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Phyto-threats project team meeting May 4th 2017 (PM session)

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/ 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.


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