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.

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.
 
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.
First Year Of Impact 2017
Sector Government, Democracy and Justice,Other
Impact Types Economic,Policy & public services

 
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 Contract Research Fund
Amount £250,000 (GBP)
Organisation Government of Scotland 
Sector Public
Country United Kingdom
Start 08/2016 
End 07/2018
 
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
 
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 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 for future management and willingness for an accreditation scheme.

Consumer survey

Mike Dunn (FR) gave a descriptive overview of results obtained very recently from the consumer survey which involved 1500 people. The data have yet to be analysed statistically. Mike ran through the questions addressed by the survey and the demographic data for the respondents who were typically members of the public who buy plants for their own home. The 19 survey questions were compiled and sent for approval by the project's ethics committee before the survey was sent out. The survey was undertaken by a survey company (Toluna) and it targeted buying habits, perceptions of the seller's biosecurity, and attitudes towards accreditation. The 1500 respondents were generally representative of the nation's demographics although 57% were aged 55 or over.

Survey results

Most people buy plants 1-2 times per year, most frequently sourcing plants from garden centres/DIY stores/supermarkets. Mariella noted that the project has not engaged these sectors yet and doing so will be important. Plant quality, cost and range were the top three factors in a consumer's decision about where to buy plants from. Evidence of good biosecurity practice by the business came out as a fairly low priority. When it comes to selecting plants to buy, plant appearance, suitability for the intended site and cost were most important. Provenance and origin of stock were very low priority for consumers.

In terms of general awareness of pest and disease threats to plants; 10% of respondents had never heard of the problem, 62% had heard of the problem but didn't know much about it, 24% had heard of the problem and felt reasonably well informed and 3% felt very well informed. Respondents were assessed for their perception of the level of risk of different potential pathways for pest and disease introduction; online and mail orders were perceived as higher risk whereas consumer's self-grown plants, specialist plant suppliers and nurseries gave most confidence as being of low risk. In terms of willingness to support an accreditation scheme; 9% of respondents chose not to buy accredited products because of the increased cost, 32% gave accredited sources little thought when making a purchase and 38% bought accredited products in some cases because they believed in the goals of the scheme. In terms of a potential accreditation scheme for plant sellers, 25% of respondents agreed with the principles of such a scheme but had concerns about the cost being passed on to consumers.

The consumers surveyed spent on average £100 per year on plants, and 45% were happy to travel further (up to 160 miles, with an average increased willingness-to-travel distance of 26 miles) and 39% were willing to pay more (on average 18% more) for accredited plants.

Overall, the results of the consumer survey indicated a general willingness to support accreditation (within reason) but it also highlighted a need for consumer engagement about the risks of spreading pests and diseases.

Discussion of consumer survey

Mike's presentation generated a number of questions such as 'are attitudes to accreditation associated with i) a greater knowledge of pests, ii) experience with existing accreditation, iii) number of plants purchased, iv) types of plant sources, v) demographic factors ?.' For example, it was asked whether the previous experiences of the consumer affected their attitude towards accreditation, ie if trees had been felled in their local area then is this likely to have increased their awareness and concern of pests and diseases?. The response was that, based on previous surveys, people generally don't notice damage to trees in their area. The point of this survey was to find out where people buy their plants and what influences their behaviour. The OPAL project, involving community volunteers including schoolchildren, might help with raising awareness of younger generations. Another question was raised as to whether the behaviour of online respondents who completed the survey could be expected to differ from the public at large. The answer from Mike Dunn was that, overall, he is happy with the survey sample as it targeted a representative population in relation to location across the UK, gender and age bracket, bearing in mind that older people tend to be more likely to buy plants than younger people.

Next steps

A survey will be designed for the forestry industry and landscapers, and the project team and Expert Advisory Panel members will be asked for their inputs in shaping the survey questions. For the nursery and garden centre survey it is recognised that these groups can be both sellers and consumers. Mariella will also link in with the Horticultural Trades Association (HTA) who are working in partnership with nurseries to develop an assurance scheme.

The comment was made that growers need clear plant health advice on which to base best practice and that any assurance scheme should include management practice guidelines. The question was asked whether the HTA-piloted scheme was just for UK growers or international. Mariella responded that the scheme was for the UK market but the HTA would like it to extend internationally. The scheme is being piloted now and could possibly be launched next year.

Economic analyses

Mariella presented a number of slides on behalf of Gregory Valatin (FR economist researcher) who could not attend this meeting. Gregory will undertake an economic analysis of consumers' willingness to pay and travel for accredited stock. Gregory will look at cost-benefits of other schemes, on potential impacts of new Phytophthoras entering the UK and potential costs of not having best practice thus increasing chances of new diseases establishing. Gregory had a number of basic questions for the project team and advisory panel including;

•What kind of accreditation scheme shall we focus on?


•What is the source of additional costs-holding plants/use of fungicides or pesticides?


•Timescale for introduction of scheme?


•To what extent are nurseries expected to take up scheme?


•Timescale for uptake?


The team will consider these questions and report back to Gregory.

Sarah Green (FR) commented on a study from Californian native plant nurseries supplying restoration plantings showing how Phytophthora infections were greatly reduced after the nurseries implemented a number of key management changes. Although there were costs to implementing these changes, the resulting benefits were clear, ie less Phytophthora and less risk of passing disease to native landscapes, so reducing costs associated with outbreak eradication.

The question was asked 'if we don't have a scheme, what would happen?'. The answers were that there must be data on the costs of remediation following outbreaks. Obtaining such data could be tricky with some outbreaks being public and some private. Essentially, we don't really know the baseline costs of disease eradication efforts. It may be possible to look at past trends and establish how action could level off the need for intervention.

The discussion returned to the topic of uptake of accreditation by nurseries; if a scheme involves too much paperwork it may restrict uptake. How do we bring growers on board?. Smaller nurseries will find it costly and not participate.

Gregory's work will assess the anticipated effects of an accreditation scheme on introduction of Phytophthoras, their spread in the UK, effects on introduction of other pests and diseases as well as spread of pests and diseases already present in the country.

A last question posed: 'What are the differences likely to be, compared to baseline risks, and how do we quantify them ?' eg. % reduction in time of species x in year y.

Glyn Jones (FERA) presentation on Future Proofing for Plant Health (FPPH) project

Glyn presented on a couple of economics-related projects he is working on. One is funded through the DEFRA FPPH programme and is looking at cost and responsibility sharing, modelling nursery networks and assessing markets for plant health and biosecurity. He is considering the public good characteristics of biosecurity, ie market failure if nurseries won't provide the biosecurity that the public wants. Glyn presented a figure showing nursery sector complexity and the impact of poor biosecurity, and the difference between a pest staying put or moving into wider environment.

Glyn commented that we are living in changing times and ran through traditional government practices and instruments for intervention, including inspection, monitoring and surveillance, quarantine and pest exclusion. Research funding allocations reflect budgetary pressure from increased and changing risks. He asked if the industry is making a move now due to concerns over Xylella and the impact of Chalara. How should an accreditation scheme be designed?.The situation is currently dynamic, with various Woodland Trust, Grown in Britain and HTA assurance schemes. The Woodland Trust want clean sourced trees, but there is a potential problem with the source, for example if the order is large then trees might have to be sourced elsewhere (ie outside the UK). Glyn also ran through a number of possible economic mechanisms to support an assurance scheme, such as i) cost sharing for outbreak control measures, ii) insurance (easier if the pathogen is defined and involves a small defined group of participants), iii) environmental bond (ie growers pay money, and if no disease they get reimbursed - this may have a positive impact on behaviour, iv) retrospective levy, v) cost sharing for risk reduction measures.

Interviews have been undertaken by Glyn and his team with some of the key players in the industry. There were some criticisms of accreditation/assurance schemes, in that if a scheme were voluntary you would likely only get growers joining who already operate best practice. If a grower were to be part of a scheme would they be subject to fewer Statutory inspections?. Generally, the idea of reduced inspections was not supported by industry, they actually like being inspected!. Questions that arose included why would growers join a scheme ?, what are the benefits to them?, what do you do about those growers who don't join?. The feedback from growers was that any scheme would need to be government-endorsed and clear, with a strategic direction. There needs to be leadership from DEFRA and interaction with policy. The responses to malpractice need to 'have teeth' to incentivise adoption of good practice.

In terms of UK biosecurity policy, proactive temporary import bans of high risk plant material are hard to achieve. It was suggested that there should be expansion of nursery licenses and inspections to other importers, for example landscapers and landscape architects. One possibility would be to base border inspections on the biosecurity rating of exporting nurseries.

In general, growers supported the notion of fewer rather than more assurance schemes and the idea of earned recognition, in that there would be benefits to members of such a scheme. There can be market distortion and there is often a mis-match between demand and time to supply. Growers said that there needs to be increased distinction of UK-grown material and a transition to more home-grown, and perhaps more co-operative working of growers in order to achieve required supply. There needs to be confidence in the domestic market.

In terms of future FPPH work, Glyn said that he would be integrating with the LWEC Phyto-threats project and would liaise with Mariella and Gregory. He will be conducting more interviews of those involved in trade and undertake a demand-pull analysis, modelling design and required uptake of an assurance scheme. Glyn also mentioned the RAPID trade project, funded by BBSRC and US National Science Foundation. As part of this project they have been modelling high biosecurity trade networks following pest/disease outbreak scenarios.

It was asked whether a UK-wide accreditation scheme should be compulsory. There followed some general discussion of this along with suggestions of a licensing scheme (which might just benefit the largest operators) and whether public benefit could be used to influence what public funds could go into the scheme.
13.00-14.30: WP3 Global Phytophthora risks to the UK - Beth Purse, Dan Chapman and Louise Barwell (CEH)

Beth began the WP3 presentation by reviewing the work package objectives; (i) risk of Phytophthora introduction, ii) risk of Phytophthora establishment and spread and iii) horizon-scanning for emerging pathogens (including assessment of tourism pathways of spread). The work package team comprises Beth, Dan Chapman and Louise Barwell (CEH), Ana Pérez-Sierra, Mariella Marzano and Mike Dunn (FR).

WP3.1 Risk of introduction

Beth, Dan and Louise have been compiling a global database of Phytophthora country-level occurrence for use in predicting risk of arrival to the UK for those species not yet present in this country. Dan and Louise will be looking at trade routes linking Phytophthora source countries to the UK. The global Phytophthora occurrence database so far includes 5838 country-level records and 1208 Phytophthora species x country combinations. The data include year of arrival (or rather 1st record in a particular country) as well as invasion status and state of establishment and spread. Data have been sourced from 5 databases: daisie/ ncbi/ gbif.org/ cabi/ westerdjik (formerly the CBS culture collection).

Dan Chapman presented on trade networks. In terms of trade pathways the focal commodities are horticultural/agricultural/forestry products. Dan has already completed an analysis framework for correlating trade networks to plant pest invasion patterns in Europe, and has looked at the best-fitting model for invasion (paper currently in press in Global Ecology and Biogeography). He has analysed national-level introduction patterns of over 400 non-native species and found that these were best explained by a model incorporating pathogen occurrence in source regions, climatic similarity between source and sink regions, and connectivity of these regions through multiple trade networks. For more recent invasions, the live plant and forest products networks gave the best model. Dan and Louise will now take this further with Phytophthora species, by adding new trade data and more refined pathogen traits that might influence invasion risk. Louise asked for thoughts about how Phytophthora traits might affect species' abilities to exploit specific commodity pathways such as live horticultural plants, cut flowers, fruit, vegetables, soil, agricultural seeds, roots, food and feed, forestry products such as fuel, wood, and travel/ tourism, and to exploit new geographic regions with similar environmental conditions.

There followed some discussion on how Phytophthora traits relate to risk of importation and what the team are hoping to find. Beth responded that they would like to correlate certain traits or groups of Phytophthora with these traits as risky. They would then see where these 'high-risk' Phytophthoras occur and identify routes correlating with volumes of trade. Richard McIntosh (DEFRA) commented that there is a policy demand for this sort of information, including information on what countries are deemed to be of lower risk so can trade can be directed towards those countries.

Beth asked for sources of data on trade interceptions and traits of the organisms intercepted. Europhyt (European Union Notification System for Plant Health interceptions) was mentioned although the team had already looked at the Europhyt database and didn't find any Phytophthora hits. APHA/FERA have an extensive database of nursery interceptions in England and Wales but mining it might be a problem as the database is so large. The WP3 Beth team can have access to the database as long as they know exactly what they want and the time period. SASA have already passed on the nursery interception data from Scotland to Beth's team.

WP3.2 Risk of establishment and spread

Beth spoke about the potential environmental drivers of Phytophthora distributions, matching patterns of occurrence with environmental data. Niche modelling will be done on site-level occurrences (rather than country-level). They have amassed a global dataset of 8067 site-level Phytophthora occurrences, covering 81 Phytophthora species in 38 countries from a variety of data sources including culture collections, unpublished data from researchers in the Phytophthora community, governmental organisations and the literature. Due to recording effort the global distribution of these records is patchy and high-impact species are more frequently recorded. For example the P. cinnamomi dataset contains 3655 location records in over 20 countries. The agricultural sector is poorly represented so far, but Beth and Louise would like to ensure that the dataset captures the distribution in all relevant sectors to get a complete picture of the distribution and the important environmental factors. Jill Thompson (CEH) offered to provide some contacts to try to fill these gaps. The site-level data collation has been extended for an additional year as some large datasets from North America and the southern hemisphere are expected.

In terms of factors affecting known Phytophthora distributions, the team will be considering host, disturbance by livestock, vehicle movement and landscaping projects, seasonal weather variability, extreme weather events, agricultural and forest management practices, pollutants causing plant stress, soil pH and other edaphic factors as well as non-climatic factors.

Beth and Louise raised the need for data cleaning, for example they need spatial precision (latitudes/longitudes). There is also the issue of species ambiguity, as some species have one or more synonyms or have been re-named since records started. The method used for species detection also needs to be taken into account. For example some records are based on species isolation into pure culture, and others based only on DNA findings. Beth and her team need to know how sensitive and specific each detection method is, whether there have been changes in methods over time, and how reliable is each one?. Beth would like to score the reliability of each diagnostic method. They don't need to do this for trade modelling but for niche modelling they do.

In the following discussion it was confirmed that there are not many examples of species complexes now separated, only P. megasperma, P. cryptogea and P. citricola. Records can be distinguished based on whether from isolations into culture, specifies-specific qPCR to detect a unique DNA sequence, standard PCR + sequencing (usually of ITS region), and the recent increased use of metabarcoding (also currently mainly based on the ITS) to detect many species in a given sample. Sarah Green (FR) will outline each diagnostic method and its reliability and pass on to Louise.

The Phytophthora traits database was completed in December 2016 for 177 species listing 15 different traits per species (including host range, mating system, survival structures, dispersal mechanisms and thermal tolerance range). It will be updated as new species are described. The modelling team are developing impact metrics using the traits database. They will carry out traits-based analyses of Phytophthora impacts to determine which traits influence risk of establishment and spread. Louise ran through some initial results on which trait syndromes best predict the global impacts of Phytophthora species.

Sarah (FR), David (JHI), Beatrice (FR) and Ana (FR) helped identify 24 Phytophthora species present in the UK, and 30 species not present in the UK which the team will use to develop the niche-distribution models.

iii) Horizon scanning

Mike Dunn (FR) spoke about assessing tourism routes, in particular gathering information on visitors to UK parks and gardens. There are 31 million visitors to the UK each year; one third of these visit public parks and gardens. Mike would like to collect more information including where the visitors come from, at what time of year and whether site managers have disease concerns. Mike asked for ideas on how to gather this information, for example from visitor books and tour operators.

The WP3 session finished up with Beth asking for the names of people/organisations who might potentially use the outputs of their work.

14.30-15.00: WP5 Synthesis and integration - Sarah Green

Sarah Green (FR) spoke about WP5 which deals with the overall project coordination, communication and interaction, promoting information exchange and interdisciplinary practice. She talked about WP5 achievements over the last year including establishment of the project data sharing tool (Huddle), the project website, the Expert Advisory Panel and the Project Board, which has met four times over the last year, as well as the two all-project team meetings held during the project's first year.

WP5 also co-ordinates the Science-Practice-Policy Network (SPPN) involving to date the organisation of a well-attended workshop (~50 attendees) held on improving nursery resilience to Phytophthora (in October 2016), a short article on the project written for the Arboricultural Association Magazine, and attendance (Tim Pettitt [Uni of Worcs] and Jane Barbrook [APHA]) at the National Plant Show in June 2016. Tim also attended the Four Oaks show and other growers' meetings to raise awareness of this project. Team members also attended international conferences over the last year and gave presentations on the Phyto-threats project.

This year the Phyto-threats team will have a stand at the National Plant Show, held in Birmingham in June. Ideas for the stand and a 15 minute seminar slot are still being developed. Sarah and Mariella will also attend the IUFRO 125th Anniversary Conference to be held in Freiburg in September and give presentations about Phyto-threats. A second stakeholder workshop will be held at FERA, York, on Oct 3-4th this year with the aim of identifying effective management options to underpin an accreditation scheme.

Finally, research result summaries which were produced for the end of year report to THAPBI will be posted on the project website.

Ethics committee.

Mariella Marzano spoke briefly about the ethics committee, set up to review project protocols. She reiterated that in order to use data or photos we need to have written permission from the source. All work packages need to be committed to the ethics values and we need to be consistent in our use of anonymity when sharing data. We all need to think about how we are getting consent for sampling, interviews and surveys, and we need to have clear protocols for retaining and storing data. These issues will be discussed further at the next board meeting.

Tour

The meeting ended with a tour of the JHI pathology lab and sequencing facility.
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 sector.

Comment: Use the term 'credibility' when talking about accreditation. Don't underestimate the influence of landscape architects and materials coming straight through Dutch orchards. How do you deal with that ?. Government involvement is a very good point, it is needed for credibility.

Comment: How is the Phyto-threats project addressing existing initiatives for accreditation schemes, for example UK Sourced and Grown and the HTA-led assurance scheme ?. Discussions have been going on with these schemes, you need to know where they have got to.

Comment: We should ask growers how they think they can persuade consumers to buy accredited plants and focus on the positives, ie more healthy, beautiful plants that improve quality for the producer and greater profits too !. What would they need for this to happen ?., what are the economics?. There should also be a clear logo/badge for such plants.

Q: What about a list of possible incentives ? and what are the scenarios ?. Best case, draconian to almost utopian. For example 'Landscapers like disease-free plants'. Or is it more likely 'you're not allowed to sell unless you have accreditation' ?. (ie accreditation is mandatory).

A: Accreditation needs to be down the whole line, from landscapers right back to source.

Economic feasibility of best practice and accreditation

Glyn Jones presented on Fera parallel activities including the Forestry Commission decision tool project (a generic decision tool for assessing response options to tree pests in the UK) which is relevant to the Phyto-threats project as it might be applied to new Phytophthora outbreaks in the future. Glyn outlined the tool including why it was needed, what it does, how it was developed and its limitations. A draft final version of the tool is now in review. Essentially, the tool was developed because of the need to provide support on the economic impact of new or unknown species in a new area within a very short timeframe. The idea was to produce a single model for all pests and diseases for all end users using a standardised framework for scenario assessment. Development of the tool required input from a wide range of end users (economists, scientists, policymakers) who formed a steering group.

Glyn ran through the model and its development in his presentation. It is a combination of a prevalence model (based on pest/disease surveillance and a rule of thumb on how hard you are looking versus the actual infested areas found plus an epidemiological model) linked to an economic impact model. Glyn listed at the end some of the model's limitations including the spread model which assumes a constant spread of the pest/disease over time. Also there are very few control options for new pests and diseases so not being able to input various control options into the model is a weakness. There are also uncertainties as to which environmental values to incorporate into the model. Glyn finished this part of his talk with the questions; will the model be used ?, should it be used ?. It is a highly generic model that can be abused. How should it be used ?.

Finally, Glyn outlined plans for a workshop to be held in November 2017 on cost and responsibility sharing by industry when pest and disease outbreaks occur. Points to be discussed at the workshop include current biosecurity activities, how an industry scheme might work, and incentives to join. There will be cross-reference with the Phyto-threats project via Mariella and Gregory.

Questions and comments:

Q: Can you put case studies in, for example P. ramorum, horse chestnut bleeding canker ?.

A: Yes, and they are there.

Q: Is this decision support only for outbreaks ?. Is there decision support for interceptions ?.

A: Probably this tool could be adapted for interceptions if it were represented as the minimum area for an outbreak.

Colin Price then gave a presentation demonstrating how an adapted version of the CARBBROD model, developed for Dothistroma, could be used in a scenario analysis to estimate the cost of potential timber and carbon impacts when Phytophthora outbreaks occur. This analysis will be done in year three of the project to explore the wider costs associated with no change to UK nursery practice (i.e. a continuation of the status quo in which new Phytophthora impacts can be expected) compared with a scenario where changes to nursery practice will reduce the likelihood of future outbreaks by new Phytophthora species.

The model is based on Forestry Commission yield models. It uses DECC (Department of Energy and Climate Change) carbon prices based on international agreed limits, or the social cost of carbon (i.e. the effect of increasing CO2 concentration), or any other carbon price schedule. Discounting is done using the Treasury's schedule of discount rates, or any other schedule, or a single discount rate. When there isn't a unique carbon price, and when discount rates vary, every year has to be evaluated on its own, and all individual values summed. Thus tracking carbon pools into the indefinite future is a challenge. Colin showed how the model predicts the optimal rotation value for Japanese larch. Sometimes CARBBROD gives better carbon values when there is infection in trees, using the DECC values. This isn't the answer we would expect. Other carbon prices give more expected results.

Questions and comments:

Q: Has CARBBROD been tested against real-world data? i.e. documented case studies? Do the predictions emulate what really happened?

A: All data come from the real world!

Q: Can you add more than just carbon values to give you a more intuitively correct answer?

A: Various impacts of trees have been looked at, for example temperature reduction, pollution absorption, flood alleviation. Carbon values are so big that they will always dominate models.

Comment: More talks with pathologists are needed since it is not clear what the primary inputs would be for the Phyto-threats project. Assuming best nursery practice, what scenarios can we predict? This is a two-way discussion between economists and pathologists on the team and we need to identify over the next six months specific scenarios of use/interest to the project that Colin can apply to CARBBROD. For example WP3 might identify specific high-risk Phytophthoras not yet present in the UK, but which might enter the country if no change in existing practice occurs, that could be applied to CARBBROD.

A: Gregory/Colin will initiate these discussions by email.
13.00-14.30: WP3 Global Phytophthora risks to the UK - Louise Barwell (CEH)

Louise began with a run through of the WP3 team members, objectives and associated milestones. For objective 3.1 (Risk of Introduction) a year 1 milestone has been to compile a global country level database of Phytophthora occurrence. The team has now amassed 13,853 country-level records covering 1601 Phytophthora species x country combinations including year of first record of that species in the country and invasion status. The team are aware of potential sources of bias in country-level occurrences such as level of pest recording activity per country, biosecurity, and the lag phase between pest arrival and first report. Louise has collected metrics on national pest reporting activity and posed the following question to the team; how can national recording and biosecurity efforts best be measured, ie are there descriptors of Plant Health Inspector activity ? Can we weight records against the number of inspections per country ?

Currently Louise is looking at assessing national pest reporting activity through the IPPC, legal instruments such as ECOLEX and level of biosecurity investment (from the FAO). The team have been doing a preliminary analysis developing the first models based on post-2000 occurrence data using predictors such as trade connectivity, recording effort and biosecurity. Live plant imports on their own explained 44.36% of variation in Phytophthora arrivals per country since 2000. When combined with metrics of recording effort per country, the model explained nearly 60% of the variation in Phytophthora arrivals. There followed some discussion on the use of the term 'arrivals' vs 'records'. Some of the post-2000 increases in Phytophthora records per country might not necessarily relate to new arrivals but rather to increased surveillance effort (ie expansion of molecular tools) reporting species that may have been present in that country for some time. David Cooke suggested weighting the new records according to species description date.

The team have also looked at trade pathways and tried to link Phytophthora reports in each country with different commodity imports. The resource trade data allow for live plant imports to be broken down into different commodity types so it should be possible to get a sense of which types of hosts seem to be transporting the most Phytophthoras. The next steps are to collate further trade networks data, to break down total Phytophthora 'arrivals' to the species level, and build in country by country climate matching metrics. Once species-level arrivals can be used as the response variable, particular traits can be assessed for whether they make species more or less likely to arrive. The final output will be to predict the arrival risk of different Phytophthora species to the UK and to simulate how this might change under different kinds of trade scenarios. So data will be sought on different projections for future global trade.

For objective 3.2 (Risk of Establishment and Spread), the team have so far collated 9907 georeferenced global Phytophthora records with 1-10 km precision. The data encompass 81 species from 38 countries. In collating these data the team are prioritising regions that are climatically similar to the UK. Louise showed a slide listing the data sources and highlighted the sources of uncertainty (ie taxonomic uncertainty due to differences in use of different ID methods, positional uncertainty, recording effort resulting in false absences etc) and how such uncertainties might be overcome.

As part of objective 3.2 the team are developing niche models for different Phytophthora species predicting global impact and risk of establishment and spread in the UK. As an example, Louise showed the global distribution model for P. cinnamomi published by Burgess et al. 2016 (in Global Change Biology) and presented a list of the potential environmental drivers of Phytophthora distributions ie animal activity, pollutants, hot and cold stress. The pathologists on the Phyto-threats project sent Louise a list of 54 focal Phytophthora species with known or potential impacts on UK tree species for the niche models, including 24 species currently known to occur in the UK - this list can be found on Huddle. These species will be used to validate how well the potential distribution of Phytophthora species in the UK can be predicted with the global niche models. The other 30 species are absent from the UK and 15 of these are thought to also be absent from Europe. For these species risk maps will be created and each one will be ranked for its potential impact in the UK.

Louise also described the global Phytophthora traits database, part of which has now been merged with a similar traits database developed by a team based in Australia and New Zealand. As a result of this merging of databases we now have a comprehensive traits database complete for 172 Phytophthora species which it is thought could be managed and updated by Scion (New Zealand) over the next 10 years as part of their long-term Phytophthora research programme. The two groups aim to publish the traits database in the near future, after which it will be made freely available online. Louise then ran through some of the traits included in the merged database (ie characteristics of sporangia, oospores and other survival structures, thermal tolerances). Not yet included in the merged database are data on species distribution, host species, genome size, disease symptoms and impact metrics. These data will be added later following the publication of some manuscripts currently in preparation.

Louise ran through some of the questions they are testing using the traits database. These include examining the value of traits data for pathogen groups, the extent to which traits databases been compiled for pathogen groups in the past and whether these traits can be used in analyses of pathogen behaviour. Also, is there a phylogenetic signal in the traits ?, ie to what extent do closely related species share traits, which traits seem to be experiencing the strongest selection pressures, and are there groups of traits that are co-evolving in response to global movement of Phytophthora ?. Another question is do hybrids share traits with parent taxa ?.

Louise then showed a Phytophthora phylogeny based on the ITS region that had been sent to her by Treena Burgess in Australia. Louise has had a first attempt at measuring the phylogenetic signal in some traits, with the outcome being that there is generally a lack of phylogenetic signal in traits. Only sterile and non-caducous species had a non-random relationship, and there was a nice correlation between trait and cumulative branch distance between two species. This analysis used a 'Brownian motion' model of traits applied by 'crawling' down branches and flipping at random. Louise asked the project team what other appropriate models could be used for trait evolution for Phytophthora ?. The response was that the project team aren't familiar with the different models but David Cooke suggested focusing on nodes as that is where species split. If Louise could circulate some of the models that she has in mind then others will able to advise. It was also noted by members of the project team that a multigene phylogeny might be better for the analyses (ie Martin et al, 2014), although the ITS-only phylogeny would probably not differ that much. David Cooke commented that it would also be nice to relate genome evolution with the trait database.

The other question being addressed is can species traits predict or explain the global impact of Phytophthora species ?, ie what makes an invasive species ?. Two impact metrics, geographic extent and host range, are being used to test this by modelling individual traits vs groups of traits ('trait syndromes'); the idea being that particular combinations of traits will help a species get all the way along the invasion pathway (introduction > establishment > spread > impact). Louise has looked at trait syndromes and the extent to which certain traits might be positively or negatively correlated. For example being caducous and causing foliar disease are positively correlated, whereas being sterile and causing root disease are negatively correlated. Heterothallism and invasive potential on roots (in particular) and foliage are key traits that co-vary and are positively correlated. It could be anticipated that heterothallism allows greater sexual recombination and adaptation.

In terms of whether trait syndromes can explain global impacts, initial results suggest that high impact species (ie those with the broadest host ranges) tend to be heterothallic, have one or more survival structures, broad thermal tolerances and fast growth rates. Host range can also be predicted by root (and foliar) disease symptoms. In general, trait syndromes are more ecologically informative about the global impact of Phytophthoras. Louise went on to suggest that it might be possible to develop a trait-based early warning signal for Phytophthora pathogens which are known to have certain traits but for which there are no data on impact, ie to try and predict the behaviour of a novel species at an early stage. In this way potential threats can be ranked in order to inform Pest Risk Assessments.

In terms of next steps, the WP3 team will publish the traits database and phylogenetic analyses, and they aim to submit a paper linking traits and global impacts this November. Louise will continue to collate data on global Phytophthora occurrences, fine tune niche models and begin preliminary niche modelling approaches. They aim to co-develop final model outputs with policymakers.

14.30-15.00: WP4 Predicting risk via analysis of Phytophthora genome evolution - Ewan Mollison

Sarah Green introduced Ewan Mollison who recently started (August 1 st 2017) on the project as a PDRA working with Paul Sharp at the University of Edinburgh. Ewan started his presentation with a project overview and talked about the different mechanisms of evolution in oomycetes ie vertical gene transfer, horizontal gene transfer and hybridisation. Horizontal gene transfer, which is the direct transfer of genes between two species rather than from parent to offspring (known as vertical gene transfer), is of interest because oomycetes are known to have acquired genes from fungi in this manner. Ewan is interested in knowing to what extent this occurs in Phytophthora. Such events can be traced in genomes since 'recently' acquired genes from another species may look quite different to neighbouring genes as they tend to retain the characteristics of their donor species. Hybridisation events can also be identified in genomes by increased genome size and chromosome number or by analysis of gene sequences. Ewan presented a slide illustrating hyphal anastomosis and zoospore fusion; two possible mechanisms by which horizontal gene transfer and hybridisation may occur in Phytophthora.

The key aims of the project are (in the shorter term, ie the next six months) to sequence and assemble the genomes of three Phytophthora species that appear less damaging but are closely related to species highly damaging to woody hosts, and over the next two years to characterise key genes involved in woody host vs non-woody host infectivity, and to look for signatures of horizontal gene transfer and hybridisation between species.

Ewan presented a brief overview of Phytophthora genomes with the most extensively studied being P. infestans, P. ramorum andP. sojae. Genome sizes are variable, for example the P. austrocedri genome is 140 Mbp and consists of 47% repetitive regions. All species with annotated genome data have from 14,000 to 18,000 genes. Ewan then showed where all the current 25 genome-sequenced Phytophthora species sit by clade using the cox2 gene to calculate the trees. He went on to describe the characteristics and phylogenetic positioning of the three species to be target-sequenced in this project. In terms of looking at woody vs non-woody host infecting species, Ewan will look at ways in which their gene complements differ, whether characteristic sets of 'woody host infecting' genes can be identified. He will start with a comparison of P. ramorum (woody) and P. sojae (non-woody) as these are the most extensively studied species. Ewan then finished up with an overview of some background work on genome sequences of P. austrocedri isolates from Britain and Argentina, looking at similarities among isolates and between isolate groups, and whether the genome sequences might tell us anything about the origins of the two outbreaks in each country.

Questions and comments:

Q: How much of the difference between Argentinian and British isolates occurred in the source population before their separate introductions into their new regions ?.

A: We have no idea of the size (ie genetic variability) of the source population and can only infer what has happened since the founder population began in each country. In this case spread has been clonal, so the differences between the two isolate groups have largely occurred in the source population.

Q: It wouldn't be surprising if these invasions were driven by multiple introductions. Is it possible to look at this ?.

A: Yes this scenario is likely, although the separate introductions were likely to have been of the same clonal strain in each country.

15.30-16.00: WP5 Synthesis and integration - Sarah Green

Sarah Green gave an overview of WP5 activities since May 2017, including Board meetings and the reports/research summaries recently posted on the project website. Sarah noted that a four month no-cost extension (ie to July 31st 2019) which applies to the whole project and its work packages has been agreed by the funders. Jill Thompson (THAPBI co-ordinator) followed up on this point where it was confirmed that the whole group can spend existing funds up to the new deadline (but the project will not be in receipt of any additional funding). Project reporting will be three months after the new deadline. Sarah will initiate changes to the Collaborative Agreement to reflect this.

There was some discussion of where and when to hold the next all project team meeting. It was agreed that CEH in Wallingford next April/May would be appropriate and Debbie will circulate a doodlepoll to confirm a date once Louise has confirmed the plan with Beth. Sarah then reported briefly on the Phyto-threat's attendance at the National Plant Show back in June 2017, and talked through the seven posters that were designed for the stand display with the aim of raising awareness of the link between Phytophthora outbreaks on trees in the wider environment and spread of these pathogens in trade. It is planned that the project team attend the National Plant Show again in 2018 with some information presented on project results. Sarah also reported briefly on the 125 thIUFRO Anniversary Congress held recently in Germany, where the Phyto-threats project was represented by a talk and poster. Jill Thompson also mentioned an event to be held at Dynamic Earth in Edinburgh next month, it will be mostly targeting school children but the project could have a couple of posters there. The next stakeholder event to consider will be the THABPI dissemination event to be held in London on February 7th 2018. Watch this space!.
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
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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, 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 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 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 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 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 stipulated as part of the plant procurement process to allow purchasers to select what they consider to be the healthiest/least risky bid rather than the cheapest bid. This needs to be taken on board by the government for example in setting plant procurement policies for local councils. During this session Mariella also asked for local authority, landscaper, garden centre and retailer contacts for interviews. Several members of the project team responded that they would be able to supply contacts, and even help with the smart survey in this way.
The third session dealt with focus groups. Three focus groups are required this financial year. These will involve small groups of selected stakeholders discussing questions around feasibility of best practice and attitudes towards accreditation. This could be done via the HTA and the pilot Plant Health Assurance Scheme; for example would they be influenced by the consumer survey? The WP2 team could also meet around APHA and retailers to have a session on best practice and accreditation. More discussion is needed on this.
Finally, Mariella presented some slides on behalf of Gregory Valatin (FR) who is looking at cost-benefits of best nursery practice. The objectives are to undertake an appraisal of the costs and benefits of options for developing best practice in UK nurseries to mitigate risks of further Phytophthora introduction and spread, both from the UK nurseries' perspective and from the perspective of society as a whole. Mariella asked the team to consider the different scenarios that Gregory could use in his analysis, including the most appropriate baseline of best practice, which nursery characteristics to assume in the analysis and how to estimate cost of benefits to nurseries as a result of introducing best practice.
There was some discussion around whether an accreditation scheme should imply no use of imported seed. Current schemes vary on this issue, with the Woodland Trust's UK Sourced and Grown Scheme not allowing importation of seed from outside the UK. Seed can certainly be a source of some pathogens. A baseline scenario should involve nurseries having implemented some, but not all, best practices, assuming some importation of stock from outside the UK. More time would be needed to explore these economics questions fully and it was decided that Gregory should speak directly to Tim Pettitt, Jon Knight (AHDB), and Jane Barbrook and Kelvin Hughes of APHA as experts in the nursery sector willing to offer advice.

WP3 Global Phytophthora risks to the UK - Beth Purse (CEH) and Mike Dunn (FR)
Beth Purse presented the WP3 work, starting off by reminding the project team of the WP objectives. For Objective 1 (Risk of Introduction) the aims are to identify the most important trade and recreational pathways linking Phytophthora source regions to the UK, to model introduction risk based on transport networks, source and destination characteristics and to test links between introduction risk and traits. One milestone was to compile a global country-level database of records of occurrence/arrivals of Phytophthora. This milestone is now nearing completion with 17,371 country level Phytophthora records, and 1417 species x country combination records obtained from various sources. These state where possible the source/recipient country, year of first record (linked to arrival?) and invasion status. There are of course large differences among countries in national recording and biosecurity effort and this is reflected in the number of records per country. In the analyses the WP3 team are looking at pre-2000 records as the potential 'source' distribution of Phytophthoras and post-2000 records as Phytophthora 'arrivals'.
Preliminary analyses have been carried out using post-2000 Phytophthora records per country as the response factor and a set of predictors including trade connectivity to pest source countries (based on total imports of live plants), biosecurity effort (amount of invasive species legislation per country) and surveillance effort (number of official pest records from IPPC). Live plant imports and surveillance effort together explained 59% of the deviance in the number of new Phytophthora species recorded in a country since 2000.
UK Phytophthora records have also been compiled from a range of sources to enable models to be developed that relate Phytophthora species frequency of interception and extent of onward spread to biological traits. To assist with these analyses Beth held a short focus session in which she asked the project team to list what they felt were the most important factors influencing Phytophthora establishment in a new location, and rate of onward spread. These were then passed back to the WP3 team.
Beth then moved on to talk about the WP3.2 work (risk of establishment and spread) in which the team have continued to build the database of global Phytophthora records. They now have 11407 records for 82 species from 38 countries. In collating these data they have been prioritising countries that are climatically similar to the UK. Their niche models will predict potential global impact of Phytophthora species and the risk of their establishment and spread in the UK, excluding those species only known to occur in soil or water (ie no known plant host), species with no known woody hosts and species with non-relevant woody hosts (ie hosts not important in the UK). Their analyses will have to account for biases in reporting effort as developed countries have much higher species reporting than non-developed countries. This will be done by mining the scientific literature, oomycete and fungal databases (including Genbank) and adjusting weighting of records for species in highly recorded areas.
The Phytophthora traits database was merged in June 2017 with a similar database compiled by researchers in Australia and New Zealand. It contains data on 179 species and will likely be maintained in the longer term by Scion in New Zealand. A phylogeny will also be included in the database at some point. A publication is planned which will use the traits database as a conceptual framework for linking biological traits with invasion success of Phytophthora. Questions to be asked include whether closely related species share similar values for traits or groups of traits, or have traits linked to invasion evolved independently in several places in the phylogeny? They will also consider strength of phylogenetic signal in traits. Beth then ran through some traits which they have hypothesised to affect invasion success (ie survival structures, thermal tolerance, sporangial features). To do this they are using an ITS-based phylogeny (from Treena Burgess in Australia) for 179 species as well as two recent multi-gene phylogenies in order to resolve deeper nodes. Beth showed a series of slides with results from analyses so far illustrating strength of phylogenetic signal from sporangial features, reproductive traits and temperature traits, as well as rate of trait diversification over time - the latter showing high within-clade disparity suggesting rapid diversification and independent evolution to share common traits among clades.
Other questions being asked in the analyses are 'do thermal traits especially cold tolerance modulate invasion of Phytophthora into temperate regions? (ie are emerging infections at higher latitudes linked to cold tolerance?) and how traits co-vary with each other (trait syndromes) and how much of this is driven by phylogeny? In terms of the global impact of Phytophthora the main question being asked is 'can species traits explain the global impact of Phytophthora?. This analysis uses impact metrics including geographical extent (number of countries in which a species has been reported) and host range (number of known host families). These data are being compiled from various international databases. The team have also looked at whether trait syndromes outperform individual traits as predictors of global impact. Their findings so far suggest that root (and foliar) disease symptoms predict a broad host range, that trait syndromes are more ecologically informative about a species' global impact than individual traits and that it might be possible to develop a traits based 'early warning' system for pathogens which have similar traits but no impact yet.
Beth finished up by running through the plans for this coming year which are to submit papers on (i) the traits database and phylogenetic analyses and (ii) linking traits and global impact. They will fine-tune their species-specific trade models, develop UK and European spread models and finalise the niche models. They plan to finalise the model outputs with policymakers and practitioners in order to develop tools that people want, ie interactive source maps and lists of Phytophthora spp. associated with key forestry species.
Mike Dunn presented on work done so far looking at tourism and recreation as a pest and disease pathway, using methods such as literature review, visitor data from susceptible tourist attractions and by conducting a survey of internationally based plant pathologists. The literature review has found numerous studies linking spread of a range of invasive organisms to tourism, including P. ramorum. A recent VisitBritain survey revealed 31 million people visited Britain over a 12 month period with a third of these visiting parks/gardens as a stated objective. Visitor data have also been collated from seven of the most popular parks and gardens in Britain, including weekly visitor data from Kew Gardens. The team are now going to look at tourism data to see if there are links between tourism and Phytophthora introductions in the UK. Sixty-one plant pathologists worldwide have responded to a survey which included among the questions whether they considered international tourism to be a potential pathway for invasive pests and diseases. Fifty-six of the respondents said yes to this question, which is backed up by data from several studies. When asked to rank levels of perceived threat of bringing in pests and disease, imported plants and trees was ranked much higher than incoming international tourists.

WP4 Predicting risk via analysis of Phytophthora genome evolution - Ewan Mollison (University of Edinburgh)
Ewan presented on the WP4 work done so far (since the WP started in August 2017) and began by outlining what can drive the evolution of a pathogen through intrinsic factors (ie duplication, rearrangement, insertion, deletion of DNA regions) and extrinsic factors such as hybridisation between species and transfer of genes between species. He ran through the aims of the work which are (i) to compare genes from available sequenced Phytophthora genomes in order to identify a core set of Phytophthora genes common to all species as well as species-specific genes, (ii) sequence the genomes of three less damaging species which are closely related to highly damaging species so that genes involved in virulence might be identified and (iii) study target genes and gene families known to be important for virulence to identify how variations in these genes change pathogen behaviour such as host range and pathogenicity.
Ewan illustrated the sequencing and assembly strategy for P. austrocedri as an example of how a genome assembly can be improved. He found that 49% of the P. austrocedri genome consists of repetitive DNA. At this point Ewan was asked whether it would be possible to correlate species with high levels of repeat content with host range of the species - the answer was yes, it might be worth looking for associations with genome size and biological traits although generally for other species genome size correlates with nothing!
Genome assemblies are now available for 26 Phytophthora species, all in varying stages of 'finished-ness'. Most genomes are released along with predicted genes and protein sequences. Ten genomes have been released purely as scaffolded assemblies and gene prediction will need to be carried out on these. Ewan presented a graph showing large variation in the number of predicted proteins (over 30 amino acids in length) among currently available genomes, with the caveat that the protein data are likely to be an over-prediction and that the gene-prediction tools will need to be refined. A graph showing assembled genome size versus repeat content also illustrated the high levels of repeat content in certain genomes such as P. alni (hybrid), P. cambivora (putative hybrid) and P. infestans. Larger genomes are often a result of expansion of repeat regions, with these repeat regions often evolving rapidly which is very useful for overcoming host resistance.
Ewan assessed the completeness of coverage of each of the 26 Phytophthora genomes by looking for the presence of 234 ubiquitous genes expected to be present in all species. His findings showed that many genes may be missing from an assembly. For example 22/26 genomes were estimated to be 90% 'complete', 3/26 over 70% complete and the P. alni genome only 37% complete. Ewan then looked for orthologous genes present in all 26 genomes and found 2,107 genes or gene clusters common to all genomes. A phylogenetic tree inferred from these 'core' genes split some of the species from the same clade (ie species in clades 1, 3 and 8) however much more work is needed to refine this analysis.
Ewan then described some analyses done using an example gene family; the xylanases (xyn), which are cell wall degrading enzymes which specifically target hemicellulose, an important constituent of plant cell walls. There are four major xylanases which have been identified in Phytophthora; xyn1, xyn2, xyn3 and xyn4. Sequences from all xyn genes found in the 26 Phytophthora genomes were aligned and phylogenetic trees constructed for each gene. The xyn1 and xyn2 genes grouped into two distinct clades whereas the clades were less clearly defined for xyn3 and xyn4. Looking at the presence/absence of each gene among the 26 Phytophthora genomes revealed that not all species contain all four xyn genes which may be due in part to incomplete assemblies, and also that xyn sequence differences occur in some species which results in their falling outside the expected clade groupings for that particular gene.
Ewan finished his presentation with a cautionary tale; strangely anomalous xyn gene sequences were downloaded for P. taxon totara because the source database had been mistakenly linked to a P. kernoviae genome download. Always check the source!
Further WP4 work will involve sequencing P. obscura, P. foliorum and P. europaea to add into the analyses, together with any newly available Phytophthora genome assemblies. The xylanase gene family analysis will be expanded and other gene families of interest will be investigated ie RXLR effector proteins.

WP5 Synthesis and integration - Sarah Green (FR)
Sarah Green rounded off the meeting with a short overview of WP5 activities since October 2017, including Board meetings and the reports/research summaries recently posted on the project website as well as the successful uploads of all project outputs and outcomes to 'Researchfish'. There was some discussion on stakeholder engagement activities planned for the coming year. It was decided not to attend the National Plant Show this year but rather to wait until next year to present project results. There was agreement for the need to engage more formally with Defra and the HTA over the pilot assurance scheme to ensure that the Phyto-threats project data can help to shape this scheme. The next stakeholder workshop will have the theme of 'securing resilient outcomes - scoping the potential of an accreditation scheme and building a framework for its continued development'. It was thought that delaying the workshop until spring next year in order to have a more complete set of results to present would not fit in well with the nursery timetable - spring is very busy. So a decision will be made soon on whether to stick to the same format of holding the project team meeting followed by stakeholder workshop over two days in October. This will be decided at the next Board meeting.








List of Participants

Contact Organisation
Jane Barbrook Animal and Plant Health Agency
Paul Beales Animal and Plant Health Agency
Daniel Chapman NERC Centre for Ecology & Hydrology
David Cooke James Hutton Institute
Mike Dunn Forest Research
Debbie Frederickson Matika Forest Research
Sarah Green Forest Research
Kelvin Hughes Animal and Plant Health Agency
Jon Knight Agriculture and Horticulture Development Board
Mariella Marzano Forest Research
Ewan Mollison University of Edinburgh
Tim Pettitt University of Worcester
Leighton Pritchard James Hutton Institute
Beth Purse CEH
Paul Sharp University of Edinburgh
Peter Thorpe James Hutton Institute
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 presented a slide outlining the structure of the project, incorporating figures on global imports /exports, global tariffs, gathered from governmental data and the World Bank, used to look for trade anomalies using algorithms/machine-learning. This highlighted non-usual datasets.
Industry data - this project is revealing the difficulties of actually obtaining species import data. For example one company provided 240 combinations of species and specifications. The work has highlighted the very complex network of business connections that changes from quarter to quarter across the year. They are looking at certain species and asking; how much is brought in and what is the UK demand? For example, lavender, for which the demand is high, so could there be a good case to increase production internally?
Costs and responsibility - much of the work has been done by Barbara Agstner (Fera) as part of her PhD. Barbara has been on a road trip around Britain visiting various nurseries and getting estimates as to the costs of implementing various biosecurity measures. This work has again highlighted the many gaps where costs are unknown. One company was able to provide costing for a range of activities - this is being shared with Gregory.
In the second part of his presentation, Glyn presented on the emergence of various industry accreditation initiatives over time, i.e. BOPP, Grown in Britain, UK Sourced and Grown, the Plant Health Alliance. Currently the HTA, Grown in Britain and others have been working on a Plant Health Management standard and assurance scheme which is ready for launch in early 2019.
Any scheme will be about applying a plant health management standard(s) that will be owned by the governing body. The standard would then be adopted by the various assurance schemes. Individuals apply to the relevant certification body to join their scheme - thus currently there are several competing schemes all of which have to adhere to the agreed standard.
A scheme will have self-assessment questions, a full audit checklist, will require an audit. Everyone would sign up to the scheme and all would have to meet the criteria. However, certification schemes could compete - they would just apply standards, and would set their charge.
Discussion
The question was asked as to what best practice recommendations are needed to feed in to the standard from Phyto-threats? i.e. step-wise introductions of recommendations into a common industry standard since certain infrastructural changes need to be applied, such as water storage and treatment, raised benches, drainage, etc to make a scheme work at preventing disease. The idea of competing schemes did not seem very efficient either and stakeholders had preferred a single, overarching UK scheme at last year's stakeholder workshop.
Gregory Valatin spoke about the cost-benefit analysis of introducing best practice in nurseries from a nursery perspective. Following an initial low response from nursery managers to the economics questions included in the WP2 survey questionnaire, Gregory joined Barbara Agstner on some nursery visits as part of the costs and responsibility sharing Fera project. Over the summer 2018 a FR intern also helped gather economic data.
Gregory listed 12 'best practices' which formed the basis of the questions. Nursery managers were asked for estimates of the cost of implementing these practices. The best practices included water testing, water treatment, storage of water in fully enclosed tanks, clean/covered storage of growing media, use of raised benches, disinfestation stations for tools/containers etc, boot washing station, vehicle washing station, quarantine holding area for imported plants, installation of drainage systems, composting/incineration system for disposal of waste plants and buying only from trusted/accredited suppliers.
In addition to questions about the costs of implementing the best practices, growers were also asked for an estimate of the cost to their nursery were it to be affected by a future Phytophthora outbreak. The cost of implementing the best practices can then be compared with the expected avoided cost of the outbreaks expected to be prevented by implementing the best practice measures. The benefit of preventing outbreaks partly depends on the frequency of the outbreaks expected to be avoided through introducing the best practice measures. It is anticipated that other members of the Phyto-threats team - especially those working on WP1, may be able to advise on the frequency of outbreaks prevented (with this information also needed for wider exploratory cost-benefit analysis from a societal perspective).
Gregory presented preliminary conclusions for a number of scenarios based on economic data gathered so far (for which there are many gaps). These included where a nursery implements all 12 best practices (i.e. the baseline is that none of the measures have been implemented to date), as well as a scenario where a nursery implements just 8 of the best practices (assuming a 'common practice' baseline of 4 measures implemented to date). In each case it was assumed that at most one Phytophthora outbreak per year would be prevented. For the scenario of implementing all 12 measures, the initial survey responses indicated that the mean cost to nursery managers of implementing best practice, whether start up or where just the annual cost is considered, is much higher than the expected benefit of avoiding the costs of dealing with an actual outbreak. For the scenario of implementing the 8 best practice measures, the initial estimates similarly indicated that the mean set-up cost of implementing the best practice is much higher than the expected benefit of avoiding the costs of dealing with an actual outbreak, with the annual costs being of a similar magnitude to the expected benefit of avoiding an outbreak. For a 'typical' (1 ha) nursery, estimates from a sector expert also indicate that set-up costs for the best practice measures exceed the benefit of avoiding an outbreak (whether introducing all 12 best practices or the 8 best practices that initial responses to the survey indicate are not already common practice). Whether costs exceed the benefits to the nursery depends not only on the frequency of outbreaks that the nursery expects to avoid (which the responses to date suggest are currently far fewer than one per year - but potentially might increase above one per year if detection rates increase due to technological improvements), but also on any sales price premium nurseries are able to obtain once they introduce the best practices. Based on the preliminary data, Gregory questioned the level of take-up of a voluntary accreditation scheme if the perceived costs to the nurseries of introducing the best practices outweigh the perceived benefits.
Some of the qualitative responses from nursery managers support the conclusion that implementing best practice to reduce the risks of Phytophthora outbreaks is not seen to be cost-effective from a nursery perspective. However, as one of the nurseries contacted had noted, the cost of an outbreak will depend on which Phytophthora species is causing the damage. Gregory also asked the question; what happens if we factor in the benefits of avoiding other pathogens such as Xylella? Although implementing nursery best practices to reduce the risk of spread of phytophthoras may not seem a priority for many nurseries, current biosecurity measures across the plant trade sector are viewed as inadequate by some nurseries. Indeed, some nurseries advocate urgent action by the government in shaping which practices are permitted - especially in the context of risks of introduction of Xylella, with mandatory restrictions needed that apply more widely to the plant trade than just the nursery sector. Information on costs is still being incorporated from personal interviews and telephone interviews carried out this summer. More economic data will also be gathered by the survey company over the next few months.
Discussion
It was asked whether outbreak costs were based on cost of loss of stock alone as it was pointed out that outbreak costs should include Plant Health inspector time, litigation costs, loss to suppliers etc. Gregory noted that the survey asked both about the anticipated loss of nursery stock, as well as other costs to the nursery, but that nurseries are frequently very uncertain about the level of costs likely to be incurred - as illustrated by the wide range of estimates and proportion of respondents unable to provide estimates for the costs of implementing specific measures. Phytophthora risks are often perceived by nurseries as low compared to other pathogens, so there appears relatively limited interest currently in in implementing measures specifically aimed at reducing risks of Phytophthora outbreaks.
The comment was made that since improved biosecurity will be good for preventing all diseases, we need to emphasise this, in addition to talking about Phytophthora. Xylella should be included since quarantine holding areas and careful plant sourcing reduces the risks of a Xylella outbreak. It was reiterated by others present that core best practices work for all, and that best practice reduced the weeding/husbandry bill. Gregory noted that a question had recently been added to the questionnaire to enquire about the costs anticipated were there to be a future Xylella outbreak at the nursery, although initial responses indicated that it was also proving very difficult for nurseries to answer this.
Colin Price presented 'some economic costs of Phytophthora: nightmare scenarios' using the CARBBROD model - a model being used as the core element for the exploratory cost-benefit analysis of introducing best practices from a wider societal perspective. Thinking in a forestry context, disease outbreaks matter economically because of curtailing rotations and timber yields, wasting forest expenditures, taking land out of production, and by reducing carbon sequestration and storage. From a societal perspective, carbon impacts are key, owing to the high social values placed on carbon in relation to climate change mitigation. One of the scenarios presented using the model was of a new and unknown Phytophthora species entering the UK (e.g. via the nursery trade) and spreading to infect Sitka spruce plantations (based on a crop of yield class 14, age 30) along similar lines to the recent impact of P. ramorum on larch, with bare land following (if no other species replaced the Sitka on upland, acid sites); and another if Sitka spruce is replaced by noble fir. Owing to the trajectory of the social value of carbon used by the UK government for policy appraisal, infection of the Sitka followed by replacement with noble fir was found to give a better return to society than not having an outbreak! This was because of the increase in the discounted social value of carbon over time (with a lower price of carbon applying to the emissions associated with losses of the Sitka than to subsequent carbon sequestration by the noble fir). Everything depends on prices and timing! In prior discussions, Gregory had suggested potential for adopting other approaches to valuing carbon (e.g. assuming a fixed carbon value in real terms) to avoid the perverse conclusion that introducing new pests and diseases to the UK could be beneficial to society: Colin noted that implementing other approaches to valuing carbon was easy to do within the model, yielding the expected conclusion, that outbreaks modelled as above did indeed have adverse economic consequences. In worst cases, the cost through infection could be many tens of thousands of pounds per hectare.
Colin also looked at a scenario involving the speculative consequences of infection of oak stands with a new Phytophthora to the UK, assuming 30% mortality, 30% unaffected and 40% having reduced growth increment. In this case the stand increment recovers and regeneration comes from surviving trees. Forest managers can thin and choose subsequently to replant either with oak or something else (e.g. sycamore). In contrast to the scenarios for Sitka, a key difference here is that continuing to grow the same species on the same site is an option.
The CARBBROD model can also be applied to a scenario involving a new disease coming in and infecting urban trees, for example a broad host-range pathogen that can take out 10% of all urban trees. The resource baseline proposed for this scenario was the urban forest from the London i-Tree Eco project survey. Colin compared the costs of trees dying due to a new disease versus those of dying due to age. Costs in terms of the associated reduction in ecosystem services were evaluated, including loss of pollution abatement, loss of aesthetic services, and loss of carbon sequestration, as well as replacement costs' being brought forwards. The costs need to be evaluated by species, age and life expectancy.
Colin closed his session by asking the floor for likely scenarios for a new Phytophthora coming to the UK and infecting Sitka, oak etc. For example how much of the crop is likely to be affected, what is it likely to be replaced with? Discussions with Colin over lunch and tea did not prove as helpful as hoped in trying to answer some of these questions. Wider enquiries will be instituted.
Appendix
Attention could be drawn to some reminders on CARBBROD, compiled by Colin and presented by Mariella to the mid-year project meeting. CARBBROD does not deal specifically with the economics of nursery practices, but with the effects of these practices on forestry plantations and woodland health based upon the likelihood of the outbreak and spread of a new tree pathogen (e.g. entering the country via the plant trade). It evaluates the consequences for timber production and carbon fixing of disease arising under different scenarios of tree age, consequences and management responses. In this project the model will be applied to important threatened species and genera (e.g. Sitka, oak, urban trees). It is flexible to allow adoption of different forms of carbon pricing, discount schedules and interactions.
In terms of future developments of CARBBROD, as the carbon effects are dominant, incorporating the effects of the new disease on litter and soil carbon (if these are known) would be useful, as well as adapting urban tree carbon for effects of disease, including landscape scale effects of disease if feasible and incorporating a simple application to scenarios of disease spread (as has been done previously for Dothistroma).
WP3 Global Phytophthora risks to the UK - Beth Purse (CEH), Dan Chapman (CEH) and Mike Dunn (FR)
Beth Purse presented the objectives and components of the work package which are;
Pathways of risk of introductions
Traits modulating introduction risk
Social factors and environmental/ecological traits influencing spread once here
Environmental niche models to map areas at most risk
Dan Chapman presented on risk of introduction of pathogens which they are addressing by modelling the risks based on transport networks and pathogen traits. Louise Barwell has accumulated a database of country level occurrences which includes 17,371 country level records with dates and 1,417 species x country combinations (the source of this information is the recipient country/ year of first arrival/invasion status).
A preliminary analysis of this database asked the question: 'Can live plant trade network explain arrivals?' There are data for total import volumes, network connectivity (imports of focal species from source countries), arrivals-trade-species-country. Arrivals detected post 2000 were from 94 countries and 56 Phytophthora species with = 1 documented arrival. The result was that connectivity (total live plant imports from countries in which Phytophthora species occur) explains about 21% of the variation in new arrivals better than total imports (i.e. from anywhere).
Moving on to risk of establishment and spread, Beth ran through the original aim of the global niche models: to predict the area of extent of impact on UK tree species of global Phytophthora species that have not yet arrived in the UK (30) and 24 species that have arrived. Of the global Phytophthora occurrence data gathered, regions climatically similar to the UK give 11,497 records comprising 82 Phytophthora species in 38 countries. Data are still to come from countries such as New Zealand, Australia, South Africa and Canada.
Looking at the habitats in which Phytophthora species are recorded, most records are drawn from closed forest types, also urban areas and cropland. Many of the species for which sufficient information is available to make niche models on risk of establishment and spread are already in the UK. Focal species not yet present in the UK have very few occurrence records worldwide. So the aims of the niche models need to be revised. For those species already present in the UK, niche models will look at their potential distributions here. For high impact invaders such as P. cinnamomi and P. ramorum new global niche models will be developed with a range of environmental factors.
Records of pathogen interceptions/escapes in the UK have been gathered from key sources (THDAS, RHS, SASA, eDOMERO). Some data e.g. THDAS have related data on interceptions to subsequent spread in the different settings, linking back to traits and trade/recreation proxies. Geographical occurrence will be linked to environmental characteristics in order to predict potential distribution.
Beth then updated everyone on the Phytophthora traits database which was merged last year with a database held by Scion (New Zealand) and which will be maintained there. Beth finished up by outlining future work which will be to submit papers on the trait database and phylogenetic analyses and traits and global impact (by January 2019), trade models, finalise global niche models, policy briefs and co-development of final model outputs with policy makers and practitioners. An example of the latter might be the production of interactive source maps from trade and tourism models.
Discussion
A comment was made that host ranges did not seem to be included in the traits database, possibly because information only comes in when disease outbreaks occur. Yet host range data are very important. Generally, when a new species is found it is tested for pathogenicity on hosts closely related to the affected host, or on hosts that closely related Phytophthora species infect. It was agreed however that phytophthoras can surprise, for example host range tests were performed on trees expected to be P. ramorum hosts based on analogy with the US, but no one expected larch! It was asked if closely related Phytophthora species have similar impact? If you look at host range at the Phytophthora species level, rather than related group level, some species have a wide host range, others narrow. It was cautioned however that wide host range doesn't necessarily mean they are more devastating on a host.
Mike Dunn presented on his work looking at tourism and recreation as a pathway for pathogens, carried out through literature search, survey of Plant Health researchers around the world, and visitor data to UK parks and gardens. Generally, it is considered true that recreation and tourism have acted as a pathway for spread of plant diseases previously, but that this pathway is perceived to be of lower risk in terms of spread of pathogens than other pathways such as traded plants and plant material.
In terms of visitor data, the 2011 Visit Britain survey on passengers visiting Britain has been useful in providing number of visitors, origin and timing of visits and, based on a questionnaire, the estimated number that are planning to visit a public park/garden while in the UK. Mike has also approached 23 parks and gardens asking for data on visitors, with a mean of 471,000 visitors pa. Very few of these sites collect data on visitor origin. Moving on to discuss domestic spread within the UK, a survey monitoring engagement with the natural environment conducted in 2017-2018 found that 62% of adults living in England reported making visits to the natural environment at least once a week.
The next steps for this piece of work are to write up the data and think about whether incoming tourists are a viable means of spread of pathogens.
Discussion
It was suggested that people travelling between (for example) National Trust properties in a single day could potentially be transferring pathogens from site to site. Bus tours, train tours etc go from site to site and it might be interesting to look at the tours and what their schedules are. Another suggestion was to check international plant propagators conference proceedings as examples of people going overseas and bringing back plant samples independently.
WP4 Predicting risk via analysis of Phytophthora genome evolution - Paul Sharp and Ewan Mollison (University of Edinburgh)
Paul Sharp explained that this work package focuses on understanding what can drive the evolution of a pathogen and allow pathogens to adapt to evolving host defences, expand host range and increase virulence. Comparative genomics may enable us to identify the genetic basis for some of the Phytophthora traits, for example evolving to infect woody hosts. Previously his group successfully completed similar work with 64 strains (genomes) of P. syringae: 38 from woody hosts and the rest from non-woody hosts. They were able to associate specific genes with woody hosts and they will try to accomplish this with Phytophthora.
The aims of this work package are to compare genes from available sequenced Phytophthora genomes, identify a core set of Phytophthora genes common to all species, identify species-specific genes or variation, sequence the genomes of three less damaging species which are closely related to highly damaging species (the topic of this talk) and study target genes/gene families known to be important for virulence.
Currently, they have Phytophthora genome information available from various sources, covering 27 species and 10 clades, but most genomes are from species in clades 7 and 8. Paul showed a phylogeny of all Phytophthora species with available genome data.
The project has recently sequenced the genomes of three less damaging species. These are;
P. europaea, clade 7, originally associated with rhizosphere of oak forests in Europe and most closely related to P. alni, P. cambivora (woody hosts) and P. fragariae, P. rubi (soft fruit hosts).
P. foliorum, clade 8, originally isolated from azaleas in US and closely related to P. ramorum.
P. obscura, clade 8, originally associated with horse chestnut soils and azaleas and closely related to P. austrocedri.
Carolyn Riddell (FR) successfully extracted high quality genomic DNA from all three species for PacBio long-read sequencing and Ewan has been assembling the genomes.
Ewan Mollison ran through the results from the initial genome assemblies. The reason for choosing PacBio over Illumina is because it gives much longer read lengths (10s of Kbps), giving better resolution of repetitive regions and greater overall contiguity. Error is random rather than systematic, so if there is very high read coverage across the genome the errors can be corrected rather than amplifying bias.
Ewan ran through an earlier assembly of the P. austrocedri genome. This species was sequenced using a 'hybrid' method combining both PacBio and Illumina reads. The hybrid assembly was hampered by not having sufficient read depth of either sequence type for optimal assembly. Pete Thorpe (formerly of JHI) re-did the assembly based on the PacBio reads only, using the Illumina reads only for error correction. The outcome was a much improved assembly (862 scaffolds compared with 43,700 with the hybrid assembly). Therefore a PacBio only assembly was pursued with the three Phytophthora species targeted here using two SMRT cells to achieve plenty of reads across the genomes.
The data for the three new genomes (P. europaea, P. foliorum, P. obscura) were presented. A good overall read length was achieved for all three species across both SMRT cells and Ewan explained how he made his scaffold assemblies and gene model predictions. In terms of genome size the estimates for each species are; P. europaea 95Mbp (has more repetitive genome content); P. foliorum 70Mbp; P. obscura 63Mbp; therefore it is safe to use 100Mbp as an estimate of genome size for all three species. The number of contigs for the three species is low (103 to 127) indicating a very high degree of contiguity in all three assemblies.
Scaffolding links contigs together with gaps of known length padded out with 'N' characters. The number of scaffolds across the three genomes is also low, ranging from 67-77, again indicating a high quality of assembly. All three species sequenced here have a very low number of scaffolds compared with other sequenced Phytophthora species (except for P. sojae which has a very complete assembly), for example most species have over 2000 scaffolds, with P. cambivora having 120,000 scaffolds indicating a highly fragmented assembly.
The three assemblies reported here have a high completeness of assembly (98%), a low level of genome duplication (~1%) and good resolution of haplotypes. The likelihood of polyploidy is low. Looking across the other genomes the trend is for larger genomes to have larger repeat content. Looking at predicted proteins the trend is less clear. The number of predicted genes is generally similar for many of the Phytophthora genomes. P. cambivora came out as having a particularly high number of predicted proteins but rather than being extra genes this is likely to be gene fragments incorrectly identified as separate genes/proteins.
Ewan showed an example of xylanases as a sample gene family which may be of interest in this study. Xylanases are an important class of plant-cell-wall-degrading enzymes.
There are four major xylanases which have been identified in Phytophthora; xyn1, xyn2, xyn3 and xyn4. Sequences from all xyn genes found in 30 Phytophthora genomes were aligned and phylogenetic trees constructed for each gene. Clades 9/10 only have 2 xyn genes, clade 8 species have 3 xyn genes and clades 1-7 have all 4 xyn genes. xyn sequence differences occur in some species which results in their falling outside the expected clade groupings for that particular gene.
Discussion
A question was asked about the use of the tool BUSCO for assessing genome assembly. Ewan explained that BUSCO tends to evaluate core genes, for example those in DNA replication and protein metabolism that are more ubiquitous. Checking that they are there would certainly provide a measure of confidence.
A non-biologist within the group asked for a digest on progress for a non-biologist! Much of the language used in this presentation was incomprehensible to those unfamiliar with the field. It was explained by Paul that, put simply, the three sequenced genomes have good sequences so they can now look for genes to see if there's an association between having a gene and having a certain trait. Also, for genes with target activity e.g. genes known to be involved in pathogenesis like xyn genes, they are now in a position to compare amongst the pathogens and non-pathogens.
WP5 Synthesis and integration - Sarah Green (FR)
Sarah Green presented an overview of coordination/ communication events since the last meeting. This included two board meetings (June and August), the minutes of which were posted on Huddle. The April team meeting report and research updates for 2017/18 were also posted on the project website.
The date and location of the next all project team meeting were discussed. It was agreed that a meeting would be held in York in October 2019, together with a stakeholder workshop. It was pointed out that this should not clash with the Phytophthora IUFRO meeting in Sardina over 17-25th October.
Sarah, Tim Pettitt and Jane Barbrook also represented the Phyto-threats project at the HTA National Plant Show in June 2018 following the offer of a stand for free! Sarah took the WP2 consumer survey leaflet to hand out, as well as the two-sided flyer on best practice, based on outcomes from nursery sampling to date. Both were well received. Sarah conducted interviews for, and completed, 7-8 garden centre questionnaires, gaining an appreciation for the difficulties of social science research! She also presented a talk at the show, following which the 'Gardening Which' magazine approached to say they would stop recommending purchasing 'bargain' (i.e. unhealthy-looking) discount plants to their readers!
David and Sarah went to the Oomycete workshop in Boston in July 2018. Their presentations covered this project, in particular how we engaged nursery stakeholders. David said their approach with validation got praise. David, Leighton and Sarah will all present talks at the 'DNA Working group meeting' in Derby, 26-27 November 2018.
Discussion
Discussion followed on the nature of the focus groups that need to be held. What should they be about? How would it link to outcomes on accreditation? We need to hold them before the end of December 2019. Sarah suggested a focus group aimed at building in more with the HTA initiative and associated groups. Mariella clarified that a focus group meant an intense discussion for a couple of hours with just 8-10 people and she said that Fera should be included.
Beth suggested a group to discuss risk model outputs, perhaps toward the autumn, either within the October stakeholder meeting or as a stand-alone. At the stakeholder workshop next year Sarah would like stakeholders to receive a clear message from each WP including practical outcomes.
Mariella returned to the questions that might be asked at a focus group with nurseries. For example how do nurseries react to what their consumers think? She wondered if there were any outstanding questions not covered or not covered adequately so far. If so, Mariella would welcome feedback.
A comment was made that we all use specialised vocabulary in our presentations. What words are washing over everyone else? It would be helpful not to use too much jargon for the public audience. It was agreed that we should always try to deliver the key messages to stakeholders in easy language to follow (maybe a glossary would help too).
Discussion of future funding options - Sarah Green (FR)
The meeting finished up with a discussion on further funding opportunities given that current project funding ends in March. There has been a no-cost extension until end of December 2019 but no further funds for staff time.
Sarah is putting together a proposal to the Defra future-proofing plant health (FPPH) programme 2019-2022. Within this she is looking to build a collaborative framework to support the continued development of accreditation. The feedback was that the timing was good for collaboration and the Phyto-threats project has lot of information to feed into scheme.
Another part to the FPPH proposal is aimed at developing a standardised nursery testing protocol for metabarcoding to be incorporated into an accreditation scheme. This would use methods already developed as part of the project but broaden the scope to include other types of pathogens such as bacteria. It was suggested that nematodes could be included too. It was agreed that community modelling for areas within the nursery prone to accumulation of pathogens would be useful.
On the question of the ability of metabarcoding to assist in nursery surveillance during statutory plant health inspections, the comment was made that, crucially, you need to isolate an organism at some stage. Also, results need to be fast so staff can go back to the nursery almost immediately.
Another suggestion was that it might be possible to tie in nursery sampling with something else of service to the nursery, for example testing peat/water/ cuttings from Kenya! Even to ants or leaf-hoppers! Technology moves on too, the processing gets faster, better.
It was asked if Sarah had seen the HTA's paper on how technology is being managed because this might give further guidance. Sarah confirmed she has had discussions with the HTA plant health lead and that he is supportive of the Phyto-threats project feeding into the Assurance Scheme.
Other thoughts on funding included developing something on the macroecology of Phytophthora and related groups. It might be possible to relate success in environmental/hosts/traits to host/pathogen relationships and latitudinal or elevational gradients i.e. what makes species successful? There could be added value of joining up research on trees with ornamental and agricultural research. The BBSRC standard grant round might be a good starting point, i.e. better predication on landscape-scale spread.
A comment was made in regard to the proposed accreditation scheme that the UK garden centre association has an annual meeting. They might be interested.
Two of the WP4 team have submitted a NERC DTP PhD proposal for continuing some Phytophthora genome work.
Another area for future consideration might be to identify where the unusual species have come from? What is the point of entry into environment? Traditional paperwork trail has been used as a tool. If you think about the nursery data, how does that Phytophthora come to be there? You can monitor sewage, fish farms, eDNA. NERC might provide support? It was also asked if there would be value in mapping Phytophthora species data for the UK? One of the bioinformaticians also works on a bacterium and is trying to identify through sequence analyses whether bacteria are transmitted vertically through seed or through the environment. They need to find the right bit of the genome, then they have to train the tool.
Following the end of this discussion the meeting was closed and Sarah thanked everyone for their contributions.







List of Participants

Contact Organisation
Jane Barbrook Animal and Plant Health Agency
Daniel Chapman NERC Centre for Ecology & Hydrology
Peter Cock James Hutton Institute
David Cooke James Hutton Institute
Mike Dunn Forest Research
Debbie Frederickson Matika Forest Research
Sarah Green Forest Research
Kelvin Hughes Animal and Plant Health Agency
Glyn Jones Fera
Mariella Marzano Forest Research
Richard McIntosh Defra
Ewan Mollison University of Edinburgh
John Morgan Forestry Commission
Ana Perez-Sierra Forest Research
Colin Price Consultant
Leighton Pritchard James Hutton Institute
Beth Purse NERC Centre for Ecology & Hydrology
Alexandra Schlenzig SASA
Paul Sharp University of Edinburgh
Gregory Valatin Forest Research
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
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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.
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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.
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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 ?.
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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.
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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.
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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.
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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.
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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'.
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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:
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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.
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The surveys will focus on disease management generally, with Phytophthora a component of that.
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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.
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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.
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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?.
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Richard McIntosh (DEFRA) asked whether the social science surveys would question about Phytophthora specifically or general disease management? - Answer was both.
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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,
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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
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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:
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David Cooke made an action point to speak to Dan, Beth and Ana about the Phytophthora species list details. David agreed to drop his species description literature collection of pdfs on Huddle.
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It was noted that some databases (ie CABI) have dubious entries with questionable provenance, ie identification of P. kernoviae in New Zealand: a post-hoc identification by sequencing of a culture collection.
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We need to be aware that plants do move WITHIN Europe and that may not show on the import-export databases.
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Open-source flight information may be helpful.
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Mariella Marzano asked whether the plant passporting scheme can be used to track movement of plants within Europe - the answer was yes, to some extent.
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Paul Sharp (University of Edinburgh, UoE) asked how many Phytophthora species are there and will we be able to spot the next 'new' species?. The answer was that there are likely to be many as yet unknown species globally and therefore prediction is a major challenge. Ana Perez-Sierra (FR) commented that SE Asia is thought to be a 'hotspot' in Phytophthora diversity and the EU POnTE project has scientists currently conducting Phytophthora surveys in Asian countries such as Vietnam (and potentially Japan).
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Jane Barbrook (APHA) commented that we should not forget that data exist from previous projects on modelling on nursery movements and hubs. Also that LWEC Phase 2 project has host-pathogen interaction modelling, including CLIMEX.
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A question was raised as to how to cope with plant imports via internet purchases? Kelvin Hughes (APHA) said that Plant Health have a relationship with internet companies and also deal with Royal Mail and East Midlands airports to check consignments. It was also noted that total volumes of plant material moving in this way is small compared to other trade pathways.
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John Speirs commented that the Scottish Government is commissioning a new project in month or so that will track Phytophthora species in key environments across Scotland. Again, data from current metabarcoding projects studying Phytophthoras in the wider environment will be useful for WP3 models.
WP4 presentation
14.00-15.00: Paul Sharp (UoE) and Leighton Pritchard (JHI) presented the overview of WP4: Predicting risk by analysis of Phytophthora genome evolution. This WP will start in April 2017 and will run for two years. Paul provided a general introduction to molecular genetics using data from a range of organisms to explain how DNA sequences can yield useful information on evolutionary processes leading to (for example) woody host adaptation, including the role of horizontal gene transfer. Paul also provided an overview of complications in DNA analyses due to hybridisation and horizontal gene transfer. This project will look at genes gained and lost across the Phytophthora population using approaches similar to those used to analyse genes associated with infection of woody hosts in Pseudomonas syringae. Leighton Pritchard presented on currently available Phytophthora genome data, describing the usefulness of different genome databases. Most Phytophthora genomes are in the size range of 30-50 Mb, although P. infestans genome is 130 Mb. The following discussion points were raised;
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Sarah Green (FR) said that money had been budgeted within the project to target sequence three Phytophthora species. Which species should these be? (to be decided). Sequencing of these three genomes should be done this year so that data are ready for the UoE PDRA to start April 2017.
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Beth Purse (CEH) asked whether genome size is related to adaptability?. Leighton Pritchard (JHI) said 'possibly' and would pass genome size data on to Beth.
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Sarah Green (FR) commented that the Phytophthora austrocedri genome is currently being sequenced - it appears to be large (around 120Mb).
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Dan asked if the extent of horizontal gene transfer could be predicted from genome size and Leighton's answer to this was 'yes, perhaps'.
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Sarah Green (FR) also commented on a paper published showing how P. ramorum (for example) has likely acquired infection genes from other oomycetes and fungal species by horizontal gene transfer [Richards, T.A. et al. (2011) Horizontal gene transfer facilitated the evolution of plant parasitic mechanisms in the oomycetes. Proc. Natl. Acad. Sci. USA 108: 15258-15263].
Stakeholder perspectives
15.10-15-50: Stakeholder perspectives were given by plant nursery participants Alan Harrison (Forestry Commission), Alice Snowden (Cheviot Trees) and Rodney Shearer (Alba Trees).
Alan Harrison is head of the forest tree and seed supply for the Forestry Commission's (FC) National Forest Estate plantings. He manages three forest nurseries at Newton, Wykeham and Delamere, growing 23 million trees, buying in 5.6 million. The FC does not buy trees from outside the UK but some of the suppliers may do. Overall they supply ~ 12K Ha planting each year. The main species is Sitka spruce which is grown in the ground or in cells in contact with soil. Approximately 12% of the stock are broadleaf spp. grown as bare root and in cells. Alan commented that they have much greater species diversity in their stock compared with 10 years ago, mainly due to the wish to diversify forests and in response to climate change forecasts. Lodgepole pine is back in favour, for example, and some of the new species are Taxus, Tsuga, Thuja, Chamaecyparis, Eucalyptus, Cedrus, Juniperus. Some of these are 'newcomers' and we know less about how they will behave in Britain.
Some of the issues raised by Alan included importation - are visual checks sufficient?. Should we quarantine them?. Also, do their existing nursery practices (ie growing directly in soil) make infection more or less likely?. Essentially the nursery wants a better appreciation of risk and what they can do about it. For example what are the risks of further host jumps in Phytophthora?, what is the risk of mutation causing increased virulence?.
Alice Snowdon gave a run through of Cheviot Trees production systems with photos. They are a forest nursery, growing cell-grown stock in polytunnels with approximately 25% of stock going to FC under contract. Broadleaves go to FC and some to foresters under grants. They also grow some Christmas trees. The stock is sold at 1-2 yrs old, mostly 1yr old. All stock is raised above ground over Mypex with mist irrigation indoors. The water source is borehole including one from gravel under a river bed. Water drains from beneath/edge of beds. Trays are always washed after use in cold water (this water would be a good sampling point), however, the nursery is considering changing this and would like to know whether it is worth the effort.
Newly sown crops can suffer from damping off. They have also had cases of patch dying of conifers, hawthorn and privet. Samples of diseased stock get sent to a laboratory for testing. Generally the lab reports show many species of potential pathogen organisms - they cannot tell the nursery which is primary. Diseased saleable plants with blackened stems and top wilt are nearly always diagnosed as Phytophthora. This is normally addressed through changes to irrigation. Sometimes conifers are found to be positive for Phytophthora - and treated with fungicides. Impact of Phytophthora currently means changes in species stocked (ie they no longer grow larch and are cautious about Juniper).
The nursery considers that involvement in this study could be risky, but they hope not. They are looking for guidance on best practice. Alice was interested to know more about the
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Australian nursery accreditation scheme and how it works. In terms of management practice, Alice wondered if the project could test irrigation water sitting in tanks in winter for Phytophthoras. Alice also wondered whether cell density in trays was important in terms of increasing ventilation (less humidity for infections) and how long to allow tree collars to dry between watering to lower risk of infections. Apparently there are very few fungicide options on the market. A phosphite-based compound was reportedly very effective but was taken off the market.
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Ana Perez-Sierra (FR) commented that trays are very important in Phytophthora transfer in nurseries and that steaming is the most effective cleaning method. Often the trays cannot be cleaned even with bleach.
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Kelvin Hughes (APHA) commented that compost/growing medium also has an important role in Phytophthora management.
Rodney Shearer presented on Alba Trees, who grow 11 million cell-grown trees (no bare root). The nursery doesn't buy in anything and nothing comes from the EU. They have recently acquired a tree nursery in Czech Republic as an export agent. In Scotland the nursery has two sites about 800m apart. One site has greenhouses and propagation, and the second site is a farm which does the growing-on. The nursery has the potential to produce 14 million trees if the market was there. Red-band needle blight has reduced the pine stock requirement; apparently there are further restrictions on movement of pine in Britain due to the presence of a unique southern strain of the pathogen not present in Scotland. The nursery has reverted to using disposable trays for susceptible crops because of disease risk, but this causes much plastic waste. They do not use compost, as tends to be from municipal waste and is not uniform. Instead they use a peat based non-sterile product from peat bogs which is tested for Phytophthoras and eelworm. Rodney did express concern about the application of notifiable diseases and exclusion zones, citing an experience the nursery had with fireblight on hawthorn. Alba Trees used to grow mainly native species but now also stock more alternative conifers. Rodney cautioned on the risks involved as we don't understand enough about their biology. Alba are not scared to have project scientists visit as they want to know what Phytophthoras they have in order to reduce risk. The nursery wants stability and they need to know the balance of risk and species.
Policy and industry perspectives
15.50-16.45: Members of the Expert Advisory Panel gave their talks from policy/industry perspectives.
Kelvin Hughes, Chief Plant Health and Seeds Inspector, APHA;
APHA have 190 staff and cover 30 UK border inspection points. There is 18h/day, 365 days/yr cover at major points of entry. They do passenger baggage checks too and general surveillance. APHA do Plant Health diagnosis with R&D done by FERA. Traditional techniques for diagnosis dominate, although they are now promoting the use of on-site molecular diagnostic instruments (ie Genie machines) for tests applicable to specific pathogens.
The UK is responsible for 1/3 of EU notifications and the current main Plant Health issues are Epitrix and Xylella. Kelvin stressed the importance of collecting plant passporting information during project sampling. It is important that the project works with PHSI in sampling although each inspector's time is chargeable and project scientists need to beware that APHA staff cannot spend extra time at nurseries without explaining to owners why.
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APHA can provide information on how to package and send project nursery samples up. We also need to make sure that project involvement does not affect APHA's ISO9000 accreditation.
John Speirs Senior Policy Advisor, Scottish Government;
The Scottish Government has roles from policy to inspectorate and scientific support (through SASA). Though Plant Health is devolved, in general, Plant Health links are strong across the UK. John Speirs is Chair of the Scottish Phytophthora steering group too. A Plant Health Strategy for Scotland was published earlier this year http://www.gov.scot/Publications/2016/03/7136
John stressed the importance of the project managing its message to industry so that it is viewed positively. John also mentioned the possibility of new EU legislation meaning that nurseries with an 'action plan' may not be inspected so frequently.
Richard McIntosh Assistant Chief Plant Health Officer, DEFRA;
Richard is head of the Plant Health Risk and Horizon Scanning team and provides direct support to Nicola Spence, Chief Plant Health Officer as well as scientific and technical training to DEFRA, FERA etc. Richard provided information on the Plant Health Risk Group (PHRG) which meets every 6 months to assess UK wide positions on specific pest issues, including horticultural pest and pathogen problems. The group monitors interception data from the UK and abroad and decides which organisms to place on the UK risk register. Pest Risk Analyses are then commissioned followed by a 12-week consultation period. Recommendations for action are then made to the Chief Plant Health Officer and escalated to ministers where necessary. Currently about 10 species are added to the risk register each month. Richard listed some of the actions required for the 15 Phytophthora species currently on the risk register (11 present in the UK - 4 widespread and 5 more limited in distribution). Richard stated that some challenges to the project include how to prioritise species as threats, dealing with the 'unknowns', and the need to offer practical and proportional guidance. In order to secure nursery participation, stakeholders need to know what's in it for them.
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Sarah Green (FR) asked what does it mean if a Phytophthora is on the risk register?. The answer was that species may be on the register as Regulated or Unregulated. Regulated species are under specific regulations and any species considered a low risk are Unregulated. Since the risk register has come into operation more and more species have been added each year. At present all species on the risk register remain on the register even if no longer considered to be a risk.
Jon Knight; Head of Research and KT, ADHB
Jon is the Head of Crop Health and Protection at ADHB which is part of DEFRA. It is a levy-raising board and a non-departmental Government Body. Its purpose is to provide independent, evidence-based information and tools for growth and sustainability. 9% of its income (ie about 700k of a total income of £7.2M) comes from the Hardy Nursery Stock sector - 12% of that is from tree production. Phytophthoras cross several sectors of AHDB so is of much interest to them. Jon can help with project in terms of providing stakeholder contacts as he has a list of 600-700 Hardy Nursery Stock sector levy payers. Jon's presentation summarised the value of the different sectors of the UK horticulture and landscaping industries including the value placed on tourist visits to UK parks and gardens, the amount (£1.4 bn) spent by tourists in gardens, the £2 bn value of UK flower/plant production, and 300k people employed in horticulture and landscaping in the UK. He also mentioned the Ornamental Horticulture Roundtable Action Plan as being of interest to the project https://www.rhs.org.uk/about-the-rhs/pdfs/about-the-rhs/mission-and-
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strategy/ornamental-horticulture-roundtable-action-plan which includes Plant Health as a focus.
WP5: Project communication and interaction
16.40-17.00: Sarah Green presented on WP5, the integration and communication platform for the project. This is a network to promote information exchange and interdisciplinary practice within the project team. The project uses Huddle to share information and for project/task management. The project board will meet monthly or every two months by phone and the whole project team will meet twice a year. There will also be annual Science-Policy-Practitioner Network (SPPN) workshops involving project scientists, industry and consumer representatives, policy makers, and other interest groups. This year's SPPN workshop will focus on scene setting and building relationships. The one to be held in the final year will focus on scoping the further development of an accreditation scheme (the goal of the project). By this stage in the meeting the discussion was brief!;
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Proposed that the next project team meeting is held at Sand Hutton, York, in early October 2016 with a visit to a local plant nursery in the afternoon. The spring 2017 meeting could be held at JHI in Dundee with visit to sequencing labs in the afternoon. Dates and places will be investigated.
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It was suggested that the project should have a presence at the National Plant Show, Stoneleigh June 21/22 http://www.nationalplantshow.co.uk/ in order to advertise the project to traders, but that this event is too soon for this year's project SPPN workshop.
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It would be best to combine the SPPN workshop this year with the autumn project team meeting at Sand Hutton and have a two day event.
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Other events which would be useful in terms of reaching out to stakeholders include the Four Oaks Trade Show http://www.fouroaks-tradeshow.com/ 6th-7th September in Cheshire and GroSouth http://www.grosouth.co.uk/ 9th November in Chichester this year
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Who to invite to the SPPN ?. Please email suggestions to Sarah Green (FR). Attendees should also include landscapers and conservation groups.
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 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 public, landscapers, and middle-men in the supply chain) and wider society. Without the knowledge of what accreditation is trying to achieve and what it represents, it cannot be expected to garner support or influence spending behaviour.

Government signs : Achieving improved awareness of Plant Health and its importance was seen by many to be the responsibility of the government and its relevant departments (e.g. DEFRA, APHA). To achieve this aim it was agreed that the problems accreditation would attempt to solve must be made visible to the point where they simply cannot be missed or ignored. Suggested strategies for public spaces included signage throughout transport networks, typified elsewhere by the large, unmissable signs (e.g. bordering Canadian highways in and out of at-risk areas). Bus shelters and airport signage were similarly suggested. The imagery used in these instances could include altered landscapes, featuring 'before and after' photographs in outbreak areas, or artificial images to demonstrate how a currently valued landscape would likely appear following a loss of trees.

Media campaigns : TV campaigns, comparable to anti-smoking and green cross code advertisements were thought to be the most effective way to bring the message around the need for accreditation into the publics' homes. This was thought to give the public little choice but to see and hear the required information. In contrast, online resources (such as videos or factsheets) are thought to have less impact - since people would actively have to seek out this information themselves it is unlikely that a sizeable proportion of the population would benefit from this form of exposure. For both TV and online content there was some concern that cartoons have a lifespan, and that beyond this the content may become ignored or tiresome if not periodically reinvented. Even with an ongoing campaign, there remained some scepticism that awareness would be long-lasting, and that many people would pay little attention to the issue until they themselves were directly impacted - i.e. through receiving diseased plants or recognising degradation or loss in a forest they used (e.g. discolouration or removal of numerous trees).

The role of growers and sellers : In addition to a government led blanket approach to raising awareness, it was agreed that growers and sellers have an important role to play owing to their first-hand interaction with consumers. As well as having signage and staff on-hand to communicate the problems associated with poor biosecurity and the goals of the scheme, it was felt that compliance with accreditation would need to be visible. This task would be best achieved with the presence of a recognisable accreditation logo that featured on accredited premises and products, alongside an explanation of the scheme's aims and requirements.

Pressure groups : Pressure groups were also suggested as a means of raising the public's awareness of risks within the trade. Greenpeace's campaign to raise awareness about the use of neonicotinoids in pest control put pressure on growers to stop using these products, leading some to suggest that similar action could be employed to address the sale of high risk plants.

Message tone and content : In terms of the tone of the information being disseminated, it was suggested that finger pointing be avoided and instead the focus be on informing about the problem and its solutions. Others felt that there was a need to go beyond informing on the threat to the landscape, and to educate customers on what goes into growing a plant - something which may chime with the large proportion of those whose buying choices are influenced by plant quality. Some went as far as to say that accreditation should include a warranty/guarantee to customers to demonstrate that the product is high-end and worth paying for. Whatever the avenue for engaging with the public, it was deemed important that the message be succinct and trustworthy. Indeed, trust in the accreditation scheme and the growers are considered vital to the public's receptiveness to supporting the scheme's goals.

2.4 Training for the trade

Integration of training into accreditation : Early discussions around the posited and emerging accreditation schemes (including the HTA pilot project) have included proposals for ongoing improvement of a nursery's practices in combination with staff training. Although the HTA pilot nurseries were described as having, "a lot to do, with few provisions" there is some optimism that inroads are being made, with DEFRA being particularly helpful in thinking about how training might be delivered.

Training options : Although the likes of SRUC's new MSc on forensic plant health were highlighted as potentially valuable courses, they tend to be in short supply. In addition, the workforce of some nurseries are without the qualifications - and perhaps desire - to attain the level of expertise suggested to be necessary, meaning this formal education approach would prove inaccessible or incongruous to many workers. Instead, the idea of having an assigned officer within the organisation (equivalent to a health and safety officer) was proposed. This could be encouraged by making the presence of such a position a compulsory requirement for accreditation.

Knowledge and skills throughout the sector : Some felt that plant health professionals should be embedded in other professions including landscape design and retail. This measure was seen as a means of reducing the promotion and demand for high-risk trees and plants (such as olive trees and Himalayan balsam). It would also presumably help move towards a sector-wide commitment to selling only those plants which are in season, and more generally, facilitating sound biosecurity becoming revered throughout the supply chain. The upcoming introduction of a training module by the Landscape Institute is one example where increasing knowledge of plant health and best practice will soon be encouraged. Meanwhile in Scotland, the Confor nursery group is looking to see how to offer and deliver training on plant health to growers.

The rewards of training : Finally, it was suggested that the best practice and training required for accreditation should be something which is promoted to the growers on the grounds that a better quality product would result. On this basis, accreditation may become an asset (a badge of honour for growers and sellers), rather than representing red tape or a tick box exercise.

2.5 Challenges

Added costs : One nursery manager queried whether accreditation would necessitate more costs for the consumer - something which may undermine a scheme and accredited businesses should plant buyers opt to go elsewhere in search of cheaper goods. They reasoned that if implemented efficiently within nurseries, biosecurity should not be excessively costly and thus the costs passed on to consumers would be negligible. However, others with knowledge of schemes elsewhere insisted that it would be impossible for many nurseries to enact management changes and improved biosecurity measures without increasing the price of its products. In addition, it was noted that any input from plant health inspections would be expensive to growers, since inspectors charge even for 15 minutes of their time. Therefore, resources need to be put in place so that a scheme can be policed without excessively burdening growers. This policing may involve inspectors and auditors being granted the power to force changes on nurseries. The idea of a yellow/red card system for those who have failed to comply was also suggested, yet the specifics about whether non-compliance would result in any loss of privileges or the incurrence of fines - and over what timeframe - require further discussion.

Limitations to accreditation : Finally, it was acknowledged that an accreditation scheme could only be expected to reduce the risk of pathogen spread as oppose to eliminate it. For this reason, some raised concerns about the robustness of a scheme's credibility in the event of an outbreak, particularly if it were to occur in the early days of a scheme being rolled out. As it is impossible to discount this possibility, the participant cautioned against overselling what the accreditation scheme could achieve.

2.6 KEY OUTCOMES

•A single, all-encompassing UK accreditation scheme is preferred


•Accreditation needs to cover the entire supply chain if it is to have impact


•Demand for accredited products should be ensured to incentivise uptake in the scheme


•Accreditation could also be incentivised by allowing access to grant funding, and through financial reimbursement when contracts to supply accredited plants are cancelled/altered


•It is necessary to raise public awareness about the need and benefits of accreditation through highly visible campaigns and signage, including a recognisable logo


•Training for growers and others in the sector should be integral to accreditation so that practices continue to improve


•For a scheme to be respected and to generate improvement it must be effectively policed
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 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