Promoting resilience of UK tree species to novel pests and pathogens: ecological and evolutionary solutions (PROTREE)
Lead Research Organisation:
Royal Botanic Garden Edinburgh
Department Name: Cryptogamic Plants and Fungi
Abstract
Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.
Technical Summary
The project will take advantage of existing experimental resources that the consortium has been building for the past few years. These include living experiments (a reciprocal transplant experiment on 3 contrasting sites including 21 native provenances; a glasshouse provenance-progeny trial; field provenance-progeny and provenance trials) and genetic and genomic resources (a large database of mutations across the Scots pine genome and capability for high-throughput genotyping; reference genome for Dothistroma; genetic markers for Dothistroma and pine tree Lappet moth). These existing resources will be made available to the project at no cost.
We will assess distribution and variation in the threat organisms using surveys and genotyping, and study pathogen evolution by characterising genetic changes in samples from different populations. We will assess variation in the host using population genomics (high-density genotyping of samples from multiple populations in trials) and quantitative genetics (analysis of variation in phenotypic traits and extended phenotype - resistance, phenology, morphology, needle chemistry, needle endophyte community). Data from the biological studies will be unified in a spatially-structured database and used, with data on distribution, density and regeneration rates to model the introduction and spread of threat organisms and their interaction with a variable pine population. The models will be used to test scenarios for management change that emerge from stakeholder interactions.
We will use workshops, semi-structured interviews and focus groups with stakeholders (identified through stakeholder analysis) to identify, test and refine options for building resilient pine populations. This will be a dynamic process, with ongoing interaction between natural and social scientists in the consortium, and with stakeholders. Finally, we will create a template for extending the analysis to other tree species.
We will assess distribution and variation in the threat organisms using surveys and genotyping, and study pathogen evolution by characterising genetic changes in samples from different populations. We will assess variation in the host using population genomics (high-density genotyping of samples from multiple populations in trials) and quantitative genetics (analysis of variation in phenotypic traits and extended phenotype - resistance, phenology, morphology, needle chemistry, needle endophyte community). Data from the biological studies will be unified in a spatially-structured database and used, with data on distribution, density and regeneration rates to model the introduction and spread of threat organisms and their interaction with a variable pine population. The models will be used to test scenarios for management change that emerge from stakeholder interactions.
We will use workshops, semi-structured interviews and focus groups with stakeholders (identified through stakeholder analysis) to identify, test and refine options for building resilient pine populations. This will be a dynamic process, with ongoing interaction between natural and social scientists in the consortium, and with stakeholders. Finally, we will create a template for extending the analysis to other tree species.
Planned Impact
See Main Document.
Organisations
People |
ORCID iD |
| Christopher Ellis (Principal Investigator) |
Publications
Anderson Stewart C
(2018)
Analysis of fungal endophytes in Scottish Sitka spruce plantations shows extensive infections, novel host partners and gives insights into origins
in Forest Pathology
Gweon HS
(2015)
PIPITS: an automated pipeline for analyses of fungal internal transcribed spacer sequences from the Illumina sequencing platform.
in Methods in ecology and evolution
Iason G
(2018)
Community-based biotic effects as determinants of tree resistance to pests and pathogens
in Forest Ecology and Management
| Description | The diversity of fungal endophytes which live in Scots pine needles are thought to protect the tree against disease. However, the actual diversity of these organisms was equivocal prior to this project, and there was limited knowldge of endophyte communities. Using Next Generation techniques this study revealed the scale of diversity of endophytes in Scots pine (c. 700 OTUs), to show that endophyte communities have clear biogeographic differences among zones, and within these zones that different tree genotypes have different endophyte communities. Additionally, a second study has now examined the effect of the tree nursery environment on the development of endophyte communities, including the collatoral effect of fungicide spraying to prevent disease on beneficial endophyte diversity. Results from this second study have revealed contrasting amplicon patterns among treatments; this shows that endophyte communities are fundamentally changed by fungicide treatments, including the declining abundance of mutualist or commensal diversity. |
| Exploitation Route | The results suggest that the forestry industry should consider locally sourced seeds in order to ensure ecological compatibility between the tree genotype and the endophytes which occur in the local environment. The study also provides information on the potential negative impacts of spraying different types of fungicide, and guidance as to the appropriate use of disease control. |
| Sectors | Agriculture, Food and Drink,Environment |
| Description | Engagement has continued through the use of the animated computer game - CALEDON - which combines the scientific results and messaging from the PROTREE project, with a novel interactive learning platform. Players must manage a simulated forest to achieve a series of goals, by developing plantings with different stock types, species and genetic diversity, to generate income and maintain biodiversity, while faced with threats of tree disease (which can be minimised through good decision-making). Our decision to generate a computer game was in direct response to the UK Animal and Plant Health Strategy (Animal and Plant Health in the UK: Building our science capability) Action 4: 'Generate a plan for developing appropriate plant health skills and career pathways'. It has aimed to encourage participation from a next generation of plant health scientists. Details are provided in our entries under Engagement Activities; the game had been showcased at Science Festivals across the UK, has featured in youth magazines as well material for forestry practitioners, and has been listed as an activity for schools curricula. The use of CALEDON continues to expand nationally and internationally. |
| First Year Of Impact | 2017 |
| Sector | Education,Environment |
| Impact Types | Cultural,Societal |
| Description | Plant Health Resource Bank |
| Geographic Reach | National |
| Policy Influence Type | Participation in a guidance/advisory committee |
| Impact | New knowledge created during the PROTREE project was used to inform an online and user friendly plant health resource bank, that was commissioned by and partly delivered as a report to the Government. This forms a part of our national capability for plant biosecurity. |
| URL | https://www.planthealthcentre.scot/sites/www.planthealthcentre.scot/files/2019-08/phc2018-11_final_r... |
| Description | Scottish Plant Health Centre of Expertise: Development of an online, user friendly plant health resource bank for the Scottish natural environment. |
| Amount | £14,000 (GBP) |
| Funding ID | PHC2018/11 |
| Organisation | Government of Scotland |
| Sector | Public |
| Country | United Kingdom |
| Start | 04/2018 |
| End | 03/2019 |
| Description | Scottish Plant Health Centre of Expertise: Expansion of plant health resource bank |
| Amount | £6,000 (GBP) |
| Funding ID | PHC2018/11 |
| Organisation | Government of Scotland |
| Sector | Public |
| Country | United Kingdom |
| Start | 04/2019 |
| End | 09/2019 |
| Description | Standard Grant |
| Amount | £13,000 (GBP) |
| Funding ID | 2017/14 |
| Organisation | Sibbald Trust |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 11/2017 |
| End | 07/2018 |
| Title | DNA Library |
| Description | A DNA library of c. 900 extractions including host and endophyte DNA, from geolocated sites and trees of known provenance. Currently stored at the EDNA facility at Royal Botanic Garden Edinburgh. |
| Type Of Material | Biological samples |
| Year Produced | 2016 |
| Provided To Others? | Yes |
| Impact | The DNA has been the underpinning resource for delivery of the PROTREE project. |
| Title | Data Platform for Scots Pine Endophyte Diversity |
| Description | Database structures have now been developed to manage the massive sequence (OTU) diversity for endophytes, across each of 360 experimental trees; 120 replicates across three common garden sites, structured by site identity, tree provenance, randomised blocks and lab codes. Tree health has been screened for individual experimental plants, and photo-documented. |
| Type Of Material | Data handling & control |
| Year Produced | 2014 |
| Provided To Others? | Yes |
| Impact | Database development is a enabling step within the PROTREE project, and the impact is in allowing clarity and accuracy for hypothesis testing and analysis. |
| Title | Nursery trial PIPITS output with taxonomic assignments from UNITE |
| Description | Next Generation Sequencing data from endophytic fungi sampled from healthy leaves of Scots pine in a common garden experiment, using controlled trials to test the impact of registered fungicides on endophyte communities as well as target pathogens. The data was generated from RNA to discriminate living from dead endophyte species. Trees were of known provenance planted; the data can be used to partition the effects of fungicides for different genotype/provenances. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2016 |
| Provided To Others? | Yes |
| Impact | Currently working on a draft paper, that describes fungicide effects on endophytes. |
| Title | Stability of Bioinformatic/DNA Extraction Protocols for Massive Sequence Data |
| Description | Fungal endophytes have been sampled from surface sterilised leaves (Pinus sylvestris) by the Research Fellow (Dr Joanne Taylor). The study is now testing how variability in fungal endophyte diversity, quantified as 'operational taxonomic units' (OTUs), depends on the options for combining DNA extraction protocols and sequencing techniques. A newly developed bioinformatics pipeline* is being used to understand whether endophyte diversity derived from Next Generation Sequencing (NGS) using 454 pyrosequencing, or using Miseq, varies across complimentary DNA extraction protocols, including CTAB or Qiagen DNeasy. Analysis of this data is enabling identification of the DNA extraction methods to achieve maximum diversity for a consistent representation of community structure. This supports the aim of the PROTREE study, to robustly quantifying hidden players (endophytes) in tree disease resistance, and provides a wider understanding of optimisation of sampling for the massive sequence diversity of unidentified fungi. * Bálint, M., P. A. Schmidt, R. Sharma, M. Thines, and I. Schmitt. 2014. An Illumina metabarcoding pipeline for fungi. Ecology and Evolution, 4 :2642-2653 |
| Type Of Material | Data analysis technique |
| Year Produced | 2014 |
| Provided To Others? | Yes |
| Impact | This is a unique optimisation study that is of high relevance at a time when the wider scientific community grapples with biological/ecological interpretation of large numbers of undiscovered taxa that are present in NGS samples, especially within mycology. The impact will be conceptual and methodological, and driven by scientific output (conference presentations, papers). |
| Title | Updated Common Garden taxonomic assignments from UNITE |
| Description | Next Generation Sequencing data from endophytic fungi sampled from healthy leaves of Scots pine across a west-east biogeographic gradient. Trees were of known provenance planted in a common garden experiment; the data can be used to partition the effects of genotype and environment on endophyte community structure. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2016 |
| Provided To Others? | Yes |
| Impact | Currently drafting a research paper in collaboration with CEH, for submission in 2017. |
| Description | CALEDON tree health computer game |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Schools |
| Results and Impact | To respond to a strategic need for capacity building around UK plant health, we adapted our planned public programmes to deliver a plant health computer game targeted to young teenagers. PROTREE scientists worked with game designers from a Dundee-based start-up to develop an interactive plant health learning game. The game was launched in September 2016 at the Scottish Learning Festival in Glasgow. Post launch the game has been promoted via 14 online networks within the teaching and forestry communities. Articles about the game have been published in Arb Magazine, Confor, Forestry and Timber News, CRANN, The Observer, The Scotsman and The Week. The game was featured on Radio Five Live. A programme of events to promote the game has now been completed and around 2,000 people have been engaged at seven events across the UK. Alongside the CALEDON game a mobile exhibit was developed for PROTREE and this will be used in conjunction with CALEDON at the Edinburgh (RBGE) and three regional botanic gardens during 2017. |
| Year(s) Of Engagement Activity | 2016,2017 |
| URL | http://www.rbge.org.uk/education/schools/resources/caledon |
| Description | Community-based biotic effects as determinants of tree resistance to pests and pathogens |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presentation as co-author at the International Union of Forest Research Organisations 125th Anniversary Congress (Freiburg, Germany) |
| Year(s) Of Engagement Activity | 2017 |
| Description | Forest Pathology Group |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Contribution of PROTREE findings to a formal group of forest pathologists that meet routinely to discuss and share information on established and emerging diseases and responses to these. |
| Year(s) Of Engagement Activity | 2017 |
| Description | Fungal Endophyte Community Analysis by NGS - Perspectives on Methodologies |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | A workshop with talks and sessions to share experiences on the application of NGS data and techniques across disciplines, e.g. fisheries, forestry, agriculture etc. |
| Year(s) Of Engagement Activity | 2016 |
| Description | Fungal Endophytes |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presentation of project results to the UK-wide Forest Pathology Group, aimed at the dissemination of information to inform UK forest health and resilience. |
| Year(s) Of Engagement Activity | 2016 |
| Description | PROTREE Stakeholder and Members Meeting |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | Final project symposium to disseminate results among participants and to key stakeholders. |
| Year(s) Of Engagement Activity | 2017 |
| Description | PROTREE Video |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Development of a short film which introduces stakeholders to the project's aims. This was a successful initiative in encouraging wider enagement, and the film is freely available and has been widely disseminated, see: https://vimeo.com/140911259. The film was released late 2015, and we expect its impact to continue to build over time. |
| Year(s) Of Engagement Activity | 2015 |
| URL | https://vimeo.com/140911259 |
| Description | The tree microbiome as part of the extended phenotype |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presentation as co-author at the International Union of Forest Research Organisations125th Anniversary Congress (Freiburg, Germany) |
| Year(s) Of Engagement Activity | 2017 |
| Description | The tree microbiome as part of the extended phenotype? |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Academic research talk to present results and discuss concepts at the Centre of Excellence in Fungal Research International Conference at Mae Fah Luang University, Thailand. |
| Year(s) Of Engagement Activity | 2017 |
| Description | Unearthed: a NERC Showcase Event |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Schools |
| Results and Impact | Presentation of PROTREE and its CALEDON computer game, to engage school children with forest management, plant health, and the excitement of a career in plant/fungal biology. |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://www.nerc.ac.uk/latest/events/archive/unearthed/ |