Modelling plant host-pathogen interactions and spread for resilient biosecurity and planting policy

Overview

Non-native plant pathogens are increasingly being introduced into new areas through global trade and travel, with major consequences for agricultural, horticultural, forestry and natural ecosystems. Since many pathogens are unknown to science or only recently described at the point of emergence, comparative, cross-species approaches have investigated the factors
that underpin pathogen invasiveness and host-pathogen interactions, to inform pathogen horizon-scanning and risk-assessment. These have revealed for example that pests and pathogens tend to be more likely to attack closely related plant species than species separated by greater evolutionary distances. For microbial taxa, biological traits such as spore morphology, optimum temperature for growth, the ability to disperse long distances, the ability to reproduce both sexually and asexually and cold-tolerance have all been associated with greater invasiveness. These frameworks need to be further contextualised at the national and landscape level, to understand how pathogen traits influence invasion success in global and local transport and landscape-scale spread and how host traits, alongside pathogen traits, also underpin the likelihood and outcome of host-pathogen interactions.
More-over, against the backdrop of further climate change and forestry policies that promote extensive woodland expansion and planting of novel species, quantitative tools are required that inform biosecurity and planting policy by predicting which tree species are resilient or vulnerable to multiple important pathogens and climate change, whilst also delivering key ecosystem functions. This is particularly critical since movement of live plants is the commonest way by which plant pathogens have been introduced into new areas.

Using modelling approaches and strong engagement with decision-makers in biosecurity (the Forestry Climate Change Working Group, Plant Healthy Certification Scheme) and experts in forest pathology and policy (Forest Research, James Hutton Institute), the student will address the following questions:

(1) How do ecological traits and species relatedness predict which host species will be impacted by key pathogen species like Phytophthora and Xylella?
(2) How do the biological and distributional traits of pathogens and hosts determine the rates of pathogen arrival in the UK, and interact with landscape connectivity to determine the pathogen species spread from horticultural plant supply chains into the UK’s wider environment?
(3) How do the traits that determine tree host resilience to pathogens co-vary with those that underpin forest ecosystem functions and resilience to climate change and what are the consequences for biosecurity and tree planting policy?

Methodology

Working alongside ecologists at UKCEH and University of Stirling and pathologists at Forest Research and the James Hutton Institute, the student will compile databases for plant hosts and priority pathogen taxa threatening UK forests (e.g. oomycete Phytophthoras, Xylella, Hymenoscyphus sp.) comprising traits, global and UK occurrence and interception data (GBIF, EPPO, CABI and UK Plant Health databases) and documented host-pathogen interactions. The student will conduct phylogenetically-informed analyses to understand whether closely-related hosts share pathogen species (or closely-related pathogens share host species), whether particular ecological traits of hosts confer resilience or susceptibility to pathogens, or whether pathogens with particular traits are able to impact a wider range of hosts in temperate environments. Combining spatial Mixed Effect models and landscape analysis, the student will analyse how current patterns of spread of pathogens within the nursery and wider environment in the UK depend on pathogen and host traits and landscape connectivity through pathways such as trade, recreation, road and river networks. Focussing in on native and non-native, current and potential future UK forestry species, the student will also review their role in ecosystem functions, how these are related to functional traits and co-vary with their resilience or susceptibility to pathogen infection and climatic change to inform future planting policy.

It is envisioned that the PhD project could provide or inform tools to:
– assist horticultural and forestry managers with assessing key biosecurity risks arising from growing and sourcing particular host plants (aligning with the requirements of the Plant Health Management Standard for pest risk analysis)
-inform forestry managers about which hosts are more-or-less resilient to pathogens in different geographical locations (aligning with current forestry site management decision support systems).

Policy context for the project will be provided by advisors from the Forestry Climate Change Working Group (FCCWG) the Plant Healthy Certification Scheme for nursery managers – item 13 on the FCCWG’s action plan) and APHA’s Plant Health & Seeds Inspectorate (who collect and analyse plant health inspection data to inform policy across the UK). There will be strong engagement with wider stakeholders throughout the project to frame the models (including focal host and pathogen taxa) and outputs.

Project Timeline

Year 1

Months 1-2: Review literature on global emergence and impacts of plant pathogens, comparative host-pathogen ecology, and forest ecosystem functions. PhD training including training in environmental data processing, and hierarchical mixed-effects models including phylogenetic and multivariate analyses. Familiarisation with existing host-pathogen interactions, trait and occurrence databases (including those already compiled at UKCEH for Phytophthoras and at Stirling for Xylella). Meet with Policy Advisors and supervisors to select focal pathogens and host taxa and discuss phylogenetic model framework for predicting host-pathogen interactions.
Months 2-6: Compile database of trait, occurrence and interaction database for focal pathogens/hosts including host climate responses and life history traits (TRY, COMPADRE data-bases)
Months 3-8: Design and conduct phylogenetically informed analyses of host-pathogen interactions
Months 8-12: Write up first ISI paper on role of traits and phylogeny in determining host-pathogen interactions, consult with Policy Advisors on how the database and model predictions of pathogen impacts on hosts could be packaged up for use by nursery managers
Within first year: Training in stakeholder engagement, external training course in phylogenetic multivariate analysis

Year 2

Review occupancy and spread modelling methods for invasive pathogens incorporating hosts and landscape connectivity.
Develop database and analysis of current patterns of spread of Phytophthora pathogens within the nursery and wider environment in the UK in relation to host and pathogen traits and pathways of spread through the landscape (landscape analysis). Consult with Policy Advisors on how the database and model predictions of pathogen spread could inform policy. Develop second ISI paper on this analysis/policy engagement.

Year 3

Develop database on ecosystem functions and climatic sensitivities of native and non-native current and future UK forestry tree species. Develop analysis of how predicted resilience/impacts of pathogens on forestry species trades off against their contribution to ecosystem functions and their resilience to climate change. Develop third ISI paper on this analysis/policy engagement. Work with Policy Advisors and Forest Research to understand how model outputs could inform current policy and tools for tree planting, including site-level Decision Support Systems such as ESC and potentially develop Shiny Apps where opportunities to inform decisions are identified.

Year 3.5

Write up short case study / experience of co-developing tools for Plant Health. Finalise thesis.

Training
& Skills

The student will receive training in a breadth of skills including database compilation, use of computing clusters and manipulation of large-scale ecological and environmental datasets using R, hierarchical mixed effects and occupancy modelling, environmental change impacts, ecosystem functions, comparative ecology, pathogen ecology and forest ecosystem functions, co-developing predictive model frameworks to meet the needs of end-users and inform policy.
They will benefit from working in an interdisciplinary, diverse and supportive supervisory team and engaging with plant health stakeholders including the Forestry Climate Change Working Group. We currently work on some of the most important plant health and invasive species threats (e.g. Xylella fastidiosa, Phytophthora, and Ragweed) and have strong links to plant health policy makers in the UK, Europe and beyond.

References & further reading

Chapman, D.S. et al (2017) Global trade networks determine the distribution of invasive non-¬źnative species. Global Ecology and Biogeography 26, 907-917.

Gilbert GS, Briggs HM, Magarey R (2015) The Impact of Plant Enemies Shows a Phylogenetic Signal. PLoS ONE 10(4): e0123758. https://doi.org/10.1371/journal.pone.0123758

Beales et al. (2019) Plant Diseases and Biosecurity, Oxford University Press, ISBN: 9780198827726

https://www.forestresearch.gov.uk/research/global-threats-from-phytophthora-spp/

More information on the Plant Healthy Scheme
https://planthealthy.org.uk/resources/

Further Information

We welcome applicants with a background in Ecology, Biology, Statistics or related fields. To enquire informally please contact Dr Beth Purse (beth@ceh.ac.uk) or Dr Daniel Chapman (daniel.chapman@stir.ac.uk).

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