Modelling plant host-pathogen associations and consequences for pathogen spread and biosecurity and planting policy

Overview

Non-native plant pathogens are frequently introduced into new areas through global trade and travel, with major consequences for agricultural, horticultural, forestry and natural ecosystems. Trade in live “plants-for-planting” is the most important pathway of arrival and set to pose a greater threat under current UK policies that promote extensive woodland expansion and planting of novel tree species.

To inform pathogen horizon-scanning and risk-assessments, comparative studies that bring data together across many species, have indicated that both biological traits and evolutionary relatedness can affect invasiveness. These dimensions structure plant-pest associations and influence host range and impacts of pathogens, and their establishment and spread in new regions. For microbes, traits such as spore morphology, optimum temperature for growth, the ability to disperse long distances, and cold-tolerance have all been associated with greater invasiveness. There is considerable scope to improve our understanding and predictions of pathogen impact on key host species, by analysing how these phylogenetic (relatedness) and ecological dimensions (traits) interact to structure plant-pathogen associations and how both host and pathogen traits and phylogeny influence pathogen success through different stages of invasion. Against the backdrop of future climate change and woodland expansion, the quantitative tools derived from this work will inform biosecurity and planting policy by predicting which tree species are resilient or vulnerable to multiple important pathogens and how this trades off against benefits from trees and their resilience to climate change.

Taking an inter-disciplinary approach, combining ecological modelling, empirical experiments on pathogen behaviour, and strong engagement with decision-makers in biosecurity and forestry, 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 such as Phytophthora and Xylella?
(2) How do the biological and distributional traits of pathogens and hosts determine the pathogen arrival through horticultural plant supply chains and landscape scale spread and impacts in the UK wider environment?
(3) Do cold-tolerance traits (related to infection and growth processes) explain strain level differences in invasiveness of temperate regions for selected plant pathogens?
(4) How does tree host species’ vulnerability to pathogens co-vary with ecosystem benefits and resilience to climate change and what are the consequences for biosecurity and tree planting policy?

This project aligns with the UKCEH-led NERC Treescapes project, newLEAF – “Learning to adapt to an uncertain future: linking genes, trees, people and processes for more resilient treescapes”.

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 global 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.
Working in the laboratories at JHI and FR, for selected pathogen species and strains with similar host ranges, the student will investigate whether growth rates at low temperature explain different observed levels of invasion into temperate regions. Building on prior reviews of ecosystem benefits and resilience to climate change of native and non-native current and potential future UK forestry species, the student will add understanding of their likely pathogen loads to inform future planting policy. The student will examine how functional traits determining ecosystem benefits co-vary with their resilience or susceptibility to pathogen infection and climatic change.

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 partner links to the Forestry Climate Change Working Group (FCCWG) that lead the Plant Healthy Certification Scheme for nursery managers 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 stakeholders throughout the project to frame the models (including focal host and pathogen taxa) and outputs.

The timeline and structure set out below is indicative only. The precise timetable and balance of activities between disciplines will be decided by the student (in consultation with the supervisory team).

Project Timeline

Year 1

Months 1-2: Review literature on global emergence and impacts of plant pathogens, modelling of host-pathogen interactions for plant health. 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.
Within first year: Training in stakeholder engagement, external training course in phylogenetic multivariate analysis

Year 2

Months 1-6: 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).
Months 7-12: Identify subset of Phytophthora pathogens for lab investigation of cold-tolerance traits versus invasion success drawing on JHI strain collection. Set up and conduct experiment at FR (extending into year 3)

Year 3

Develop second ISI paper on this lab investigation of cold-tolerance traits versus invasion success.
Integrate pathogen associations into existing host databases 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 and be packaged up in online tools to help nursery managers comply with Plant Health Management Standard.

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, empirical pathogen ecology, 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 Plant Health and Biosecurity Alliance. 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

Gougherty, A.V. & Jonathan Davies, T. (2021) Towards a phylogenetic ecology of plant pests and pathogens. Philosophical Transactions of the Royal Society B: Biological Sciences, 376 (1837) https://doi.org/10.1098/rstb.2020.0359

Chapman, D.S. et al (2017) Global trade networks determine the distribution of invasive non‐native species. Global Ecology and Biogeography 26, 907-917.
Barwell, L., Perez-Sierra, A., Henricot, B., Harris, A., Burgess, T., Hardy, G., Scott, P., Williams, N., Cooke, D., Green, S., Chapman, D., Purse, B., 2021. Evolutionary trait-based approaches for predicting future global impacts of plant pathogens in the genus Phytophthora. JOURNAL OF APPLIED ECOLOGY 58, 718–730. https://doi.org/10.1111/1365-2664.13820

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

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

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 (dan.chapman@stir.ac.uk)

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