Phytothreats biannual all project team meeting
5 October 2016, APHA, Sand Sutton, York
This event provided an opportunity for the project team to meet in its entirety, including new team members Peter Thorpe (JHI), Louise Barwell (CEH) and Debbie Frederickson-Matika (FR), together with an overseas member of the Expert Advisory Panel (EAP) Susan Frankel (US Forest Service), and other UK-based EAP members David Slawson (OPAL), John Morgan (FC), Richard MacIntosh (Defra) and Kelvin Hughes (APHA). The objectives of the meeting were to share research updates for each workpackage (WP) in the morning, and to promote team-wide understanding of the plant trade and nursery sampling challenges through a visit to Johnsons of Whixley nursery in the afternoon.
David Cooke outlined WP1 objectives as using metabarcoding to analyse Phytophthora community structure in nurseries and associated ecosystems with the aim of informing disease management and best practice and to model Phytophthora communities. David reviewed WP1 sampling methods and reiterated the need to extend networks for nursery sampling. David is involved in a number of related projects that can feed into this one, including a THAPBI Phase 2 project on Early Detection and a Scottish Government funded project looking at Phytophthora diversity in different ecosystems in Scotland. Data on Phytophthora diversity in a range of wider ecosystems can be modelled together with data on nursery Phytophthora diversity. David then gave an overview of the metabarcoding approach to be used from sampling in nurseries through to analyses of Phytophthoras present in each sample.
WP2 Presentation – Mariella Marzano (FR) and Gregory Valatin (FR)
Mariella started her presentation with a review of work planned for the social and economic research. This package will cover the feasibility analyses and development of ‘best practice’ criteria for a nursery accreditation scheme. There are three key parts: social-the applicability of best practice criteria; cost-benefit analysis; the development of best practice criteria to underpin guidelines for an accreditation scheme.
In general the project team need to be aware of all the other initiatives in terms of accreditation schemes, for example Richard MacIntosh (Defra) mentioned the Woodland Trust Accreditation Scheme.
Gregory Valatin asked what the expected uptake of an accreditation scheme might be, pointing out that if low the overall impact would be small.
There was also a short discussion on a 2016 paper by Whittet et al in Land Use Policy journal "Supplying trees in an era of environmental uncertainty: Identifying challenges faced by the forest nursery sector in Great Britain”
This study involved a survey of forest nurseries in Britain in relation to supply of locally sourced seed and domestically produced planting stock for native woodland and hedging markets. It will be important to follow up on which nurseries were surveyed to avoid overlap.
The discussion ended with the comment that consumers’ willingness to pay will be affected by the availability of cheap plant imports.
WP3 Presentation – Beth Purse (CEH), Dan Chapman (CEH) and Louise Barwell (CEH)
Beth outlined the approaches for WP3 objectives 1) assessing risk of introduction of Phytophthoras to the UK via trade and recreational spread, 2) risk of establishment and spread following arrival, and 3) scoping knowledge gaps to try to predict likely future introductions. The WP team will identify and rank Phytophthora threats to the UK and link invasiveness to different traits.
Sarah (standing in for Paul Sharp, University of Edinburgh, who was unable to attend the meeting) gave a brief overview of the objectives of WP4 which aims to predict risk via analysis of Phytophthora genome evolution. This will enable a better understanding of the genetic mechanisms by which Phytophthoras can infect woody hosts, adapt to new hosts, and the extent to which they can acquire new genes through hybridizations or horizontal gene transfer. WP4 does not start until April 2017, however the project has funding to target sequence three Phytophthora species (to be completed this year) and the focus of Sarah’s presentation was how to select these species.
13.30-17:00: Visit to Johnsons of Whixley plant nursery
After lunch the project team hopped into a minibus driven by David Cooke for the 30 min trip to Johnsons of Whixley, one of the largest wholesale plant nurseries in the country, supplying mainly the amenity sector. The team was hosted for the afternoon by Ian Nelson, production manager, who provided a lively, honest and energetic tour of facilities and account of business practices as well as responding to the many questions asked by the project team. This was a very useful experience for all members of the project team, particularly those not directly working with nurseries, who finished the visit with a much greater understanding of what is driving the trade and associated management practices.
Phytothreats start-up meeting April 21st 2016
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.
Project introduction presentation (Sarah Green, Forest Research)
NB: presentation links will open in a new window
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.
Mariella Marzano (FR) presented the work plan for WP2: Feasibility analyses and development of ‘best practice’ criteria.
This work is split into three parts:
- a social analysis of nursery best practice
- a cost-benefit analysis of best practice
- 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.
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 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.
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.
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).
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 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.
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.
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. 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.
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.
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 which includes Plant Health as a focus.