points - ie incoming plants/water/pots/ground. So far the team have carried out 18 sampling missions at 15 nurseries (6 in England, 1 in Wales, 8 in Scotland). This has resulted in 1009 samples (everything in triplicate) including plant roots (93) from a range of 35 hosts, 132 water filter samples and 170 samples of buffer associated with each filter. Water samples came from water washed through plants, boreholes, ponds/ditches, equipment washing (eg trolleys) and water control blanks. To date, 395 samples have been PCR tested for Phytophthora. David described some of the necessary changes to lab protocols to improve the efficiency and accuracy of processing. Data were presented showing the number of Phytophthora-+ve samples for 10 nurseries (labelled 1-10 and not named in the presentation). Sample types were broken down into water filter, water buffer and roots. There were clear differences among nurseries in relation to the number of Phytophthora +ve and -ve samples, and this could be related to practices observed during the sampling missions. David did outline the issues of working with each sample in triplicate, ie when 2 samples are negative for Phytophthora and 1 is positive, and how they deal with such results. There was discussion on the different nursery sizes and practices and how that relates to the number of findings per nursery as this should be taken into account when presenting data. Hard evidence is required linking practice to Phytophthora findings. Mariella Marzano (FR) made the point that a survey of management practices accompanies each nursery sampling visit so that a basis of best practice/worse practice can be developed in relation to Phytophthora findings. Participating nurseries are willing to know their results in order to improve their practice. Nursery data include turnover/plant species sold to help interpret findings. Detailed (fine-scale) sampling is only done for nurseries that volunteer. The question was asked whether sampling was designed to avoid bias, ie if you focus on a sick area of plants within a very large nursery you will bias the data. This is more a problem for plant samples than water samples. David Cooke confirmed that detailed notes accompany each sample collected, including whether samples were collected on a random basis or due to presence of disease symptoms. A broad-scale survey is due to start soon in which plant inspectors will be collecting root samples for the project from nurseries during their routine Plant Health inspections. In particular it will be important to clarify with inspectors where and what they should be sampling. This element needed further discussion between APHA and JHI. David made the point that the aim of the broad scale survey is not to repeat the statutory testing but rather to look more widely across nurseries for a different insight that will help inform the goals of the Phyto-threats project. It was suggested that nursery samples are collected from areas not expected to have disease (for example where plants are apparently healthy), just to check what Phytophthoras might be 'hiding'. In such cases the foliage could look healthy but perhaps the pathogens are present in the roots or soil. Some Phytophthoras such as P. gonapodyides could just be 'root nibblers' and not viewed as pathogenic. The consensus was that it is still useful to know the distribution of non-aggressive Phytophthora species to see how they are distributed. The presence of these species might indicate a route in for other more pathogenic Phytophthoras. It was asked whether information is available on where nurseries with Phytophthora-positive samples have sourced their plants, ie from plant passport numbers, and whether such information could be used to know what pathogens are in those areas where plants are imported/bought in from ?. David Cooke responded that data on plant sources are with each nursery and could be obtained from some of them, however, the true origin of the plants might not be known by their plant passport number. The length of time that plants have been in a nursery is a factor included on the nursery questionnaires. David Cooke listed the Phytophthora findings to date by sample type, showing a higher proportion of positive samples from roots than water, although this would reflect the fact that sickly plants are targeted for the root sampling. Different production methods included; •Water sources; mostly borehole, some mains plus rainwater and river water ('filtered'). •Plants in cells/pots above ground or on the ground, or bare root grown in the ground (ie forestry nursery). •Production systems included wholesalers/holding/importing to production on-site. •Premises included garden centres/nurseries/mixed/horticulture/hedgerow/forestry tree growers. •Generally good plant health awareness was observed but fungicide use was widespread. David then showed examples to illustrate sampling points, such as water sources and types of plants sampled. In terms of the next steps for the nursery sampling; David Cooke is to discuss the broad scale sampling with Jane Barbrook (APHA) and Alexandra Schlenzig (SASA), as well as co-ordinating the OPAL sampling with David Slawson. For OPAL, water samples from streams and other waterways will be collected by OPAL community volunteers in Plymouth, Cardiff, North Wales and Glasgow. David Slawson emphasised the need for good photographs and descriptions of sampling methods for the volunteers, and also expressed the need for rapid feedback on OPAL results to enthuse and engage OPAL volunteer interest. The fine scale sampling of the 15 partner nurseries will also be repeated in June/July and again at the end of the year. A question was asked whether root samples are also taken from plants sampled by water flow-through (ie plants are placed on a tray and watered to capacity, left to stand for 30 mins or so, and the water flow-through in the trays then sampled). If so, this would provide an interesting comparison of the two methods in terms of Phytophthora detection. David Cooke said that where possible roots were sampled from plants also subject to flow-through sampling, although sometimes time constraints prevented this. At the moment there is also a backlog of samples requiring DNA extraction from the previous round of sampling and getting this done will be a priority. The first 176 Phytophthora-positive samples will be run through Illumina sequencing in May 2017. This will produce 15M barcode reads=156K reads per sample; each read approximately 250bp in length. Synthetic control samples will also be included in each sequencing run as a test of error rate. Bioinformatics analyses Pete Thorpe (JHI) presented on the bioinformatics pipeline that he and Leighton Pritchard (JHI) have developed called METAPY - this pipeline is a key output from the project and will soon be publically available on GitHub for use by the wider scientific community. Pete began by describing the system for Phytophthora identification from sample collection, to DNA extraction, nested PCR of the ITS1 region with Phytophthora- specific primers, DNA library preparation, Illumina sequencing and analysis of sequencing reads by the bioinformatics pipeline, METAPY. Pete explained that other pipelines tend to use one clustering tool (ie to align sequence reads to a reference sequence in a database), however, each clustering method can vary and so METAPY produces individual results for five different clustering methods (Blastclust, Swarm, V-search, CD-hit and Bowtie) so that results can be validated by comparing the different methods. Pete ran through the different clustering methods and showed results from a control sample containing a DNA mix of ten known Phytophthora species. He explained reasons for variation and false-positive results for each clustering method. Blastclust was the least discriminating method and reported 27 species; many of these false-positives were species in the same clade. Bowtie, on the other hand, only detects species with a 100% match to the reference sequence in the database and reported only 7 species in the test. CD-hit found 20 species, Swarm 16 and Vsearch 16. The reference database is yet to be adjusted for species which have highly similar or matching ITS sequences and this might sort out some of the false-positives. METAPY can also be set to error-correct reads before identification (Illumina can be prone to error - these sources of error are known and can be automatically corrected). METAPY is currently used for the ITS1 region but can be edited for other genes. Pete then described the main issue with using the ITS region which can exist in 50-500 copies in the Phytophthora genome based on assessment of ITS copy number using qPCR. The short reads produced by the sequencing method can't resolve repeat/repetitive regions and so these get collapsed to consensus sequences. Perhaps a different sequencing method such as PacBio, which produces longer reads, will help to resolve this. Pete is re-assembling ribosomal DNA regions for all Phytophthora genomes to determine copy number and within-genome variation. The question was asked how Phytophthora hybrids might be identified using the bioinformatics method. David Cooke agreed that chimera detection in the pipeline might throw them out and thus identifying hybrids will be tricky. Ana Pérez-Sierra (FR) mentioned the POnTE project which is assessing both ITS1 and the Cox region for Phytophthora detection to see how resolution compares. For other fungi, for example powdery mildew, the single copy B-tubulin gene is used for barcoding. It was also asked whether the different ITS sequences present within an individual would show up in the metabarcoding data given the very high number of ITS reads produced with Illumina, so that within-species variation would be identified. Or, is it only the predominant and more abundant ITS sequence that gets resolved?. Sarah Green (FR) described the scenario with P. austrocedri that had arisen in a previous metabarcoding study in which some samples yielded high numbers of reads of an ITS sequence typical of the UK lineage plus a few reads of an ITS sequence typical of the Argentinian lineage. Initially it was thought that the Argentinian lineage might be present in Scotland - however, subsequent analysis of the P. austrocedri genome revealed that the UK lineage also has the Argentinian-type ITS sequence in the repeats, probably at lower copy number. David Cooke responded that some species do have multiple ITS types and he wants to build them into the reference database. Beth Purse (CEH) commented that the WP3 team are receiving data on global Phytophthora distribution based, in many cases, only on ITS sequence detection. Ca we be confident in these data?. David Cooke replied that whereas some species have identical ITS sequences and cannot be resolved, the majority of Phytophthoras can be distinguished based on ITS. Taxonomic irregularities can also cause difficulties. The WP3 team will need to have clarification over which species can be confused so that they can mine the data that they have compiled. Can they trust the Blast analyses used to identify species?, and is there a timeline for species identification?, ie before a certain date the identifications would have been based on morphology alone and thereafter more likely to have resulted from mainly molecular tools or a combination of both. David Cooke replied that from about 1998 onwards, Phytophthora researchers were using molecular tools and thus data are more likely to be reliably discriminated. The trick is to avoid over-interpretation. We also need to take care not to interpret previously uncharacterised sequences as new species just because they are not on the reference database. There was then a discussion/comment that ideally we should know the range of ITS ambiguity in each Phytophthora genome so it can be incorporated in the analyses. The existing reference database of Phytophthora ITS genomes is still being worked on and accuracy of the database is key to the outcome of analyses. Currently it is believed by the team that METAPY gives the best likelihood of a given Phytophthora species being present compared with other pipelines. 11.00-12.30: WP2 Feasibility analyses and development of 'best practice' criteria - Mariella Marzano (FR) and Mike Dunn (FR) Mariella began with an overview of the social and economic research being carried out by herself, Mike Dunn, Gregory Valatin (all FR), Colin Price (contractor economist) and Tim Pettitt (Uni of Worcs, nursery engagement) and she reminded the project team of the WP2 objectives, listing milestones and outputs. Essentially this WP has three key parts; i) social analysis to assess applicability of nursery best practice criteria, ii) cost-benefit analysis of implementing best practice and iii) which elements of best practice that should underpin an accreditation scheme. So far the WP2 team has mapped the stakeholder networks and created a stakeholder database. The consumer survey was supposed to be done in year 2 of the project, but since there was early interest in this work the survey was conducted in year 1 (more detail to follow). The team have done some context building; interviewing science team members and members of the Expert Advisory Panel to get a sense of what is needed, and Mike Dunn (FR) has also joined the WP1 team on nursery sampling visits. They are exploring existing values within the sector, experiences, and practices on disease and management. They are planning to conduct interviews and undertake participant observation at nurseries starting this summer. One of the key factors to assess will be potential attitudes and willingness to join an accreditation scheme. The team will also do wider industry focus groups but they have yet to finalise the methods. They will be led by the data as it comes in. More surveys are being developed for landscapers, nurseries and garden centres, including supermarkets and superstores. They will prepare questions on the supply chain, disease threat perspectives, current management, policy tools etc and obtain information on decision management, where can and can't nurseries change, perspectives fo |
| Year(s) Of Engagement Activity | 2017 |
| URL | https://www.forestry.gov.uk/fr/beeh-antjyz |
| Description | All-project team meeting Oct 3rd 2017 |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Study participants or study members |
| Results and Impact | Phyto-threats project team meeting - October 3rd 2017, APHA, Sand Hutton, York The aim of this meeting was to bring the entire project team and members of the Expert Advisory Panel together to share and discuss research progress since the last all-project team meeting on May 4th 2017, and to outline and receive feedback on future research plans. The meeting started with a welcome by Sarah Green (Forest Research, FR) and brief introductions from everyone present including their affiliations. 09.30-11.00: WP1 Phytophthora distribution, diversity and management in UK nursery systems - David Cooke (JHI) and Pete Thorpe (JHI) David Cooke introduced the WP1 team and reminded everyone of the WP objectives and methods used for the fine-scale sampling of the 15 partner nurseries, including some of the practical issues. A simple questionnaire is applied to each nursery to collect basic data and to get to know the manager, asking for example how material comes onto site and where it goes off site, where material comes from, where it goes to, what water sources are used (ie borehole/river/pond) and how it is treated, and whether the manager has any particular concerns. David explained that sampling involves collecting material from known and unknown Phytophthora hosts, some common to all sites and a mix of symptomatic and asymptomatic. Plant tissue collected is mostly roots. For water sampling, water is passed through batches of potted plants in trays which are left to sit for 30 mins or so. This allows for any Phytophthora propagules on the roots or in the potting soil to be flushed out. The flow-through water is then collected and filtered to trap Phytophthora propagules on the filter. Water supplies and water collection areas (ie puddles, irrigation ponds, drainage ditches) are also tested and filtered. David reminded everyone, and planned to reiterate to stakeholders at the workshop the following day, the importance of water in Phytophthora spread and that water management in nurseries is a critical area to get right in order to control disease. On each nursery site the team evaluates potential disease control points and contamination hazards but it's always a balance between time available and the need for detail. In terms of a sampling update for the fine scale sampling, the WP1 team have carried out 34 sampling visits to the 15 partner nurseries (6 in England, 1 in Wales and 8 in Scotland). Thus each nursery has been sampled at least twice, and a third round of sampling is currently underway, with a total of 1700 nursery samples plus associated meta-data collected so far. Just over 400 samples have been PCR tested for Phytophthora: this includes 93 plant root samples from 35 different host types, 132 water filter samples and 170 samples of buffer associated with the filters. Isolations have also been attempted from selected samples, resulting in three confirmed P. austrocedri findings and a finding of P. cambivora on shelterbelt trees. For the OPAL community sampling, carried out through co-operation with David Slawson and Vanessa Barber of the OPAL project, the sample kits were sent to the volunteers in June 2017 and a training course/skype video made by David to inform volunteers of the sampling protocol. Ten samples from OPAL have been received to date from various sites in North Wales, all collected by one of the OPAL volunteers. David also showed a leaflet that is being used to explain the project and to aid understanding of Phytophthora diseases. The broad scale nursery sampling is carried out as part of the national statutory sampling programme in liaison with Alexandra Schlenzig (SASA) and Jane Barbrook (APHA). This element of the project targets 50 nurseries/garden centres in England and Wales and 25 in Scotland (to be sampled in 2017/18). Sample packs were sent out to Plant Health Inspectors earlier in the summer and 27 sample packs have been returned so far (ie representing 27 nurseries; 11 in Scotland and 16 in England and Wales). Each sample pack contains 5-10 different root samples per nursery as well as a limited amount of information on each nursery. For Phytophthora detection using metabarcoding, the Phytophthora-specific PCR assay is the first key to understanding how many samples are Phytophthora +ve. Currently JHI has a large backlog of samples, and they are splitting the lab processing with Forest Research, who are dealing with the root samples. There are no data yet on Phytophthora species findings as the first Illumina plate failed quality control, probably due to sample loss during one of the clean-up stages in the library preparation. The plate is being redone with the aim of completing the Illumina runs this month. The sequencing runs will also include synthetic control sequences generated as a test of; a) sequencing error, b) indexing error and c) sensitivity range. The team at JHI have been putting together a database of known, verified Phytophthora ITS sequences, comparing databases from Santi Català, Treena Burgess and a database developed by David Cooke. Phylogenetic trees have been produced for each database so that duplications and variations among sequences can be observed, including sequence errors, for sample one problem has been the truncation of even some type-strain sequences. A new database is being constructed through manual editing of the phylogenetic trees for the existing databases, for example if three sequences for a given species are identical in each database then any of the three sequences can be used, and any sequences with errors are discarded. David presented some of the slides he plans to show at the stakeholder meeting the following day, including Phytophthora findings by nursery (anonymised), findings by sample type, and observations while sampling. In terms of risk of Phytophthora coming onto site there is the need to keep water sources clean, to be aware of the health and source of plant material coming in (this presents high risk especially if from EU or third countries), and to consider biosecurity for staff and visitors as mud is a problem in some nurseries. He recommended a concrete pad for delivery/despatch areas. In terms of Phytophthora dissemination on site, plant to plant spread tends to be least problematic in cells raised above ground, and since puddles are oftenPhytophthora +ve then drainage is important. Infection by Phytophthora has been picked up in shelterbelt trees and having nursery 'hospital/recovery' areas is not a good idea. Rapid disposal of sick plants is optimal. David also recommended quarantining new plant material if possible - this material is often put at the back of the nursery in unkempt areas. David then went on to show photographs of some of the issues encountered during the nursery sampling, ie puddles, muddy and/or flooded ground, soggy possibly Phytophthora-infected roots. Photographs of good management included covered water-holding tanks, collection ponds that are lined and free of vegetation, well-built drainage ditches, graded surfaces that minimise puddling in key parts of the nursery, for example where vehicles move in and out, plants sitting on raised benches, on well drained gravel or clean mypex with good spacing between plants. The next steps for the WP team are to complete this autumn round of sampling, accelerate the lab testing, run the metabarcoding analyses to identify the species present, complete the computational biology platform, report species findings to nurseries and begin data interpretation. Questions and comments: Q: What about the implications of finding Phytophthora in the nursery - what do they do about it ?. A: Being aware of symptoms is important and we make management recommendations when reporting on where samples have proven to be positive for Phytophthora. For example if roots from a specific supplier are consistently Phytophthora +ve then avoid that supplier. Also, not all Phytophthoras are pathogens - although we need to be careful when making this statement, for example P. gonapodyides is also a pathogen as well as being fairly ubiquitous in water. Comment: It is early days yet in the project and as results come in they will help to indicate how nurseries can reduce Phytophthora through making changes to certain practices. In the longer term the project will be able to offer very good advice, very targeted, to guide management. Q: What about findings of statutory importance ?. A: Findings based on DNA data alone cannot be a basis for statutory action. The nursery manager however needs to be aware and Plant Health kept informed. Q: Is there competition between so called pathogenic and non-pathogen Phytophthora species, and if you get rid of the non-pathogens are the pathogens more likely to take hold ?. A: Interesting point. A study in Austria is looking at the question of whether some Phytophthora species are outcompeting others, and investigating the interactions among species. Q: What is the best way of killing Phytophthora in plant disposal areas ?. A: By composting to a standard that ensures the required temperatures are reached. There are numerous published studies on this. For example Fera protocol on P. ramorum suggests that composting will be effective in killing this species. Any waste disposal system will need to be built into the accreditation system. Bioinformatics analyses Pete Thorpe (JHI) presented on the metapy bioinformatics pipeline developed by himself and Leighton Pritchard at JHI. This pipeline is freely available on the github open source site. Pete reminded everyone of what the pipeline does including the five clustering tools. A new clustering tool has been recently published (ZOTU: Exact Sequence Variants: Callahan et al. 2017). ZOTU explicitly tries to correct PCR and sequencing errors and has now been incorporated into metapy. There was some discussion on ZOTUs versus OTUs. Leighton Pritchard explained that ZOTU tries to account for systematic sequencing errors before it clusters sequences. This is different from biovariation, which we are interested in. Pete then showed the mathematical model that ZOTU uses for this correction. Pete also emphasised the importance of the database as the critical determinant of classification accuracy and he showed the differences in outputs from the five clustering tools, and explained the need to trim the ITS sequences to include the ITS1 region only. Blastclust is not specific enough and so will be removed from the pipeline. The next steps are to verify the pipeline and database with the control samples from the sequencing plate and to write a Bayesian based clustering/probabilistic model. Questions and comments: Comment: In the POnTE project, which compares metabarcoding detection of Phytophthora with a traditional baiting method, sometimes metabarcoding has not found a species when it has been baited out of the same sample!. Something is not right if this happens. A: Metabarcoding is never going to be 100% accurate, however we are striving to get it better. If a species is not being picked up then this may be because the sequence is not present in the database. The database team are meeting to discuss this. Comment: One issue has been with false positives, due in some cases to ITS sequence variability within species. Most ITS sequences for species in Genbank are Sanger-generated so will be the most abundant/easily amplified sequence in that species that is deposited as the Genbank reference sequence. Illumina sequencing has such great read depth that it will also generate reads for less abundant ITS sequences in a species. For example an ITS sequence present in P. gonapodyides also seems to match P. mississippiae. In these cases the less abundant sequence will occur at low read numbers in the presence of higher read numbers of the most abundant sequence. So it can be picked up, though this emphasises the need for data verification/interpretation by those who know the species and their sequences. A: Yes there will be sequence variants within species - these can be pulled out and identified. 11.00-12.30: WP2 Feasibility analyses and development of 'best practice' criteria - Mariella Marzano (FR), Glyn Jones (FERA) and Colin Price (free-lance academic consultant) Mariella reminded everyone of the WP2 team members, objectives and methods, including the consumer survey (1500 respondents) which explored the plant buying habits of the public (reported on at the last project team meeting on May 4th) and the interviews with nursery managers, of which six have so far been conducted. An on-line smart survey has also been produced targeting a broader range of consumers including nursery owners, garden centres, landscapers and plant-buying members of the general public. This survey is being circulated via a number of on-line avenues. For the nursery interviews, carried out by Mariella, Mike Dunn and Tim Pettitt, a range of questions are asked on what influences their decisions, where nurseries are least and most able to change, and their perspectives on accreditation. The aim is to interview all fifteen partner nurseries in the project this financial year. Mariella then ran through a number of slides illustrating some of the comments/perspectives received so far from nursery managers on issues such as plant health, consumers, biosecurity practice/challenges and accreditation. Some points to consider on best practice are that even nurseries who don't import might unknowingly buy plants from another nursery that does import. Some nurseries aim to be 'green' by re-using plastic pots etc, however reducing plastic waste in this way also increases disease risk. In terms of accreditation there is cynicism. Source is an issue, for example a plant that came from Holland and arrived in Scotland - is it fair to say it's locally sourced ?. Also, landscapers are asking for plants based on design rather than asking nurseries what's possible and suited. This pressurises nurseries to arrange risky imports. If a nursery cannot import then the customer will just get it elsewhere. Some nursery managers feel that accreditation is just a tick-box exercise; customers don't ask for it, and there is little support for accreditation at present. The most popular place to buy plants now is at the big retailers and garden centres, and these are viewed as being not so concerned with biosecurity. There also seems to be a perception that accreditation would not change the behaviours of fellow nurseries. However, some nursery managers might consider accreditation if the costs were not prohibitive and the required actions not unreasonable, if there was a safety net and a demand from the consumer. Mariella then posed a suggested list of questions for the focus session at the stakeholder workshop to be held the following day and the ensuing discussion largely centred around those questions. Questions and comments: Comment: Other projects led by Fera are asking similar questions and we're finding that retailers have less interest in talking about pests and diseases than growers. A: It's about figuring out how to talk about pests and diseases. Garden centres and superstores don't want negative messages. Comment: At the stakeholder meeting tomorrow we should talk about the consumer survey message on willingness to travel further to support accreditation. There is willingness, and it is important to show this. Comment: Are we using the wrong language to talk about accreditation ?. It's not about enforcement or accreditation having 'teeth' but rather 'what's in it for me ?'. For example, if we get accredited and there is a big government planting scheme, will you buy our plants in preference?. Think of the positive benefits, not what will happen if we don't become accredited. Perhaps the question tomorrow needs to be phrased 'what would you like to see from government?'. Could the government make the climate more effective for accreditation?', ie if the government has a planting scheme would the government only use accredited plants ?. A: We shouldn't mention the government specifically, but rather ask the question 'what support is needed for accreditation ?'. Then this doesn't focus on support from a particular |
| Year(s) Of Engagement Activity | 2017 |
| URL | https://www.forestry.gov.uk/fr/beeh-asrfsc |
| Description | Article in the Newsletter of the International Society for Plant Pathology |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | The purpose of this activity was to engage plant pathologists with expertise in forest health about their experience and knowledge of the importance of tourism as a potential pathway for introducing Phytophthora to new regions. It provides a link to a questionnaire which can be completed by such experts. The article also engages plant pathologists in the project efforts to collate global occurrence data for Phytophthora pathogens. Prior to this newsletter, we engaged with over 150 global plant pathologists via email about occurrence data and the tourism questionnaire. We expect to use the same and global contact network to disseminate our model and questionnaire findings at the end of the Phytothreats project. |
| Year(s) Of Engagement Activity | 2010 |
| URL | http://www.isppweb.org/newsletters/mar18.html#6 |
| Description | Attendance and project stand at the National Plant Show |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | National Plant Show, Stoneleigh Park, Warwickshire, June 20-21st 2017 Phyto-threats project had a stand and seminar slot at the National Plant Show, held in Stoneleigh Park, Warwickshire, June 20-21st 2017. This is one of the largest plant trade shows in the UK, featuring over 160 exhibitors and receiving around 1400 visitors, representing garden centres and retail nurseries, as well as wholesale nurseries, online and mail order retailers, landscapers, garden designers, consultants and local authorities. The purpose of the Phyto-threats stand and seminar was to raise awareness of the link between the plant trade and Phytophthora outbreaks in the wider environment, and to inform growers of the role they can play in helping to reduce the spread of Phytophthora through best management practice. The stand received a steady number of interested visitors on both days, with a good number of these visitors willing to participate in an online survey designed by members of the project team to assess perspectives on accreditation based on best practice. It was also very useful for the project team to gain a greater understanding of what drives the plant trade, and how trade networks work across Europe and beyond. One of the project team (David Cooke on day one and Sarah Green on day two) gave a 15 minute presentation to the audience entitled 'Save our trees", again aimed at raising awareness of the link between plant trade and Phytophthora outbreaks on trees, demonstrating how Phytophthoras prosper in nursery environments and management practices which can reduce risk of Phytophthora spread and infection. |
| Year(s) Of Engagement Activity | 2017 |
| URL | https://www.hortweek.com/phytothreats-research-project-aims-reduce-phytophthora-spread/plant-health/... |
| Description | Conference presentation |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | White, R.M., Young, J., Marzano, M., and Leahy, S. (2018) Prioritising stakeholder engagement for forest conservation during austerity. Pathways conference presentation, Goslar, Germany 16-19 September 2018. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Conference presentation at IUFRO |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Conference presentation on PHYTO-THREATS: An analysis of Phytophthora communities in plant nurseries? IUFRO World Congress, Curitiba, Brazil, October 2019 . |
| Year(s) Of Engagement Activity | 2019 |
| Description | Cooke D. 2019 Phytophthora: a European view of the threat. Presentation at National Phytophthora preparedness workshop. 5-6 June 2019 St. Kilda, Melbourne, Australia |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Invited to present research data and knowledge on European perspective to an Australian working group preparing for invasive Phytophthora pathogens. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Cooke DEL 2022. Insights from probing Oomycete diversity at different taxonomic scales. 21st Annual Meeting of the Oomycete Molecular Genetics Network. Aug 22-25, Brno, Czech Republic. |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Presentation at international conference |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://omgn.org/ |
| Description | Cooke DEL, Brierley J, Toth IK, Randall E, Humphris S, Jones J, Cock PJ. 2022. Applications of DNA metabarcoding for plant pathogen tracking and diagnostics. Crop Production in Northern Britain Conference. Online 1-2 March 2022 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presentation at conference of scientists, practitioners and agricultural advisors presenting power of new metabarcoding methods for investigation of microbial diversity |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://www.cpnb.org/ |
| Description | Cooke DEL, Randall E, Clark B, Thorpe P, Cock PJ, Pritchard L, Pettitt T, Frederickson-Matika D, Green S. 2019. Phytophthora eDNA barcoding for natural ecosystem surveillance. Proceedings of the Oomycete Molecular Genetics Network, 10-12 July 2019. SAMS, Oban, Scotland. |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | Presentation at key international conference on Oomycete biology (Oomycete Molecular Genetics Network). |
| Year(s) Of Engagement Activity | 2019 |
| Description | Cooke DEL, Randall E, Keillor B, Cock P 2022. eDNA metabarcoding as a powerful tool to track plant pathogens. Presentation at Underpinning National Capacity DNA technologies, skills and infrastructure workshop, Perth, UK Dec 2022. |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Attendance at workshop to link research to stakeholder application |
| Year(s) Of Engagement Activity | 2022 |
| Description | Discussions with BBC Science Correspondent on BBC article covering risks of spread of plant pathogens via trade and links to wider environment disease outbreaks |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | Discussions on plant health risks and Phytophthora diseases with BBC Science Correspondent Pallab Ghosh whose team will visit Scotland on March 16-17th 2020 to film a piece about the Phytophthora ramorum epidemic on larch and the spread of these Phytophthora diseases via the plant trade. Filming will also take place at one of the partner nurseries who are improving their biosecurity practices. The link between potential spread of plant diseases in trade and killing of trees in our wider environments will be emphasised for the public This piece will potentially reach a very wide audience. |
| Year(s) Of Engagement Activity | 2020 |
| Description | Dissemination of final project findings and management recommendations to all 15 partner nurseries |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Final sampling results across three years were reported to all fifteen partner nurseries in the fine scale survey. A comprehensive cover email explained the sampling and analyses procedures again, and 'walked' the reader through the results output which took the form of a simplified Excel spreadsheet listing sample metadata (date sample collected, sample type, host species, any symptoms recorded, location on nursery, plant passport number etc) and indicating whether that sample was positive or negative for Phytophthora in the PCR. For all positive, sequenced samples the Phytophthora species detected by metabarcoding were listed. Each nursery also received a separate 1-2 sided word document briefly outlining the key Phytophthoras found at that nursery, the implications and recommendations on mitigating management measures. For instance if water sources were found to contain Phytophthora then water treatment measures, or using covered water supplies, were recommended. Hosts found to contain high Phytophthora diversities or quarantine regulated pathogens were noted as 'high risk' as were the nursery green waste and spent compost dumps. Most nursery managers responded with questions and comments in relation to improving practice. Four of the partner nurseries have now joined the Plant Healthy Certification Scheme. |
| Year(s) Of Engagement Activity | 2021 |
| Description | Dissemination of nursery results to date to all project partner nurseries at intervals throughout the project and at the end |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | Updated spread sheets showing the results of Phytophthora testing of nursery samples were sent to all project partner nurseries in December 2018. The spread sheets contained information on sample type (water/root) and date of sampling, host (including stock identifiers and presence of any symptoms), location of sampling, and whether the sample was positive or negative in the PCR test for Phytophthora. The implications of the findings so far were discussed via email/phone with a number of the partner nurseries. As the project progressed there was evidence of partner nurseries improving practice based on advice delivered by the science team as a result of Phytophthora findings, for example raising plants off the ground, improving drainage and taking decisions not to trade in high-risk hosts. Nurseries also started asking questions of growing media suppliers - what are the processes of sterilisation and can they guarantee pathogen-free components?, and seed suppliers - has this seed come from disease-free orchards? In relation to raising from locally collected seed native plant stock destined for restoration planting at ecologically vulnerable sites, one nursery manager is now considering offering dedicated growing of stock to high biosecurity specification close to each restoration site and well away from the main commercial premises. Another partner nursery has now employed a full time Plant Health specialist to train staff on plant health issues, audit existing plant health processes within the nursery, and to update plant health standards. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Ethical considerations when using powerful diagnostics in research - experiences from working with plant nursery stakeholders |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Other audiences |
| Results and Impact | Sarah Green and Mariella Marzano were asked by the Scottish Plant Health Centre to give a presentation to one of the regular meetings of the Science Advisory and Response Team on the ethics of detection, drawing from my experiences of working with plant nurseries as part of the Phyto-threats project. There was much discussion afterwards on this often overlooked topic and a request made to write a blog for the Scottish Plant Health Centre. |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.planthealthcentre.scot/about-us |
| Description | Final all-project team meeting November 2019 |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Study participants or study members |
| Results and Impact | The aim of this meeting was to bring the entire project team together to share and discuss research progress since the last all-project team meeting on November 20th 2018, to outline planned outputs and to discuss next steps for continuing collaborations now that the project is finishing. Full report is available on the Phyto-threats project website with links to presentations (see below URL). |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.forestresearch.gov.uk/research/global-threats-from-phytophthora-spp/phytothreats-meeting... |
| Description | Improving nursery resilience against threats from Phytophthora |
| 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 | The aims of this first workshop were: • to introduce the scientific aims of the project • to develop collaborative networks across individuals and groups with an interest in working towards collective best practice in nurseries • to share lessons and experiences around the challenges and opportunities of managing disease threats • to identify nurseries and other stakeholder groups and individuals who could and would become involved in the research The meeting was attended by c45 academics, nursery managers, Plant Health inspectors, foresters, policy makers and others Richard McIntosh (Defra) provided a policy context for plant health in the UK. He emphasised the value of healthy landscapes and the benefits they can provide. Increased vigilance is important but also having the capacity to quickly intervene in the event of an incursion. Richard outlined the 5 'Ps' approach (predict, prevent, protect, prepare, partnering) and highlighted the range of approaches the government is taking pre-border, at the border and inland. He posed a challenge to the audience to think of how they could incorporate a 5'Ps' approach to their business. Mike Harvey (Maelor Forest Nurseries) highlighted the changes they have seen in their nursery over the last 20 years, particularly in the numbers of new pests and diseases and he noted the limited range of tools that nurseries have to deal with damage and control. Maelor have invested in Integrated Pest Management which guides use of water, clean areas and purchasing behaviour. Ian Nelson (Johnsons of Whixley) presented a trade perspective and noted the complexity of the trade network. Business is largely driven by price and profit. He said that UK growers currently cannot meet the UK demand for plants and therefore import from abroad. However, he recognised that the inspection regime in other countries may not be as robust as in the UK. Ian called for greater education amongst customers such as landscape contractors to look for alternatives to plants that can host serious diseases. David Edwards (Tilhill Forestry) started by describing the devastating impact that Phytophthora ramorum has had on larch forests in South Wales. David explored the efficacy of different approaches to deal with P. ramorum but also the huge challenges of trying to predict the next outbreak. He made a plea for prevention rather than cure for tree health and warned that any solutions should not impact heavily on the economics of forestry (e.g. abandoning Sitka Spruce). A panel discussion chaired by Sarah Green (FR) elaborated on some of these challenges, highlighting the dilemmas of 'unknown unknown' as well as 'known unknown' harmful organisms. The use of correct tools for detection was said to be important and discussions touched on the closure of high risk pathways. The value that plants add to the environment is believed to be highly under-valued by society, which facilitates the desire for cheaper products and imports. Reducing bureaucracy was considered to be key to making changes in the sector as well as seeking opportunities to increase the quality and quantity of UK plant production. Each of the 4 project Work Packages presented a 5 minute introduction to their work. Work Package 1 (presented by David Cooke from James Hutton Institute) focusses on understanding Phytophthora distribution, diversity and management in the UK nursery system. The team are developing a diagnostic system that can detect Phytophthoras and identify individual species using DNA methods. The team have been collecting samples at a number of nurseries. David thanked the nurseries who have volunteered so far and welcomed more participants. Work Package 2 (presented by Mike Dunn from Forest Research) involves social science and economics. The core focus on WP2 is a feasibility analysis and development of 'best practice' criteria. The research will involve exploration of nursery practices and issues they deal with on a daily basis as well as attitudes towards best practice guidance and accreditation. A consumer survey will be undertaken to understand better plant purchasing behaviours and public attitudes towards accreditation and what this could entail. Work Package 3 (presented by Bethan Purse from Centre for Ecology and Hydrology) involves modelling global Phytophthora risks to the UK. The team are mapping trade pathways from source countries and ecological zones and linking ecological traits of all known Phytophthora species globally to likely impacts if they were to arrive in the UK. They are looking to learn lessons from past introductions in order to develop a predictive tool. Work Package 4 (presented by Sarah Green on behalf of Paul Sharp from the University of Edinburgh) will look at predicting risk via analysis of Phytophthora genome evolution. Questions that this work package will explore include how Phytophthoras have evolved to kill trees, why they are so adaptable and how they can hybridise. The team will sequence the genomes of three Phytophthora species which will add to a comparative analysis of genomes across a range of Phytophthoras. Two international speakers provided an overseas perspective on Phytophthora risks and nursery accreditation. Susan Frankel (US Forest Service) focussed on California and the impact of Phytophthoras on native plants and wildlands. She noted the unintended consequences of restoration projects that are introducing Phytophthoras. The US National Plant Board have started a certification scheme with 8 nurseries currently signed up (pilot phase). Susan emphasised that complying with the certification standards required a lot of work but the nurseries involved are then free from intensive inspection per pest. There is also a voluntary accreditation scheme that involves following best practice guidance. Susan recognised that the scheme was not easy and she said you couldn't claim to be Phytophthora-free but you could claim to have done everything possible to be disease-free following a systems approach. Giles Hardy (Murdoch University, Perth) was unable to attend in person but presented a video on the Australian NIASA scheme (available as a slideshow without sound on http://www.slideshare.net/ForestResearch1/niasa-nursery-industry-accreditation-scheme-of-australia-a-working-model) whereby production nurseries and those involved in growing media sign up to follow best practice management guidelines. This scheme has been in operation since 1997 and the guidelines are now in their fifth edition. Giles described the guidance in detail including crop hygiene, crop management practices, general site management and water management. Giles also described in detail a method for composting. Alongside the nursery accreditation guidelines there is also a national nursery and garden industry biosecurity plan which focuses on risk mitigation. There followed a workshop session led by Mariella Marzano (Forest Research) to explore what a nursery accreditation scheme would look like in the UK. Feedback suggested that accreditation might need to be tailored for different stakeholders but possibly under a single umbrella. A scheme could include different levels of standards to encourage businesses to improve their practices. A number of practicality issues were raised and need further exploration. However, there was a strong consensus that any scheme should have minimal bureaucracy. It was felt that there would need to be consumer support for any scheme to provide an incentive for nurseries to be involved. Decisions over what the scheme should include would best be made by representatives from a mix of sectors. Brexit might provide an opportunity for the UK to promote its own best management practices and to have more control over quality of imports. There are practices (e.g. mail orders, garden shows, illegal trade in plants) that could undermine an accreditation scheme. The scheme would require consumers to be informed and supportive. Jon Knight gave a keynote listener talk, reflecting on the day's discussions. He emphasised that we need to understand market constraints and explore how to ensure that regulations and legislation work better for the sector and consumers. He noted that capacity will have to be increased if we are to produce more 'home-grown' plants but businesses need to be profitable in order to keep trading and that currently involves importing from abroad. He highlighted that if there is a desire to change trading practices then consumers need to be willing to pay more for 'home-grown' plants and that involves recognising the value e.g. of a disease-free environment. He made a plea for models to provide some foresight on future risks to facilitate traders becoming more resilient. |
| Year(s) Of Engagement Activity | 2016 |
| URL | http://www.forestry.gov.uk/pdf/FR_Phytothreats_Oct6th2016_Green.pdf/$FILE/FR_Phytothreats_Oct6th2016... |
| Description | Keynote presentation by Louise Barwell "Trait-based approaches for invasion risk assessment of Phytophthora pathogens" at Dieback Working Groups Disease Information Group Conference, Australia, September 10th-11th |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | The theme of the online conference was "Phytophthora Dieback - Tools for the Future" and aimed to bring together experts, speakers and the public. Speakers presented on a range of contemporary Phytophthora Dieback issues, including; developments with new research and technology, insights on industry engagement and land management. ranging from local, to state and international perspectives. Our project presented the novel trait-based approaches and tools for horizon scanning for risks from global Phytophthora species affecting forestry, horticulture and agriculture. |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.dwg.org.au/event/dig-conference-2020/ |
| Description | Manned the James Hutton Institute stand at the Royal Highland Show in Edinburgh 20-21 July 2019 discussing the Phytothreat projects role in forest and natural ecosystem health |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Public/other audiences |
| Results and Impact | The Royal Highland Show is a major event in the Scottish calendar for communication of key science messages to the wider public and other interested stakeholders. David Cooke helped to present the work of the PhytoThreats project in the context of Hutton's research portfolio of forestry science. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Meeting of the Science and Advisory Reponse Team of the Scottish Plant Health Centre, Forest Research, January 31st 2020 |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Other audiences |
| Results and Impact | Sarah Green presented a talk on the Phyto-threats project; focusing on the outcomes of the nursery sampling, linking Phytophthora findings to management practice, support for accreditation and implications of the findings for Plant Health in Scotland in face of proposed new planting schemes. Mariella Marzano then convened discussion groups around the question: Is our current plant health biosecurity framework fit for purpose? The main outcome of the meeting was the action point for the Plant health Centre Sector leads to draft a letter to the Scottish Plant Health Centre Steering Group outlining the biosecurity concerns over ill-thought through, rapidly executed woodland expansion programmes, the need to have an overarching strategy to ensure Plant Health and biosecurity is a priority when planning schemes. |
| Year(s) Of Engagement Activity | 2020 |
| Description | Meeting with the Horticultural Manager of the Horticultural Trades Association |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | Sarah Green, Mariella Marzano and Debbie Frederickson-Matika of the Phyto-threats project team held a one-day meeting at Forest Research's Northern Research Station with the Horticultural Manager of the Horticultural Trades Association (HTA), Alistair Yeomans. The aim of the meeting was to discuss progress with the HTA-led Plant Health Assurance Scheme and Plant Health Standard (being developed by the HTA together with industry), to present results from the Phyto-threats project to date which might be used to underpin the assurance scheme, and to decide upon the best way of communicating project results to the HTA and industry. It was agreed that the Phyto-threats project data can provide the supporting scientific evidence to justify nursery infrastructure and management improvements required as part of the Plant Health Assurance Scheme. The Phyto-threats project data will be disseminated in the form of technical fliers and webpages to the HTA, industry and policymakers developing the Plant Health Standard over the next 6-8 months so the project will have impact in shaping this new, UK-wide Plant Health Accreditation Scheme. |
| Year(s) Of Engagement Activity | 2019 |
| Description | OECD-funded workshop on "Rapid evolution in the spread of invasive species", CEH, Wallingford, UK, June 2019 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | CEH co-convened this OECD workshop with Stirling University which involved 12 participants from universities, public sector research institutes and plant and animal health. Louise Barwell, Dan Chapman and Beth Purse all gave talks on the analyses undertaken in Phytothreats to predict the behaviour, spread and impacts of Phytophthoras from biological traits, trade, biosecurity and climatic factors. Discussion with the other participants centred around the ways in which human activities are altering evolution of pathogens during invasion and the knowledge gaps in understanding these processes. These lead to an report to the OECD and a review paper for submission in 2020. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.oecd.org/agriculture/crp/documents/conference-organiser-report-evolution-invasive-specie... |
| Description | Phyto-threats all project team meeting - April 2018 |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Study participants or study members |
| Results and Impact | Report on Phyto-threats project team meeting April 26th 2018 Held at CEH, Wallingford, Oxfordshire The aim of this meeting was to bring the entire project team and members of the Expert Advisory Panel together to share and discuss research progress since the last all-project team meeting on October 3rd 2017, and to outline and receive feedback on future research plans. WP1 Phytophthora distribution, diversity and management in UK nursery systems - David Cooke (JHI), Leighton Prichard (JHI), Pete Thorpe (JHI) and Tim Pettitt (University of Worcester) David Cooke introduced the entire WP1 team, including those involved in nursery sampling, processing in the lab, and analysing data, and he reminded everyone of the WP objectives and methods. He noted that processing of the filters from the water samples is very time consuming and that processing only the buffer solution that the filters are placed in might yield the same information with much less sample preparation time. They will be comparing buffer and filter samples from a subset of nursery samples to ensure that they are not missing any phytophthoras trapped on the filters. For the fine scale sampling they have now obtained 49 sample sets from the 15 partner nurseries (6 in England, 1 in Wales and 8 in Scotland). Some results have now been reported back to all nurseries and this has promoted a more positive attitude among nursery managers towards the project. The WP1 team now have 2292 samples from 150 different host plant species, plus associated metadata. Of these samples, 1660 have been PCR tested for Phytophthora, including 617 from plant roots, 193 water filters and 850 buffer samples associated with water filters. They have also carried out isolation from some samples, yielding P. austrocedri, P. cambivora and P. lateralis. The team have been testing new methods for DNA extraction and have moved on to using kits rather than the phenol/chloroform method. A question was asked about how sick plants were targeted - by eye?, or does the nursery manager ask the team to test specific plants? The answer was both, and that field notes and photos are taken of sampled plants so that results can be linked back to symptoms. For the OPAL community sampling of local waterways, in cooperation with David Slawson and Vanessa Barber, the WP1 team have received 26 samples to date from three locations (north Wales, south Wales and Glasgow). These have been PCR tested for Phytophthora and about 50% are positive. This sparked some discussion on the usefulness of rolling out in the future the OPAL citizen science/public engagement element to a broader project looking at pathogens in the wider environment, particularly for early detection in sentinel plantings. For the broad scale sampling, 64 nurseries have been sampled to date; 25 in Scotland and 39 in England/Wales. Samples usually involve 5-10 root samples per nursery. So far 408 root samples have been received. Root extractions have yet to be done on these samples. Sample packs for the 2018 broad scale sampling have been sent out to PHSI. David then showed a range of photographs of plants sampled across nurseries and other general observations and reiterated that messages about management are being communicated to nursery managers. He presented a slide showing progress since the last project team meeting in October 2017, including data on the large number of samples processed during this time as lab testing has been accelerated. The first Illumina plate has been run and analysed, and results from the PCR testing and Phytophthora species data were reported back to nurseries in March 2018. David went on to show a number of graphs summarising PCR results by substrate and nursery and emphasised that data interpretation in relation to management practice is needed next. There was a question on whether the sampler affects the number of positives, and that it might be good to see if certain people are getting higher numbers of PCR positive samples. The answer was that there is a fairly large team of people sampling most nurseries and that the team always includes at least one experienced plant pathologist. The sample team usually walks around the nursery first thing and decides together where possible which plants to focus on. Another question was asked about whether the distribution of PCR positives and negatives could be plotted across nurseries to look at outliers, ie those nurseries with particularly high or low numbers of Phytophthora positives, and that could be related back to management practice. The discussion moved on to how the nursery sampling data can be analysed statistically, for example, how can we show that a particular practice results in a high Phytophthora load? It was suggested that the project establishes a small working group to decide how to analyse the data statistically. David showed a slide summarising the Illumina run carried out with the first set of positive PCR samples. Samples containing synthetic control sequences at different concentrations were included on the plate to test the sequencing error rate, the indexing error to set an acceptable threshold read number (currently 50-100 reads) and the sensitivity range. David stressed that the species data obtained in this first sequencing run are preliminary and that full validation is required against a set of reference Illumina sequences obtained from 45 known Phytophthora cultures already set up on a control plate due to be run in May. This should provide important data on ITS1 sequence variation within species. David then went on to show an example of the results files sent to the nursery managers back in March, including a cover letter explaining the methods and what the results are likely to mean. A brief comment was included on each Phytophthora species reported by the sequence data, ie its usual hosts and whether it is regarded as an aggressive species or not. David also discussed the Illumina findings and challenges - ie most species were Phytophthora, with some downy mildew or Nothophytophthora. There were low levels of Phytopythium in the sequence data. He ran through an overview of species found in some samples, for instance a high diversity of species particularly in river and puddle samples. Some species results were unexpected and we need a means of examining false positives. Reporting results back to managers is also challenging as the implications for management are not always clear. Summary findings will be reported back to the Plant Health Risk Group via Jane Barbrook of APHA. David also pointed out the dynamic nature of Phytophthora taxonomy, showing examples of the clade 6 phylogenies in 2003 (12 taxa) versus 2015 (30 taxa). He finished his presentation by outlining ongoing and future work; that the nursery sampling will be completed in 2018, many more Illumina plates need to be run and the need for data interpretation in relation to management practice, ie practices need to be related to Phytophthora findings. A question was asked about relating DNA findings to actual viable propagules and that it would be useful to back up the DNA data by doing isolations/colony plate counts. This was addressed in part by a presentation from Tim Pettitt (below). Tim Pettitt (University of Worcester) was able to demonstrate some results from his baiting and plating water samples conducted at a subset of nurseries sampled in this project. His data showed numbers of viable oomycete spores in different water samples that had also been PCR tested for Phytophthora. He recorded zero viability of oomycetes in a treated water sample (filtered and chemically treated) that was positive for Phytophthora in the PCR test. Therefore we do need to be careful in interpreting data because presence of DNA in a sample does not necessarily indicate viable propagules ie the PCR test is not a good indicator of viability. Tim also demonstrated his amendment to the water sampling methodology using a bike track pump used to push water through a bottle containing the water sample linked to several filters. This greatly speeds up the process of water sampling and reduces potential for cross contamination of samples. He uses bottles of fizzy water - they are sterile and the fizzy water can be used to clean the filter heads and tubes, then replaced with the sample water. Leighton Pritchard gave a presentation on the bioinformatics element of the WP1 work, entitled 'Classification Performance Evaluation'. Through the use of sound tracks illustrating distortion of spoken phrases to represent the sequence 'noise' that the bioinformatics pipeline has to deal with when attempting to assign a sequence to a species, he demonstrated the importance of removing the 'noise' from a sample containing sequences (ie 'noise' meaning the sequences and sequence fragments that we are not interested in) so that the sequences are assigned to the correct species. He reiterated the importance of training and test sample sets, for example the 45 known Phytophthora species that will be Illumina sequenced so that we are clearer about which ITS1 sequences belong to which species. This will help us determine true positives and true negatives from false positive and negatives in our nursery samples. The question arose about how much importance we attribute to distinguishing between closely related species. This would depend upon the species e.g. distinguishing P. rubi or P. fragariae would be not important. Sometimes it's necessary to take a look at the sequences and determine manually. Some difficulties encountered include reference sequences that appear to differ but are actually from the same isolate sequenced by different labs. Pete Thorpe discussed some of these conflicts in his presentation. Pete Thorpe finished up the WP1 presentations by running through the metapy pipeline (to remind us of the methods and clustering tools). He also presented an update on the Phytophthora ITS1 reference database in which Sanger sequences have been obtained for 40 Phytopthora isolates and run through metapy to check the accuracy of the database. Some sequences did not cluster to the database but did match 100% to sequences in Genbank; these entries were added into the database. The performance of each clustering tool in metapy was tested on the Illumina sequence data generated from four samples containing mixes of DNA from known Phytophthora species. For each clustering tool Pete tested the sensitivity, precision, false negative rate and false discovery rate. Some species with very similar ITS1 sequences cannot be separated by most of the clustering tools e.g. P. capsici. Bowtie can separate them, but only if the ITS1 sequence is a perfect match with the database sequence. Basically Swarm performed best in terms of the above criteria but none of the tools were perfect. Manual assessments are necessary when determining which species of a species cluster is most likely to be the one present. Pete also talked about the error rates in the Illumina sequence output. Four random synthetic control sequences were synthesised with the same mean length and base composition as the Phytophthora database sequences but with no BLAST hit and processed in the same way as the nursery samples. Errors can occur during PCR, through Taq error and during Illumina sequencing. He showed the frequency distribution of errors in the control sequences and where on the sequences the mismatches occurred. Errors also include indels and chimeras. The majority of the error variation occurred within two mismatches. Looking at the sequences, when the clustering threshold was set at 3 mismatches then P. ramorum was mis-identified as P. lateralis; at 2 mismatches, P. ramorum was correctly identified. Since a large amount of the dataset was represented within one mismatch of the control sequences a strict 99% threshold was used to cluster sequences. WP2 Feasibility analyses and development of 'best practice' criteria - Mariella Marzano (FR) Mariella started the WP2 presentation with an overview of milestones and outputs, and outlined progress so far, including the public consumer survey and resulting publication - a 'glossy' summarising the results of the public consumer survey which was produced for the THAPBI dissemination event in February. The online consumer 'smart survey' aimed at the public, nurseries, garden centres and landscapers has been distributed via horticultural magazines and email, although participation to date has been very limited. The WP2 team have been carrying out interviews with managers of the partner nurseries, liaising with FERA/HTA over the pilot assurance scheme, and liaising with FERA on the cost and responsibility sharing project, in which Gregory Valatin (FR) accompanied FERA economists during a number of nursery interviews to gain an understanding of the costs of different management practices. The next steps for WP2 are to increase participation in the online 'smart survey'. This could be done by using some of the budget to pay a company to conduct the survey for the project team. The WP2 team also need to improve economic data gathering through interviews with nursery managers. Interviews to understand purchasing habits and attitudes towards accreditation are also going to be carried out with retailers and garden centres, local authorities and other managers of large parks and gardens, as well as the landscaping sector. A series of focus groups will also be held in response to the interview and survey findings on appetite for accreditation. Mariella ran through the questions asked in the nursery interviews and presented some of the findings so far in terms of nursery manager perspectives on disease threats, what they think about management for best practice, and what influences their plant purchasing decisions. She found that appetite for accreditation tended to be based on the size of the nursery and business objective. Some of the perceived benefits are that accreditation will provide reassurance to the customer as well as a training/'safety net' for the nursery (in terms of compensation). Participating nurseries would also be 'seen to be doing something' and it would allow traceability. Some of the perceived challenges are that there is currently little consumer awareness of the need for accreditation, the benefits of accreditation need to outweigh the cost of membership, and there was scepticism as to whether accreditation would change behaviours. Additionally, there is the common misunderstanding that we are trying to impose yet another scheme, instead of providing scientific evidence that would feed into a scheme. Not every nursery has got the message about disease threats so engagement on this issue will be important, and how would accreditation be policed? One comment was that there needs to be an update on progress of existing assurance schemes in the UK, looking to see how these could be run. Mariella confirmed that the WP2 team will resume engagement with the HTA and Defra over the pilot assurance scheme to ensure Phyto-threats project findings are used to influence the development of the scheme. Mariella then held three discussion sessions. In the first session she asked the project team 'what is 'best practice'? She listed twelve nursery 'best practices' and asked if all of these should form the basis for accreditation and whether other best practices should also be included. This resulted in some discussion with one comment being there was a need for continuous monitoring of stock as part of accreditation criteria. This would require staff training. Another comment was that plant protection products can often 'mask' symptoms rather than solving the problem, and that this needed to be considered within accreditation. In the second session project team members were asked to get into pairs to discuss which key questions the WP2 team should be asking of retailers, garden centres, local authorities and landscapers. Questions should include what are their key suppliers? what is their biosecurity knowledge and experience?, what are their purchasing practices and what influences them? and what are their perceptions of consumer demand?. One important point raised during this session was the need for biosecurity and plant health to be s |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://www.forestresearch.gov.uk/research/global-threats-from-phytophthora-spp/phytothreats-meeting... |
| Description | Phyto-threats all project team meeting - November 2018 |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Study participants or study members |
| Results and Impact | Report on Phyto-threats project team meeting November 20th 2018 Held at FR NRS Roslin The aim of this meeting was to bring the entire project team and members of the Expert Advisory Panel together to share and discuss research progress since the last all-project team meeting on April 23rd 2018, and to outline and receive feedback on research plans including proposed funding for continuing strands of the project beyond this financial year. WP1 Phytophthora distribution, diversity and management in UK nursery systems - David Cooke and Leighton Prichard (JHI) David Cooke started off his presentation by introducing a new member of the WP team; JHI bioinformaticist Peter Cock replaces Pete Thorpe who has taken up a position at St Andrews University. Nursery samples To date the team have completed 59 sampling missions across the 15 partner nurseries, collecting 4016 samples of which 2165 have been PCR tested for Phytophthora. The lab team have determined that processing the buffer for DNA, rather than the filter on which the DNA was originally collected, gives lots of DNA yield, so they are no longer processing filters. The team are still working their way through the fine-scale nursery root samples. The broad-scale sampling has resulted in root samples from 101 nurseries; 36 in Scotland and 65 in England/Wales. With 5-10 root samples per nursery a total of 653 samples have been returned. Top hosts returned from the broad scale sampling are: Rhododendron, Viburnum, Pieris, Juniperus, Chamaecyparis, Hebe, Fagus, Olea, Taxus, Prunus. It will be interesting to see which hosts turn out to be Phytophthora positive. These root extractions are under way. For the OPAL wider environment sampling of water courses (now finished) a total of 26 samples have been received. Sample processing Much effort has gone into root extraction optimisation. JHI tried automation with a Qiagen kit but the result was not good. They are automating with PowerPlant Pro kit, which is currently being used for the fine-scale root samples. PCR test results to date show that ~ 50% of samples are positive overall. The frequency of positives varies from nursery to nursery (ranges from 30-70%). These results will be presented by management practice, not by nursery, in public fora. Positives for roots are slightly higher than 50%. There are 1600 samples still to process. Since April this year more samples have been sequenced using Ilumina on plates containing nursery samples as well as samples from other Phytophthora metabarcoding projects - which all help to validate the results. David gave an overview of the Illumina rationale which Leighton will cover in his talk later, reminding everyone that sequencing outputs are 250 bp reads, 15M barcode reads, 156K reads per sample. Synthetic controls are included on each plate to give an estimate of technical error rate and sensitivity range. Also included on one of the plates were 45 samples from cultures of known Phytophthora spp. David went on to present some of the nursery sample findings from two of the nurseries: P. megasperma /P. gonapodyides clade 6 P. cryptogea clade 8a P. obscura clade 8d P. quercina clade 12 Plus some (closely related) downy mildew species Samples from another nursery yielded DNA reads matching: P. nicotianae clade 1 from Choisia sp P. occultans/P. citrophthora/ P. terminalis clade 2 from Pachysandra sp, Data on Phytophthora species detected in nurseries will feed into the community modelling (linking with WP3) which will assess factors such as nursery size, management practices, suppliers and geographical location on Phytophthora species assemblages detected. Nursery Phytophthora data will also be linked to Phytophthora data from natural ecosystems in concurrent projects (i.e. Ponte) and community eDNA /metabarcoding. Next steps are to complete sample processing and barcoding, re-run samples where contamination is suspected, validate the data with the new bioinformatics classifier (involving Leighton and Peter Cock), and feedback data to nursery managers and the WP3 modelling team. Discussion During the discussion a point was raised that some PCR positives initially reported back to nurseries as Phytophthora positive have subsequently been identified by sequencing as downy mildew species i.e. other oomycetes. How we are reporting back to nurseries in light of this? It was agreed that downy mildews are also important pathogens and should be reported to nursery managers, but not included in the data as Phytophthora +ves. Another comment related to the urgent need to report back to nurseries soon as they are overdue sample results, also, that it would be interesting to see if there are any changed behaviours according to results. David agreed, and said we would be able to relate photos of incidence/symptoms to results in the feedback. It was asked whether peat or peat alternatives had been tested? The answer was no, potting mix was not tested as part of this project. A final question: can the species data be related back to circumstances/ best practices? The answer was yes, this is the plan for the analyses. Leighton Pritchard (JHI) Leighton's presentation focused on the question of what was really being measured by Illumina sequencing. He reminded us that there are real stakes from our results (i.e. the consequences of a regulated pathogen turning up in a nursery might mean closure) so we need to be held to a higher standard of accuracy than other types of studies. ITS1 marker sequences are used in the metabarcoding analyses. We assume one species means one ITS1 sequence, but this is not the case! Leighton ran through the metabarcoding method and described three 'pinch points'. These are: 1. Having a comprehensive database 2. Whether barcodes are precise enough 3. And how 'individualising' are the oomycetes ITS1 sequences? Synthetic control sequences are used to help set an error rate for each sequenced plate and to check for levels of cross contamination in test samples. Synthetic control mixes are comprised of 4 unique sequences with a base composition similar to Phytophthora ITS1. In the tests that Leighton conducted (on one of the plates) the four synthetic sequences were used at six different combinations and at three different dilutions i.e. 18 synthetic control samples in total on the plate. Analyses of the Illumina output showed that some synthetic control samples contain 1000s of sequence variants, differing from the actual control sequences by up to 10-15 bp. How much is real variation? Leighton presented a plot showing the variants and how different they are from the original sequence that was put in. Leighton also spoke about the dilution effect: at the most dilute, worryingly, an artefact of 1 snp difference is seen. Some sequences can't be matched to the input sequences and are likely to be contamination. These occur at a threshold of 100. So, setting a threshold above 100 gets rid of a lot of variants. If a DADA2 clean-up is performed, the threshold is reduced to 20 variants. Also seen are PCR artefacts in low abundance (i.e. when PCR amplification introduces variation) and what appear to be contaminating sequences from environmental samples. So what is in the contamination? Many look like ITS1 sequences; many don't. Most cross-contamination comes from soil bacteria, some are oomycete sequences. The synthetic sequences pop up too at low abundance in some of the environmental samples. These are easily recognised as cross-contamination and their abundance (in terms of read counts) in samples across the plate can be used to set thresholds. Leighton then went on to explore the 'one species, one ITS1' concept. Many species have more than one ITS1 sequence since the ITS region can occur in a Phytophthora genome in anything from 40-170 copies. If a single isolate is Illumina sequenced then one major cluster should result. One of the plates contained ~40 single isolate samples to test for ITS1 sequence variation across a range of species. However, from a single isolate up to 2000 sequences resulted! Thus a single isolate does not give 1 single sequence. The resulting clustering of sequences by Swarm produced up to 150 OTUs (operational taxonomic units) (mostly 40-60) from a single isolate. However, many of these sequences are variants occurring at low abundance. Removing all amplicons occurring at abundance of less than 20 before clustering reduces the number of OTUs per isolate to around 6. The next question is 'how are the OTUs present within each isolate 'individualising'? By looking at the Jaccard distance between OTU members among isolates it can be seen that several OTUs are unique to individual Phytophthora species and some are common to several sequenced species. If one species has a specific 'classifier' (i.e. unique OTU) as well we can ignore the ambiguous ones. Leighton asked 'what is a classifier?' Associating input sequences with species classes, this is the classifier. So if you change anything in the method, the classifier changes. Leighton and bioinformaticist Peter Cock are currently developing the automation of the 'classifier' process. This includes building the reference database framework based on trusted sources. The next step is to create a training dataset. This will be combinations of reads from single isolate controls, individualising sets for a species, applying and evaluating the current pipeline and applying validated classifiers to old and new samples. Discussion A question was asked about the timeframe by which we can have confidence in the latest plates to present the results back to nursery managers. Leighton said he couldn't give a definite date, but hopefully fast! He thought early next year was achievable. Another question related to whether there were data on isolations to go with these sequence outputs? It was confirmed that there were P. lateralis/P. cambivora isolations with DNA samples from the same material progressing down the pipeline. However isolations were never intended to be done as part of this project. It was mentioned that a Scottish Government-funded project is generating companion data from live (baited) organisms as well as metabarcode data from the same soil and water samples. We're assuming that what is in a sample represents a threat but this may not be so. Detectable live presence may be a better marker. Another comment related to the sequencing process: the synthetic control in most abundance gave the same reads when replicated and those sequences that were spiked appeared in the correct order. The lowest dilution of synthetic sequences was not found or was equal to background noise, which is good. It shows this as a robust and accurate tool. In this respect, testing with control sequences, we seem to be at the forefront of metabarcoding. It was pointed out that the nested PCR itself could potentially introduce error and there was general concurrence on this point given that the technique is so sensitive. It is recommended when starting up to use blanks and do a control plate before anything else so that an estimate of cross-contamination can be made. However, overall, when considering what species have been found in nursery samples to date, the results make sense. Pathogens appear on expected hosts (i.e. P. austrocedri on juniper, P. lateralis on Chamaecyparis, P. pseudostugae on Douglas fir, P. occultans on Buxus). If a result looks erroneous, this has usually been present at very low read number and is most likely to be cross-contamination. Hence the need to set a read threshold below which results are not considered as true. On the question of doing some qPCR validation of results, the answer was yes, this had been done, but as part of other metabarcoding projects. WP2 Feasibility analyses and development of 'best practice' criteria - Mariella Marzano (FR), Mike Dunn (FR), Gregory Valatin (FR), Glyn Jones (Fera) and Colin Price (external consultant) Mariella opened her presentation with a brief reminder of the objectives of WP2. She then went on to update the team as to where they are with the different sectors: Nursery interviews - the team have conducted 19 nursery interviews so far and are aiming to have interviews completed by Jan/Feb 2019. One of the problems has been that there are so many questionnaires in circulation because of the competing accreditation schemes that nurseries have been deluged by questions and become fatigued! The team have, however, managed to interview several on-line retailers and garden centres, where previously they were short of inputs from these sectors. A survey company has been recruited to take up the task from here. Landscapers - Mariella explained that after engaging with landscapers e.g. LI (Landscape Institute) and BALI (British Association of Landscape Industries) she was made aware that her team's questions were too generic and not specific enough. This will need further discussion in the focus groups. 'Landscapers' are more accurately landscape architects, contractors or garden designers, each with different roles and implications for biosecurity. Furthermore, individual contracts determine how much impact landscapers have in choosing plants: they may be told what to plant; may be able to offer choices or alternatives; and depending on the client base they may or may not have biosecurity awareness. They may have access to a reference guide (for example the LI is releasing a 'biosecurity toolkit' document for their members). A good question to investigate is at what stage in the process is biosecurity important, if at any? Glyn Jones and Barbara Agstner of Fera have done a lot of groundwork on cost-sharing. This will be presented by Glyn later. Retailers/Garden Centres - Mariella attended a recent workshop that involved large retailers. Discussions indicated the feeling that customers trust that this sector is doing things correctly and expect quality, and retailers are wary of negative messaging. However, customers are now starting to ask more questions e.g. on plant origins. Through interviews one issue raised was that customers can take their diseased plants to the garden centre to ask experts for advice on ailing plants!, thus, potentially disseminating pathogens into the garden centres. There seems to be an opportunity here for a plant health message to the public. Mariella then posed a question to the floor - the WP2 team had proposed to do a series of focus groups in the later stages of the project, so what should the focus groups be about? This will be discussed later during the WP5 presentation. Mike Dunn - Mike has been exploring biosecurity issues with public parks/gardens. Both sectors have an interest in plant health standards, which is driven by the obligation they feel to meet visitor requirements, not driven by pest/disease concerns. Generally, visitors want and expect to see exotic species. The National Trust has bronze/ silver /gold plant health standard checklists of what factors to consider when procuring. Mike and team have also developed a Local Authority question framework and plan to interview 15-20 Local Authorities. The consumer survey, including gathering of more economic data, is now going to be the responsibility of a survey company and telephone surveys will be conducted on 50 each of nurseries, garden centres and landscapers, to be completed by February 2019. Questions will elucidate location within the supply chain and key biosecurity factors. Discussion Mariella asked for input on how to integrate all the data from the surveys of the three main sectors and how to disseminate advice. It was agreed that packaging up information and advice from the project and making project data accessible to stakeholders would be key. A comment was made that the team's choice of target groups was correct, particularly the landscapers. The 'landscaper' sector could have some biosecurity weaknesses, because following the planning and approval stages there are apparently few subsequent checks and balances to ensure that plans are followed. Glyn Jones presented on the Defra Future-Proofing Plant Health (FPPH) work of relevance to the Phyto-threats project, outlining three projects as follows; Early warning system/pathways analysis - Glyn pre |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://www.forestresearch.gov.uk/research/global-threats-from-phytophthora-spp/phytothreats-meeting... |
| Description | Phyto-threats project stand, display and presentation at the National Plant Show |
| 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 | The Phyto-threats project and three team members returned to the National Plant Show again this year, held in Stoneleigh Park, Warwickshire, June 19-20th 2018. This is one of the largest plant trade shows in the UK, featuring over 160 exhibitors and receiving around 1400 visitors, representing garden centres and retail nurseries, as well as wholesale nurseries, online and mail order retailers, garden designers, consultants and local authorities. The Phyto-threats stand had a poster display aimed at raising awareness of the link between the plant trade and Phytophthora outbreaks in the wider environment, and offered fliers with results from the consumer survey on 'attitudes and behaviours of the UK's plant buying public' as well as some preliminary results from the ongoing nursery surveys for Phytophthora. The project also had a seminar slot on both days in which the nursery survey work was presented including Phytophthora findings to date and key messages so far in terms of management practices linked to high levels of Phytophthora infestation. Once again the stand received a steady stream of interested visitors over both days which enabled some very useful networking opportunities. It does appear that awareness of pest and disease issues in trade is rising, largely due to concerns over Xylella but also Phytophthora. Project team members took the opportunity to distribute a nursery and garden centre survey questionnaire aimed at improving our understanding of the supply chain; the perceived benefits (or not) of an assurance scheme; the basis of these attitudes (e.g. experiences of pests and diseases; use of measures for managing tree disease); and the willingness to pay extra or to travel further to buy accredited products. Information gained from this survey will be used to guide the development of effective accreditation. The survey is also available online. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://www.forestresearch.gov.uk/research/global-threats-from-phytophthora-spp/phytothreats-meeting... |
| Description | Phyto-threats stand and seminar at the National Plant Show, 18-19th June 2019, Stoneleigh Park, Warwickshire |
| 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 | Members of the Phyto-threats project team attended the National Plant Show for the third year running. The project had a display stand with proejct information in the form of posters, fliers, technical reports on the project's outcomes to date. Members of the project team also gave a 15 minute presentation on both days to the general audience focused on the outcomes of the nursery survey, management practices linked to high Phytophthora infestation levels and evidence to support accreditation. The stand once again received a steady flow of visitors (nursery or garden centre managers or other types of plant producer/purchaser) with good discussion on plant health risks. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://hta.org.uk/event_listing/hta-national-plant-show-2019.html |
| Description | Phyto-threats start-up meeting |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Policymakers/politicians |
| Results and Impact | The aim of this meeting was to bring the whole project team together with a range of stakeholders to present the workpackage (WP) objectives, research approaches and programmes of work in order to generate shared understanding, discussion, commentary and advice. The aim of this meeting was to bring the whole project team together with a range of stakeholders to present the workpackage (WP) objectives, research approaches and programmes of work in order to generate shared understanding, discussion, commentary and advice. Action points arising from the meeting are highlighted in green. There were 25 attendees at the meeting comprising the project science team, nursery stakeholder participants, representatives from policy and industry, and the THAPBI coordinator. Project Overview 9.00-9.30: The meeting started with an overview of the Phytothreats project by Project Coordinator Sarah Green (Forest Research, FR). Sarah provided some general background on Phytophthoras, setting the scene with descriptions of five 'emerging' Phytophthoras now causing damage to trees in Britain, stressing the link with trade in terms of introduction and spread of these pathogens. She gave a brief description of the project WPs and objectives and finished with an overview of the day's agenda. Introductions 09.30-10.00: Social scientist Mike Dunn (FR) led the 'ice breaker' session which involved 5 mins of getting to know your neighbour before having to stand up and introduce them to the room. It's amazing what some people collect for hobbies !.The session helped to set a relaxed and informal atmosphere for the rest of the meeting. WP1 presentation 10.00-11.00: David Cooke (James Hutton Institute, JHI) outlined plans for WP1: Phytophthora diversity, distribution and management in UK nursery systems. Objective 1 of the WP is to use metabarcoding to analyse Phytophthora community structure in different nursery management systems and Objective 2 is a Phytophthora community modelling analysis. David outlined the proposed methods for sampling, with a brief account of sampling theory and bioinformatics and pointed out potential challenges and technical issues that need to be considered. David also gave a quick account of Phytophthora barcoding literature; for example a recent study of four Scottish streams found the DNA signals of 45 'species' of Phytophthora. This emphasized the need for a baseline of the 'background' level of Phytophthoras present in the wider UK environment. David's talk was followed by a discussion session which is summarized as follows; ? Vadim Saraev (Forest Research) asked how many nurseries would be surveyed, ie how would the project ensure that the sample size of nurseries was representative of the industry as a whole?. This prompted comment on ensuring that sampling was done across a broad range of nursery management practices. Currently the project has 8 partner nurseries signed up in Scotland and 4 in England & Wales. These probably represent the more pro-active nurseries in terms of willingness to manage disease. The challenge is to get those operating less optimal practice in terms of disease management. 2 ? How to appeal to nurseries in order to get engagement?. Rodney Shearer (Alba Trees) commented that we are trying to change the mindset and create a positive ethos so nurseries should be positive. ? What happens if we find a Quarantine Pathogen (QP)?. This issue was making some nursery managers and particularly the traders (ie garden centres) reluctant to participate in the project. Sarah Green (FR) asked if the project could have exemption from the legal obligation to report QP to Plant Health and instead report findings back to the nursery and work with the nursery to manage the problem through the project. The return comment was that although a finding based on DNA data is not sufficient evidence in itself to justify statutory action, any finding would still need to be reported. We should be able to reassure nursery managers that there will be a delay between sampling and results coming out so it is unlikely that inspectors will be called to the nursery, especially when the finding has been in water and not associated with an actual diseased plant. ? It was asked whether we could define a 'threshold' signal of reportable Phytophthora in the sample. The data from each sample will be in the form of DNA sequences and are quantifiable to a certain extent (ie number of DNA sequence reads per species in the sample) so the answer was, yes, this could be possible ie we would only report on QP if there were at least 'x' number of DNA reads present ?. ? It was reiterated that statutory action only happens with symptoms and an isolate from statutory sampling. Kelvin Hughes (Animal and Plant Health Agency, APHA) stressed that the project cannot avoid the legal need to declare something and that plant passports and tracing plant histories may well result in international implications of detection. It was however agreed that there could be some negotiation on this matter and Kelvin suggested that Plant Health Policy members of the Expert Advisory Panel need to discuss the issue of QP findings and report back to the WP1 team before nursery sampling starts. ? Sarah Green (FR) and John Speirs (Scottish Government) made the point that other research projects are analysing Phytophthora diversity in soils and water in the wider environment in Britain (mainly Scotland at this stage) and that the data will link in very well with Phytothreats. Sarah also said that these other projects are detecting quarantine regulated Phytophthoras at various wider environment sites including those not reported to have had Phytophthora outbreaks so this raises importance of having 'negative controls' of non-nursery sites. This would allow nursery data on Phytophthora diversity to be viewed comparatively to a 'background' level of diversity in the wider environment. ? Sarah Green (FR) asked whether the big trader/distributors such as supermarket and garden centre chains are subject to the same Plant Health inspections as smaller businesses?. The answer from Kelvin Hughes and Jane Barbrook (both APHA) was yes, their distribution centres are inspected. It would be useful to get these companies on board with the project. Alice Snowdon (Cheviot Trees) commented that small nurseries can use the data to improve their businesses whereas large distributors may feel they have something to lose, but nothing to gain. ? Alice Snowdon (Cheviot Trees) asked how many quarantine Phytophthora species per plant/batch are usually found and how many plants for sale are found infected with quarantine Phytophthora pathogens per year?. Jane Barbrook (APHA) commented that this has improved from a few % to <1% now. 3 ? Jill Thompson (THAPBI Coordinator, Centre for Ecology and Hydrology, CEH) commented that we should be aware of which stakeholders are also being contacted by other THAPBI projects in order to avoid 'stakeholder fatigue'. ? Jon Knight (Agriculture and Horticulture Development Board, AHDB) asked whether we are contacting ALL nurseries and suggested the AHDB list could be used to raise awareness of the project. WP2 presentation 11.30-12.30: Mariella Marzano (FR) presented the work plan for WP2: Feasibility analyses and development of 'best practice' criteria. This work is split into three parts; i) a social analysis of nursery best practice, ii) a cost-benefit analysis of best practice, and iii) developing best practice criteria to underpin guidelines for accreditation. Important to the research will be effective stakeholder mapping and understanding existing values, experiences and practices, and attitudes towards accreditation through a minimum of 20 interviews (of different stakeholders) per year. The cost-benefit analysis will involve nursery and consumer surveys to assess cost of implementation of different disease management measures and willingness to pay for accredited stock. There will be exploratory scaling up of survey values to a national level. The analysis will also enumerate the impacts of failure to adopt best practices. An Ethics Committee has been established to review the social science methods and a first meeting (a few weeks ago) has approved the approaches to be used. This committee will reconvene every six months. Anonymization of data will be crucial. The subsequent discussion raised the following points: ? Participant observation will be important and it would be a good idea for social science team members to visit nurseries and work alongside staff for a day. ? The surveys will focus on disease management generally, with Phytophthora a component of that. ? There must be good communication between WP1 and WP2. Mariella should be kept informed as to when WP1 team visit nurseries so WP2 can come along on same day. ? Rodney Shearer (Alba Trees) noted that Plant Health legislation means that each nursery has a nominated person for plant health so that is probably the best contact for WP2. ? Kelvin Hughes (APHA) said that a public survey of attitudes is best if done early on in the project as a subsequent survey can follow up at the project end to see if there has been a change in public attitude. Can Plant Health improve because it is not needed (due to improved buying behaviour?) rather than policy folk putting up more rules?. ? Richard McIntosh (DEFRA) asked whether the social science surveys would question about Phytophthora specifically or general disease management? - Answer was both. ? Jon Knight (AHDB) asked what was meant by 'consumer' since volumes (in terms of plant movement) are important. Thus it will be key to get landscapers into the survey of attitudes. These consumers are more price sensitive and less questioning than the public?. Jon made the point that the British Association of Landscape Institutes (BALI) would be a good contact point - e.g trees for HS2 - people are planning now. This was endorsed by John Speirs (Scottish Government Plant Health), yes, 4 landscapers are important. Also the Woodland Trust who have pledged for 6 million trees in 2016. John Speirs offered to pass on BALI contact. Jill Thompson (CEH) is talking to Woodland Trust in Oak project in May if we need connections. Thus the surveys may need to distinguish between 'domestic' consumers and 'landscaping' consumers. ? Mariella's original thoughts were to speak only to British organisations/contacts but after discussion it was agreed some European organisations would be beneficial to the project. Therefore European contacts will be investigated. Alice Snowdon (Cheviot Trees) suggested that the European Forest Nursery organisation (EFNI) would be a good contact. EFNI deal in bare root trees. ? Rodney Shearer (Alba Trees) suggested talking to those setting the rules in the plant trade. For example a clause in contracts is needed to say plants should be provided by accredited supply when supplying grant-aided forest schemes. He commented that HS2 will most likely be supplied by plant traders rather than nursery propagators due the way the whole planning has been run. ? John Morgan (Forestry Commission Plant Health, FCPH) asked whether the consumer survey will aim to catch all markets - forest sector or horticulture? Will the two streams be considered separately?. The answer was that it would need to consider both and build both in. ? Jon Knight (AHDB) asked if we could ask major wholesale traders (Aldi, B&Q, Dobbies) if they think they can sell a pricier product?. If they say yes will they pass the benefit on to the grower? They may not and that's a problem for producers. ? Sarah Green (FR) asked what does grown in Britain mean?. Cuttings can be grown in Britain but probably imported (e.g. Poinsettia) - look at web site (Growninbritain) or homegrown scheme for clarification. ? Alexandra Schlenzig (Science and Advice for Scottish Agriculture, SASA) commented that accreditation will need to be generic and not aiming for "Phytophthora free". Rodney Shearer (Alba Trees) reiterated this as we cannot say nurseries are "disease free" - "disease not found" is more realistic. The aim of the accreditation scheme is for more effective disease management not eradication. ? A comment on fungicide use led to a private discussion within the Cheviot Trees team - they do use fungicides incorporated into compost some but products have been taken off the market. Also, legislation is more complex as the old rules about agricultural fungicides being approved automatically for non-food horticulture use have changed and there is now a cost to get approval for horticultural use - AHDB are involved in this. WP3 presentation 13.00-14.00: Beth Purse and Dan Chapman (CEH) presented an overview of the programme of work for WP3; Global Phytophthora risks to the UK. The presentation was split into three parts as follows: WP 3.1 Trade pathways and risks of introduction: Dan Chapman (CEH) has been working with EPPO on plant pest pathways and predictions of high risk pathways. He presented on 5 connectivity networks between countries based on trade - import vs export matrix and the link with climate similarities and Phytophthora presence/absence data. GDP of a country in the network is also important (as a proxy for effort into biosecurity). The best model uses climate-weighted connectivity through multiple pathways. Host breadth increases invasiveness of pests and pathogens in general - but in this project this will be related specifically to Phytophthora Trade pathways will be ranked, linked to ecological traits of Phytophthora and risk of a pathogen being introduced modelled based on position in transport networks and source intersection. This project will refine the temporal resolution of arrival and spread, incorporating air transport and more pathogen traits in the analysis. WP 3.2 Risk of establishment and spread: This work will identify Phytophthora spp. with the greatest capacity for establishment and spread under UK conditions. Models range from statistical inferences on observations to detailed models based on organism traits. However pathogen spread varies with invasion stage/extent and pathogen biology might not be well known. The project needs good global incidence data on Phytophthora species from other sources to make more detailed niche maps. Pathogen niches in the UK will be mapped and best-performing modelling methods applied to 40 focal Phytophthora species to predict invasiveness a) can do this by overlapping information on environment in one country compared to that in other countries, b) for more detailed mapping can use Phytophthora biological trait data and specific modelling against climate. Survival traits are also important, ie chlamydospores vs oospores. David Cooke (JHI) commented that dead wood is not a substrate for Phytophthora survival. Ten focal species will be identified for the modelling (from the UK Plant Health Risk Register). After validation with these species a further 25-30 species outside Europe will be identified for application. Pathogens from agricultural crops will be excluded. Data will be sourced from EPPO, CABI, GBIF, DAISIE and PhytophthoraDB. WP 3.3 Horizon scanning for emerging pathogens - scoping knowledge gaps: Mariella Marzano presented this section, the aim of which is to understand patterns of human movement and how pathogens are transferred to the UK. The focus will be on tourism and other recreational pathways. Mariella raised the question of how to find out who is coming to the UK for recreational purposes and what could they be bringing in terms of plant/soil material?. This work needs data on person and plant movement. Could the project use data from border security?. Priority should be given to known Phytophthora source regions. David Cooke (JHI) commented that visitor books in guest houses might be a useful source of information. The potential policy impacts of WP3 include contributions to the UK Plant Health Risk Register, global ecological trait databases, publication of habitat/climate suitability maps for pathogens. The following general discussion/action points were made: ? David Cooke made an action point to speak to Dan, Beth and Ana about the Phytophthora species list details. David agreed to drop his |
| Year(s) Of Engagement Activity | 2016 |
| URL | http://www.forestry.gov.uk/fr/beeh-agfkx2 |
| Description | Presentation at 6th International Oomycetes Workshop: Phytophthora, Pythium, Downy Mildews and related genera. Boston, USA, July 2018. |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presented project results to international audience of scientists at workshop Cooke DEL, Randall E, Clark B, Thorpe P, Pritchard L, Pettit T, Frederickson-Matika D, Green S. 2018. The validation of eDNA barcoding in the study of Phytophthora diversity for plant health testing and natural ecosystem surveillance. 6th International Oomycetes Workshop: Phytophthora, Pythium, Downy Mildews and related genera. Boston, USA, July 2018. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://apsnet.confex.com/apsnet/ICPP2018/meetingapp.cgi/Session/2089 |
| Description | Presentation at ISSRM conference |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | I gave a conference presentation at the ISSRM conference in Utah, USA. The intension was raise awareness about plant biosecurity practices to an applied academic audience. The panel was focussed on social dimensions of tree health |
| Year(s) Of Engagement Activity | 2018 |
| Description | Presentation at Phytophthora symposium |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Keynote speaker at the New Zealand Plant Protection Society Phytophthora Symposium. Title of presentation: Plants, pathogens and practice: bridging the gap between knowledge and action to better manage plant health |
| Year(s) Of Engagement Activity | 2019 |
| Description | Presentation at UK DNA Working Group Conference 26-27th Nov 2018. University of Derby. |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presented methodology and data to a group developing similar methods for examining organisms in UK ecosystems. Promoted discussion and future potential collaborations on shared use of resources. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Presentation at the UK DNA Working Group meeting in Derby, November 2018 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Other audiences |
| Results and Impact | Attended the UK DNA Working Group meeting and presented a talk entitled 'Metabarcoding reveals a high diversity of woody host-associated Phytophthora spp. in soils at public gardens and amenity woodlands in Britain'. This event was a forum for researchers and policymakers to share information on metabarcoding methods used in analyses of environmental samples, with a view to being able to share data and approaches. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Presentation at the UK DNA working group meeting |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Sarah Green attended the UK DNA working group meeting in London 27-17th January 2020 and gave a presentation entitled 'A metabarcoding analysis of Phytophthora communities in UK plant nurseries and links to management practice'. The talk elicited questions and discussion around the issue of the proposed massive increase in woodland planting across the UK for climate change mitigation CO2 offsetting and flood emission purposes), where will the planting stock come from? and are biosecurity risks being taken into consideration by organisations involved in large scale plantings? The message put across was that these proposed plantings need to be well-thought through, with species, seed source, Plant Health risks being carefully considered through a longer lead-in time to avoid risks associated with stock importation. |
| Year(s) Of Engagement Activity | 2020 |
| URL | http://www.ukeof.org.uk/our-work/ukdna |
| Description | Presentation on consumer survey (biosecurity practices and appetite for accreditation) at APHA Multiples day |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | I presented some of the outputs of the social research in the Phyto-threats project including consumer survey results and some highlights from research with nurseries about biosecurity practices and attitudes towards accreditation schemes. The aim was to inform the major retailers in the audience and request their participation in the research |
| Year(s) Of Engagement Activity | 2018 |
| Description | Presentation to the North East Branch of the Landscape Institute on risks of spread of Phytophthoras via trade and mitigation through best practice |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | Sarah Green presented a talk to the North East Branch of the Landscape Institute on 26th Feb 2020. The talk focused on the threats posed by Phytophthora pathogens in relation to the impacts these diseases are having on trees in our wider environment. Sarah presented an overview of the recently completed research looking at the diversity of Phytophthora species in UK plant nurseries and links to management practice. The project has highlighted the risks of spread of Phytophthora through trade and into our wider landscapes via planting schemes and emphasises how prioritizing good biosecurity practice right down the plant supply chain can help to mitigate spread of plant diseases, not just Phytophthora but also pathogens such as ash dieback disease and Xylella. The talk concluded with a discussion on the potential for a UK-wide accreditation scheme to increase plant health standards across the country and whether members of the LI would support such a scheme. Feedback from the Landscape Institute was received as follows: 'Your talk was genuinely eye-opening and something that I think we're going to be focusing on to a much greater degree hopefully - both as a profession, but also as a business. We very much hope to be able to propagate your research findings to a much wider audience across the Landscape Institute, and we will remain in touch about this' |
| Year(s) Of Engagement Activity | 2020 |
| Description | Presentation to the Oomycete Molecular Genetics Network 20th Annual Meeting, July 10-12th 2019, Oban, Scotland |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Ewan Mollison (PDRA) presented a talk entitled 'Highly contiguous genome assemblies for three Phytophthora species generated from PacBio sequencing'. He described the sequencing and assembly of the genomes for three species of Phytophthora currently regarded as less damaging than their close relatives. P. europaea was first found associated with the rhizosphere of oak trees and is closely related to the highly damaging species P. alni; P. foliorum was first found on azalea and is closely related to P. ramorum; and P. obscura was first found in association with horse chestnut and kalmia, and is closely related to P. austrocedri. All three genomes were sequenced to approximately 100-fold coverage using PacBio long reads and following assembly, scaffolding and polishing produced highly contiguous assemblies for all three with N50 values of 6.40 Mbp (P. obscura), 7.50 Mbp (P. foliorum) and 10.97 Mbp (P. europaea). Completeness of coverage estimation using BUSCO indicated a very good coverage of the gene-space of the three organisms: of 234 BUSCOs associated with stramenopiles 98 - 99% were identified as being "complete", with only around 1% of these classed as duplicates, suggesting that a good resolution of the haplotypes has been achieved during assembly. Repeat modelling and masking indicated repeat contents of 29 - 35% and Augustus gene prediction identified between 19,441 and 19,658 possible gene models for the three species. Discussion focused around the highly contiguous and apparently complete genome assemblies which should provide a valuable resource for studying genes associated with pathogenicity in highly damaging Phytophthora species. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://omgn.org/about-2019/ |
| Description | Presentation to the Society of Garden Designers - Scotland |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | Sarah Green of the Phyto-threats project team gave a presentation at the annual Christmas dinner of the Society of Garden Designers, Scotland, in December 2018. The group wanted to hear about the risks of spread of diseases through the plant trade, what makes a 'good, clean' nursery as opposed to a nursery operating poor practice, and what sort of symptoms to look out for when receiving plants from a supplier. There was a lot of discussion on procurement processes, for example would garden owners be prepared to pay more for locally grown or certified stock (most thought that they would), and much concern that, as a professional garden designer, you should be thinking about the risks of importing pest and diseases into the country. In fact, supply of healthy plants from reputable sources should be part of your 'marketability' as a business. At the end of the evening the group expressed the opinion that they were now much better informed in terms of understanding the riskiest elements of the plant trade, and would make greater efforts to ensure that plants are purchased from reputable nurseries with a documented Plant Health Management plan. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Reporting results to date from nursery sampling to all partner nurseries |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | Results to date on Phytophthora findings in nurseries in relation to host type and management practice have been communicated to the fifteen partner nurseries being sampled twice a year as part of the Phyto-threats project. In March 2018 a covering letter explaining the sample processing methods was sent to each nursery manager along with datasheets outlining which of their nursery samples (ie host plant or water source and where it was located on the nursery) have been analysed to date and whether the sample was positive or negative for presence of Phytophthora. For positive samples which have been sequenced so far, information on the actual Phytophthora species (or in some cases closely related oomycete species) detected was also reported. Where a Phytophthora species has been found the nursery manager has been given information on its likely role as a pathogen, its habitat and type of hosts affected, and whether it is a quarantine regulated species or new species report for the UK. This has resulted in a dialogue between project team members and nursery managers on why certain samples had Phytophthora and ways in which infection risk can be reduced, in particular through better management of water supplies, raising stock off ground etc. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Scottish Plant Health Centre Workshop: 'Feedback on tools for assessing risks from plant pests and pathogens', September 2020 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | As part of this workshop, risk assessment and predictive tools and databases developed during the Phytothreats project were presented to cross-sectoral stakeholders to gain feedback on whether they had the potential to inform decision making around planting and biosecurity risks in different types of planting scheme. Broader questions around information sources that inform planting and biosecurity decisions and knowledge gaps affecting these decisions were also explored. Stakeholders included representatives from horticulture, agriculture, forestry and natural environment; policy makers and practitioners, including from inspection, NGOs, national agencies, nurseries and associated networks. Key outcomes were an improved understanding of how these tools could be better tailored to different types of decision makers involved in planting as well as of the key knowledge gaps affecting decision making. The tailored improvement of such tools is being taken forward in submitted PhD and grant applications in partnership with some of these stakeholders. |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://loubar.github.io/PHC-plant-health-biosecurity-risks-Scotland/index.html |
| Description | Stakeholder workshop on Phytophthora disease threats in UK nurseries and wider landscapes: what's here, what's coming and what we can do about it |
| 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 | In 2019 a final stakeholder workshop attended by c45 stakeholders representing nursery managers, landscape architects and garden designers, Plant Health inspectors, foresters, academics, policy makers and others was held to share the latest science findings from the project, to provide an interactive demonstration of science outcomes and tools and to explore how the project's science outcomes can best be used to support the continued development of accreditation and Plant Health policy. An update was provided on the 'Plant Healthy Assurance Scheme' being developed by the Horticultural Trades Association together with industry and Defra. It was clear that the project's work on analysing Phytophthora diversity in nurseries has identified hosts and practices of high biosecurity risk that can be targeted in the Plant Health Management Standard which forms the basis of the 'Plant Healthy' scheme. The work on assessing the feasibility of accreditation from consumer and nursery perspectives will assist in securing uptake and consumer support for accreditation. Continued liaison with those developing the Plant Healthy Assurance Scheme as well as with policymakers and practitioners over predictive models will ensure that project outcomes are used to support pest risk analyses and the risk register. A full report on the workshop with links to presentations is available on the Phyto-threats website (see URL below). |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.forestresearch.gov.uk/research/global-threats-from-phytophthora-spp/phytothreats-meeting... |
| Description | Stakeholder workshop on Reducing Phytophthora in trade and designing effective accreditation |
| 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 | Reducing Phytophthora in trade and designing effective accreditation - October 4th 2017, APHA, Sand Hutton, York Sarah Green, Phyto-threats project co-ordinator, welcomed everyone and introduced the aims of the workshop. These were to: •share key science findings from the Phyto-threats project which might help underpin accreditation •understand existing UK assurance schemes and how they might be supported •generate ideas for how an accreditation scheme should work in order to be effective The meeting was attended by c50 nursery managers, Plant Health inspectors, foresters, academics, policy makers and others. This report provides an overview of the presentations given on the project team's research; existing and emerging schemes (UK Sourced and Grown scheme and HTA's pilot project); and Defra's position on accreditation. Slides accompanying these talks are available on the Phyto-threats project website (see link above). The report also includes the outcome of discussions when attendees were asked to share thoughts and experiences on 'how to give accreditation teeth'. 1.1 RESEARCH HIGHLIGHTS Sarah Green (Forest Research) welcomed the delegates and provided an overview of the project, reiterating the aim to address global threats from Phytophthora species, and to mitigate disease through nursery best practice. The progress of the project to date was summarised, and it was stressed that a number of lessons had been learned surrounding appetite for accreditation, and drivers and challenges facing nurseries (both from partner nurseries and from the overseas perspectives of Susan Frankel (USA) and Giles Hardy (Australia) who featured in last year's workshop). Sarah concluded by outlining the aim of this workshop: to explore how to make accreditation work and how it should be supported. In addition, the workshop served as an opportunity for partners to hear about the specifics of the research implemented over the past year. Dave Cooke (James Hutton Institute) spoke on the sampling procedures used during his team's visits to nursery sites, and the subsequent findings the ongoing analyses are yielding. Samples from fifteen partner nurseries have been collected, including 8 nurseries in Scotland, 6 in England and 1 in Wales. In total over 1700 samples have been collected to date. Analysis of these samples is ongoing. Over 400 samples have been PCR tested for Phytophthora (93 from plant roots of 35 different hosts; 132 water filters; and 170 buffer solutions associated with the filters). The analysis is key to understanding which Phytophthora species are found in nurseries and which management practices contribute to spread or mitigation. This information is expected to help inform nurseries which Phytophthora species represent an emerging threat, allowing proactive action to be taken. Early analysis appears to be demonstrating that mud and puddles, unmanaged shelter belts and 'hospital areas' for sickly plants all increase the risk of Phytophthora being harboured. Mike Dunn (Forest Research) summarised the findings of a consumer survey from 1500 UK plant buyers. The results showed that the public have little awareness about the threats from newly introduced pests and diseases, or the specific pathogens already present. Moreover, when choosing where to buy plants, quality, cost and range of plants are the most important drivers. Presence of biosecurity practices and plant provenance are unimportant in comparison. In terms of acquisition, the most relied upon sources are garden centres (used by 80% of the sample), DIY stores (56%), supermarkets (48%), self-grown from seed (47%) and nurseries (36%) - highlighting the value of an accreditation scheme that could encompass more than just nurseries. Data on purchasing behaviour demonstrated that many of the public buy other accredited/certified products (e.g. Fairtrade products) on the grounds that they agree with the ideals of the scheme, but also because the status implies a high quality product. Forty-five percent stated they would be likely to travel further to buy accredited plants (mean distance of 26.2 miles each way), and 39% reported they would be likely to pay an additional premium (mean premium of 18%). It was acknowledged that the general public represent one of several different types of consumer for nurseries. Further research into other customers (e.g. landscapers) is ongoing. Dan Chapman (Centre for Ecology and Hydrology) moved away from thinking about nurseries to look at the national and global scales of plant movement and colonisation. Particular attention was paid to variations in environmental conditions, and the associated implications for the level of risk posed by different Phytophthoras. This process has involved tapping into global databases on trade and looking at reports of Phytophthora introductions, understanding links between traits and impact, and working towards predicting 'invasiveness' in the UK (on the basis of traits and the country's climatic conditions). Pursuing this research may aid in assessing whether a newly discovered or introduced Phytophthora will be problematic. As such, it is relevant for national scale biosecurity planning, and collaborators connected to the UK plant health risk register. 1.2 EXISTING AND EMERGING SCHEMES Lee Dudley (Woodland trust) described the Woodland Trust's UK Sourced and Grown (UKSG) assurance scheme relevant to forest nurseries. Prior to the scheme the Trust were 'spot buying' plants from mainland Europe, though this was considered a problem in light of the ash dieback outbreaks. After research and face-to-face discussion with nurseries it was decided that contract growing and seed collection would represent a more secure means of attaining healthy trees from within the UK. Nurseries and seed collectors are now encouraged to seek accreditation, and produce assured products for the Trust. Staff training, seed handling, traceability, stock control, biosecurity, plant quality and quantity, care of soil and water, and seed receipts are all assessed as part of the accreditation process. A total of 30 nurseries were approached for inclusion, leading to 19 agreeing to be audited and subsequently passing, and an additional one requiring corrective action. As a result, an estimated 56.8 million plants have been assured. While the contracts are significant to the forest nursery sector (£2-3 million per year), a huge gap is predicted between what is being supplied by forest nurseries and the number of trees that are expected to be needed in the future. It is hoped that more nurseries and seed collectors will be encouraged to join the scheme, which offers a guaranteed market for assured produce and is a good advert for the nursery. Growth of the scheme will continue to reduce the reliance on spot buying. Tim Edwards (Boningale Nurseries) provided an overview of the HTA Plant Health Assurance Scheme which is now in its pilot stage. The scheme includes 10 nurseries of varying size and type that are currently being audited as a means of testing the proposed standard for the scheme. It was noted that the nurseries participating are likely to be better than average at managing for biosecurity risks having volunteered to be part of the pilot. However, auditors are noting a number of shortcomings such as a lack of risk assessment, the absence of records of disposals, and a need for further staff training. Those involved are said to be pleased with the process which is helping them to become exemplars within the sector - something which customers such as retailers and amenity planters look favourably upon. A project meeting in November 2017 will explore the governance of the scheme and establish an independent entity that will own and oversee a refined standard for future use. All nurseries will be offered the chance to get up to speed for when the scheme rolls out to avoid giving undue advantage to those participating in the pilot scheme. 1.3 DEFRA's POSITION ON ACCREDITATION Nicola Spence (Defra's Chief Plant Health Officer) acknowledged Defra's interest in accreditation as well as preventative measures, for example through more thorough host inspections (particularly for highly susceptible species). To illustrate the scale of the challenge faced, Nicola referred to the growing risk register, which typically receives 5-10 new additions at each monthly meeting, and emphasised the need for 5 P's within the trade: predicting, preventing, protecting, preparing and partnering. Defra's stance is that nursery accreditation could be an important element in shaping the UK as a trusted provider of quality plants (with reduced pest and disease risk) and thus a bigger exporter. Reducing the number of imports and employing measures on those that do still need to be imported (e.g. quarantining) could not only lower biosecurity risk but also foster financial resilience within the industry. This resilience could be furthered by restructuring of a grant scheme currently operating for Phytophthora and a limited number of other pathogens. Defra and APHA should remain a source of information on plant pests and diseases via the plant information portal. In addition, Nicola agreed with a suggestion that Defra should influence planning and development policy to insist on the use of accredited nurseries or products during developments, once a standard had been agreed upon as to what is a bio-secure plant. 2. How to Give Accreditation Teeth: Uptake, Compliance and Impact 2.1 Accreditation coverage Need for extensive coverage : In order for an accreditation scheme to have impact it was agreed that it would need to be; endorsed by the government, critical to the business, and to encompass the products/practices of as many actors within the supply chain as possible. This coverage is deemed necessary given that retail outlets received criticism for current practices, such as offering 'bargain priced plants' which had been retained so long as to increase the probability that they harboured pathogens - something which would not be tolerated with the sale of food or animals. Challenges for widespread inclusion: Developing and implementing a scheme capable of maintaining relevance and appeal to all of the actors within the supply chain is considered a key challenge, undermined by a number of factors. UK nurseries were said to be too small to satisfy the enormous customer base resulting in a sizeable market share for non-specialist traders including supermarket and DIY chains. While the establishment of UK cooperatives emerged as a potential means of rolling out accreditation to a larger number of growers, it was noted that at present different actors appear to be pursuing their own approaches rather than uniting towards a single cross-cutting, standardised approach. For example, one DIY store are said to have a new 'unification scheme' which may involve selling only their own branded products, similar to the Ikea model. Other groups have sought to improve the quality of plants by using suppliers accredited under the BOPP scheme. While these developments serve to demonstrate that many have come to recognise the value of some form of assurance/accreditation approach, it is possible that the diversity of what is being proposed will lead to confusion among customers. Building on existing frameworks : Examples given of successfully established, widespread schemes included sustainable timber schemes and pesticide schemes, raising the question as to whether lessons could be learned from these, or if there was an opportunity to 'piggyback' - adding biosecurity best practice to an existing scheme. It was agreed that ideally the UK should have a single, recognisable assurance scheme and that existing schemes (ie UKSG, HTA, BOPP) should be amalgamated, yet how this could be achieved was not clear. International coverage: While discussions focussed on encouraging accreditation coverage among the different stakeholders in the UK, others felt strongly that a UK wide accreditation scheme would in fact need to be mandatory for all growers if it were ever to be effective. Certain nursery managers and DIY chain representatives went further still, expressing that accreditation should extend not only to countries on the continent - from which the UK receives the majority of its plants - but also to countries outside of Europe. This, they believed, was necessary to ensure that the plants arriving to and leaving from European nurseries could be considered "safe". 2.2 Support needed within the trade Ensuring demand for accredited plants : Growers investing in enhanced biosecurity practices seek assurance that their products will be in demand. One way to help ensure this is for the government to insist that contracts must specify the need for accredited trees/plants. However, at present Local Authorities are routinely awarding contracts to the lowest bidder, with little to no attention being paid to plant type, quality or health. More generally, contract growing has not been successful because of a tendency for schemes to be put on hold or not to materialise at all. As a result, it can be extremely difficult to match supply with demand. Ideally procurement/contract growing should nominate an accredited supplier to ensure that plants and trees purchased arrive from a site with the necessary biosecurity practices in place. In addition, there should be a guarantee that the plants/trees will be needed and therefore purchased. This would ensure that growers can manage their supply without fear of the demand disappearing at short notice, and losses being incurred. Benefits for accredited growers : In the event that a contract is terminated or amended (thus reducing the number of plants/trees required) growers would require an insurance policy or compensation to offset any costs invested in producing the order. By making access to this type of insurance scheme available only to those growers that had been accredited, it would be possible to discourage acquisition of plants from riskier pathways typified by the 'white van man' - since traders ineligible for the insurance would be subject to wasted resources when a contract is cancelled, and therefore be at a disadvantage in the marketplace. Other suggested benefits to holding accreditation included eligibility to grant funding and access to different markets (i.e. allowing for the purchase of plants from certain places). Again, these measures would potentially put those without accreditation at a disadvantage and reduce their market share. Insurance providers : While it was suggested that the government may oversee the administration of financial incentives/reimbursement for those with accreditation, there was a degree of cynicism about how likely this would be. Nevertheless, some did view revisions to the government's post-Brexit budget as an opportunity to introduce such measures. Other insurance providers were also suggested though it was acknowledged that more discussion would be needed to outline the specific circumstances required for reimbursement, and what level of reimbursement would occur. At present insurance policies which reflect the complexities of the trade were said not to exist, prompting some to highlight a need for the insurance sector to adapt. Consistent support : In addition to a proposed role in reimbursement, there was also consensus that the Government would need to offer wider support for an accreditation scheme, and be consistent in its efforts to encourage its uptake and effectiveness, for example, by outlining a joined up vision between departments (less silo-ing). Consistency should be visible from the national level (e.g. increasing border controls and inspections), down to local governments, who are considered important due to their role in dealing with outbreaks on the ground. Many also noted a desire for the government to act in an educational role through the provision of more information on the cost of outbreaks, so as to highlight the extent of financial impacts which result. 2.3 Awareness and Education Importance of awareness and education : Discussions around education and raising awareness were deemed relevant to plant buyers (including the plant buying p |
| Year(s) Of Engagement Activity | 2017 |
| URL | https://www.forestry.gov.uk/fr/beeh-atuhqv |
| Description | THAPBI dissemination event 7th Feb 2018 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Policymakers/politicians |
| Results and Impact | The Phyto-threats project had a stand and presentation at a dissemination event for THAPBI-funded projects in London on 7th February 2018. The event was attended by more than 70 delegates, comprising researchers, members of the funding bodies and stakeholders representing DEFRA, forestry, botanic gardens, landscapers, horticultural traders, community nurseries, woodland and conservation charities, estate managers and local government. Key-note speakers were Lord Gardiner (Parliamentary Under Secretary of State for Rural Affairs and Biosecurity), who stressed the importance of translating research into practical solutions for tree health, and Nicola Spence (Chief Plant Health Officer at DEFRA), who highlighted the value of the inter-disciplinary nature of the projects and outlined DEFRAs policy and strategy for plant health. David Cooke gave a ten minute overview of the Phyto-threats project,, along with the lead investigators from the other 7 THAPBI projects. The Phyto-threats team were then able to "speed-network" with small groups of stakeholders in ten minute sessions. This was an opportunity to disseminate some initial findings from the project. There was particular interest in the Phytophthoras being found in nurseries sampled by the Phyto-threats team and in discussing alternative management practices. Another popular discussion point was the online survey assessing consumer attitudes to nursery accreditation. A paper report summarising the initial results was picked up by a large number of stakeholders. For the Phyto-threats team, it was valuable to identify possible contacts for future co-development of trade tools to help plant buyers and policy-makers assess the biosecurity risk associated with imported plants. New avenues for gathering data linking international tourism and Phytophthora spread were also identified |
| Year(s) Of Engagement Activity | 2018 |
| Description | Talk by Louise Barwell at 9th Meeting of the IUFRO Working Party, Phytophthora diseases on forest trees, October 2019, La Maddalena, Sardinia, Italy. |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Louise Barwell, gave a talk entitled "Trait-based approaches for predicting future global impacts in the genus Phytophthora." presenting global databases on occurrence and traits of Phytophthoras and analysis which indicated the potential of biological traits to be used in horizon scanning, to predict the impacts and spread of individual Phytophthora species. This resulted in interest from students and other academics in the analytical methods and databases used but also in interest from decision makers in using the models presented as tools for risk assessment. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.iufrosardinia2019.org/program/ |
| Description | Talk by Louise Barwell at Invasive Species Session of British Ecological Society Annual Meeting 2019, 10 - 13 December 2019, Belfast, Northern Ireland. |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Louise gave a talk entitled "Trait-based approaches for invasion risk assessment of Phytophthora plant pathogens" to an international audience of academics and students which sparked discussion around accessible global databases for plant pathogen species and analytical methods used to predict impacts of pathogens from their biological traits. This lead to a potential collaboration where the Phytopthreats databases will be integrated into the Global Database of Alien Pathogenic Fungi. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.britishecologicalsociety.org/events/annual-meeting-2019 |
| Description | Understanding drivers of Phytophthora emergence through the plant nursery trade in Britain |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Key note presentation to the 10th Meeting of the International Union of Forest Research Organisations Working Party (IUFRO) 7.02.09, Phytophthora in forests and natural ecosystems, Berkeley, California, USA, 19-25 June 2022. The conference was attended by ~60 people from all around the world who carry out research into forest Phytophthora diseases. The talk was well received and sparked much questions and discussion. |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://nature.berkeley.edu/matteolab/?page_id=6539 |
| Description | Webinar presented to the England Juniper group |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Third sector organisations |
| Results and Impact | A webinar was presented to the juniper England group (which also includes interested parties based in Scotland and Wales) including data from the Phyto-threats nursery surveys, highlighting the findings of Phytophthora austrocedri in a number of nurseries associated not only with juniper but also with other hosts such as Chamaecyparis and Leylandii. Also presented were other Phytophthora species found on juniper, and emphasis given to the risks posed by the practice of collecting juniper seed from vulnerable sites, having the seed raised at commercial plant nurseries under contract, and then replanting the junipers back out onto the original juniper woodland site. Much anecdotal evidence suggests that this practice of supplementary planting has resulted in the inadvertent introduction of P. austrocedri to juniper woodlands as a result of contamination of nursery stock. Data from nursery surveys underlines this risk. There was considerable discussion afterwards and acknowledgement that planting is risky and that alternatives such as promoting natural regeneration of existing juniper woodland are preferable. Impacts include an agreement to rewrite the Defra and Scottish juniper planting guidance in 2021 and further meetings planned to discuss current understanding of natural regeneration in juniper and how it can be improved through management so as to reduce reliance on planting. |
| Year(s) Of Engagement Activity | 2020 |
| Description | at British Crop Protection Council Diseases Review 2018 - 'Problems in high value crops' |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presented work to new audiences and met future collaborators and funders. Cooke DEL, 2018. Phytophthora diseases of potatoes, fruit and trees and other crops. Presentation at British Crop Protection Council Diseases Review 2018 - 'Problems in high value crops', NIAB, Cambridge 12 Oct 2018 |
| Year(s) Of Engagement Activity | 2018 |
| Description | eDNA and Plant Pathogen Metabarcoding presentation at SNH 'Sharing Good Practice' event on "The Use of Technology to gather data about the natural environment" |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Other audiences |
| Results and Impact | David Cooke gave a talk as part of a Scottish Natural Heritage-organised event entitled 'Sharing Good Practice' on "The Use of Technology to gather data about the natural environment". It was a very good meeting and linked him to an eDNA group of UK mostly aquatic biologists. |
| Year(s) Of Engagement Activity | 2017 |