FUTURE OAK: Characterising and engineering the oak microbiome to future-proof an arboreal icon
Lead Research Organisation:
Bangor University
Department Name: Sch of Natural Sciences
Abstract
Tree declines caused by climate perturbation, anthropogenic stressors and disease outbreaks have resulted in recent forest mega-disturbances and are a major global concern. Until recently, progress has been hampered by a lack of high-throughput analytical approaches for systems-based analysis of the multidimensional factors that drive declines. Our previous research on Acute Oak Decline, a complex decline disease of native British oak, has highlighted how microbiome shifts to a 'pathobiome', are associated with tree disease. This work challenges the one pathogen = disease paradigm, leading to new hypotheses on the role of microbiomes in health and disease, and highlighting the need to revise classical disease paradigms to include the microbiome. The microbiome is a major determinant of plant health, and we hypothesise that the oak microbiome can be manipulated to improve host fitness and disease suppression. Here, we propose a landscape-scale analysis of the oak microbiome and metabolome in health and disease, to inform the design and validation of engineered microbiomes for disease suppression. Microbiome engineering is an emerging research frontier with many novel applications. The project will address new hypotheses regarding how complex multidimensional interactions between the tree host and its microbiota, encountered pathogens, and the environment, influence host fitness and disease susceptibility. The research will initiate a new frontier in forest microbiome engineering and precision medicine to future-proof iconic tree species and the ecosystem services they provide.
Technical Summary
Forest disturbances mediated by climate perturbation and tree disease outbreaks represent a significant global challenge. Tree declines are complex and involve both biotic and abiotic stressors, and consequently, limited progress has been achieved in understanding the multi-dimensional interactions between the host and its associated microbiota, pathogenic microorganisms, and the environment, that underpin tree health and disease. However, recent developments in high-throughput analytical approaches for nucleic acid sequencing, metabolite profiling and microbial isolation, coupled with advances in machine learning computational approaches, now enable systems-based analyses of the multi-scale interactions that confer unprecedented insights into complex tree diseases. This proposal addresses new hypotheses on the role of the microbiome in health and disease, using Acute Oak Decline (AOD), a complex decline disease mediated by abiotic predisposing factors and biotic (insect and bacterial) contributing factors, as a model system. The project will deliver a systems-based analysis of AOD at the landscape-scale, representing the most comprehensive analysis of a tree disease to date, and the first to integrate host, microbiota and ecological factors at this level (Obj. 1). Consequently, these data will be used to identify and isolate oak microbiota associated with host fitness and disease suppression, validated by experimental ecology approaches (Obj. 2). Engineered microbiomes will be designed and tested to engineer the oak microbiome for increased resilience and host fitness (Obj. 3). Finally, we will assess the feasibility and management implications of deploying engineered microbiomes to address tree health challenges (Obj. 4).The project will provide a paradigm-shift in our understanding of the factors that drive complex tree declines, initiating a new era of microbiome engineering to future proof global forests and the ecosystem services they provide.
Planned Impact
Complex interactions between plant hosts and their associated microbiota significantly influence the health status of an individual. The plant microbiome (the collection of plant-associated microorganisms and their encoded genes) is therefore a major determinant of health and productivity, promoting nutrient availability, resistance to environmental stresses, and defence from pathogens. Climate change and increasing outbreaks of disease represent a major threat to global forests that support the most diverse ecosystems in the biosphere, provide key ecosystem services, and valuable forest products. However, advances in high-throughput DNA sequencing technologies are transforming our understanding of plant-microbiota interactions and will play a central role in the future preservation of global plant health. In addition, engineering plant and animal microbiomes using cultivated disease suppressive microbiota is an emerging research frontier with many novel applications. Here, we will undertake a UK landscape-scale analysis of the oak microbiome and metabolome in health and disease, to inform the design and validation of engineered microbiomes for disease suppression. Microbiome engineering is an emerging research frontier with many novel applications. The project will address new hypotheses regarding how complex multidimensional interactions between the tree host and its microbiota, encountered pathogens, and the environment, influence host fitness and disease susceptibility. The research will inform future efforts to select optimal environmental conditions, microbiome composition and host genetics for tree health and resilience, initiating a new frontier in forest microbiome engineering to future-proof iconic tree species and the ecosystem services they provide. This project will be the first to focus on the core microbiome of oak trees and will address a key knowledge gap in oak microbiome research. Although AOD is the disease focus in this project, similar decline diseases are being described globally, with reports of similar oak diseases and detection of bacterial agents related to the cause of AOD described globally. The reports highlight that AOD is likely an underreported and emerging global issue and represents only one of the many current threats to oak, notwithstanding Xyllela fastidiosa, that has not currently been detected in the UK, but remains an imminent threat. Consequently, data on the healthy core microbiome and disease suppressive microbiota obtained in this project could translate to suppression of other pests and pathogens of oak at the EU and global scale, such as Chronic Oak Decline, Phytophthora spp., Oak Processionary Moth, and bark boring beetle attack, for example, and the tools and approach can ultimately be translated for application in other at-risk tree species. Microbiome engineering for disease suppression is a new frontier in plant and animal health and represents a promising approach to safeguard the health of forest biomes. The research proposed here therefore has global relevance and will feed into international efforts to protect native oak species globally. The project outputs would also directly align with DEFRA's 'Tree Health Resilience Strategy', part of the UK government's 25-year plan to improve the environment through protecting broadleaf woodlands from pests and disease.
Publications
Finch J
(2022)
Spectral binning as an approach to post-acquisition processing of high resolution FIE-MS metabolome fingerprinting data
in Metabolomics
Dandy N
"How to recognise a healthy forest: perspectives from private forest managers in Britain."
in Forest Policy and Economics
Title | 2 minute video animation about the FUTURE OAK project |
Description | The animation introduces the FUTURE OAK project. It discusses current threats to native oak in the UK, and the importance of the plant microbiome in promoting health. The animation the introduces the overarching aims and onjectives of the FUTURE OAK project and acjnowledges the project funders. |
Type Of Art | Film/Video/Animation |
Year Produced | 2021 |
Impact | The animation will be released this week and we will report on this next year. |
Title | Bac-Stop Open Day |
Description | Cutting edge tree research technology on display and engaging discussion with researchers on site at our Bac-Stop project 'Open Day'. |
Type Of Art | Artistic/Creative Exhibition |
Year Produced | 2022 |
Impact | Engagement with wider audience. |
URL | https://twitter.com/BactPlantDis/status/1547918441918525446 |
Title | Oak Research Annual Stakeholder Meeting |
Description | Visual images of our BACSTOP and Future Oak Stakeholder meeting. |
Type Of Art | Artistic/Creative Exhibition |
Year Produced | 2023 |
Impact | Raise awareness |
URL | https://twitter.com/BactPlantDis |
Description | DiversiTree: diversifying our woodlands to increase resilience |
Amount | £516,525 (GBP) |
Funding ID | NE/X004449/1 |
Organisation | Natural Environment Research Council |
Sector | Public |
Country | United Kingdom |
Start | 08/2022 |
End | 08/2024 |
Description | Knowledge Exchange Skills Scholarship (KESS) 2 |
Amount | £70,000 (GBP) |
Organisation | Bangor University |
Sector | Academic/University |
Country | United Kingdom |
Start | 08/2020 |
End | 07/2023 |
Title | Fieldwork - collection of oak tissue |
Description | A validated protocol for the collection of oak tissue for DNA extraction in the field. ~200mg of leaf tissue is collected from the north and south faces of the upper 25% of the crown of each tree sampled. ~200mg sapwood and phloem is collected from breast height from the north and south face of each tree. ~500mg of root and associated rhizosphere soil is collected from the north and south face of each tree from within 1m of the trunk. All collections are done maintaining sterility, to avoid contamination from humans. |
Type Of Material | Biological samples |
Year Produced | 2021 |
Provided To Others? | No |
Impact | This protocol was used to collect 1,050 samples for processing for the project. |
Title | Isolation methods for oak microbiota |
Description | Two methods for isolating the oak microbiota were optimized. Initially a homogenate is produced from oak samples (1 g of leaves, 1 g of rhizosphere and 5mm stem cores) by blending and/or grinding. In the first method, the homogenates are then diluted/suspended in buffer phosphate solution and plated out onto agar plates (Reasoner's 2 agar, potato glucose agar and nutrient agar). An aliquot of the dilutions is used for the second isolation method, where samples are diluted in tryptone soy broth and dispensed in 96-well microculture plates. All cultures are incubated at room temperature for one week. Individual colonies are picked from agar plates and grown in broth in 96-well formats. Microbial isolates are preserved by adding glycerol to the liquid cultures and freezing them up at -80ºC. Both methods are required in order to capture a higher diversity of the oak microbiota. |
Type Of Material | Biological samples |
Year Produced | 2021 |
Provided To Others? | No |
Impact | - The methods optimized were shared and discussed with other members of research projects from the Plant Bacterial Disease programme funded by the BBSRC, NERC, Defra and the Scottish Government. - A large culture collection, comprising 20,000 oak associated isolates, was produced. |
Title | Method for DNA extraction from oak tissue |
Description | A set of validated protocols for the homogenisation of tissue and extraction of DNA from oak tissue, including leaf, sapwood and phloem, and root tissue. This involves mechanical disruption, cleaning extracts using (phenol)-chloroform, and precipitation of DNA. |
Type Of Material | Biological samples |
Year Produced | 2022 |
Provided To Others? | No |
Impact | This protocol will be used for the extraction of DNA from all samples collected during fieldwork, allowing downstream project objectives to be met. |
Title | Acute Oak Decline decline index for all trees in study |
Description | Phenotypic measurements to construct the AOD decline index were taken for all 350 oak trees in the study. These will be used to construct a decline index denoting the severity of AOD on each tree. |
Type Of Material | Data handling & control |
Year Produced | 2021 |
Provided To Others? | No |
Impact | This will be used to help identify disease suppressive microbes in the MWAS. |
Title | Collection of microbial isolates with suppressive properties against AOD bacteria |
Description | This collection contains around 1,000 microbial isolates that have been tested in vitro and have shown potential for suppressive activity against Brenneria goodwinii, a key bacterial pathogen in the development of Acute Oak Decline. The database for this collection includes information such as the site, tree and type of tissue from where the microbial isolate were obtained, details of the isolation method, and location of the isolate within a 20,000 oak microbial collection. |
Type Of Material | Data analysis technique |
Year Produced | 2022 |
Provided To Others? | No |
Impact | Isolates contained in this collection are a resource for further research on synthetic communities or engineered microbiomes with plant pathogen-suppressive functions. |
Title | Metabolome fingerprinting data - Future Oak |
Description | Metabolome fingerprinting data generated from flow infusion electrospray ionisation ultra-high resolution mass spectrometry (FIE-HRMS) of phloem and sapwood woody tissues collected from the 300 trees in the study. |
Type Of Material | Data analysis technique |
Year Produced | 2022 |
Provided To Others? | No |
Impact | This data will be used to identify land-scape scale patterns in the chemical composition of oak tree woody tissues associated with Acute Oak Decline and integrated with phenotypic decline indexes and microbiome data in a metabolome and microbiome-wide association study (MMWAS). |
Title | Metagenome test - before and after NEBNext Microbiome enrichment kit on 6 samples |
Description | We extracted DNA from two leaf, root and stem samples, and applied the NEBNext Microbiome enrichment kit to each sample. We then performed metagenomic shotgun sequencing at 12Gb coverage to explore the viability of this approach for our samples. |
Type Of Material | Computer model/algorithm |
Year Produced | 2021 |
Provided To Others? | No |
Impact | We decided not to use the kit in our further work. |
Title | Oak microbial culture collection |
Description | 20,000 isolates from foliage, rhizosphere and stem of 150 oak trees collected from 30 sites across the UK. |
Type Of Material | Database/Collection of data |
Year Produced | 2021 |
Provided To Others? | No |
Impact | The microbial culture collection is, to our knowledge, the largest one produced from plant-associated microbiota. |
Title | Qualitative Interview Results - Future Oak |
Description | Qualitative data generated during semi-structured interviews with woodland managers focussing on arboreal management and woodland health, particularly with regard to oak trees. |
Type Of Material | Database/Collection of data |
Year Produced | 2022 |
Provided To Others? | No |
Impact | This data is being used as the core of one paper already close to submission and shall be used similarly in subsequent writings. |
Title | Quantitative Survey Results - Future Oak |
Description | Quantitative data generated via the 2021 British Woodland Survey in association with Sylva Foundation focussing on the management and health of oak trees and all woodlands within the UK.. |
Type Of Material | Database/Collection of data |
Year Produced | 2022 |
Provided To Others? | No |
Impact | This data has been used as the substance of one paper already submitted and shall be used in other subsequent papers. |
Title | Taxonomical identification of oak microbial culture collection |
Description | A database with the taxonomical identity and composition of the bacterial and fungal isolates contained in the microbial culture collection has been created by means of amplicon sequencing methods and bioinformatic analysis. |
Type Of Material | Data analysis technique |
Year Produced | 2022 |
Provided To Others? | No |
Impact | This dataset provides insights about the cultivable fraction of the oak microbiome and can be used as a tool for the selection of specific microbial isolates of interest. |
Description | BACSTOP-FUTURE OAK partnership |
Organisation | Forest Research |
Country | United Kingdom |
Sector | Public |
PI Contribution | The BACSTOP and FUTURE OAK projects have been working collaboratively to share knowledge and expertise relating to oak health. This has included discussion on methods and protocols, shared research objectives and research design, collaborative meetings and engagement events. It is likely that in kind contributions will be reportable next year. |
Collaborator Contribution | The BACSTOP team have provided knowledge exchange and support in organisning live webinar events that we were also able to take part in. |
Impact | Joint stakeholder webinar. Enhanced methods and protocols. Knowledge exchange and enhanced research design. |
Start Year | 2020 |
Description | BACSTOP-FUTURE OAK partnership |
Organisation | Forest Research |
Country | United Kingdom |
Sector | Public |
PI Contribution | The BACSTOP and FUTURE OAK projects have been working collaboratively to share knowledge and expertise relating to oak health. This has included discussion on methods and protocols, shared research objectives and research design, collaborative meetings and engagement events. It is likely that in kind contributions will be reportable next year. |
Collaborator Contribution | The BACSTOP team have provided knowledge exchange and support in organisning live webinar events that we were also able to take part in. |
Impact | Joint stakeholder webinar. Enhanced methods and protocols. Knowledge exchange and enhanced research design. |
Start Year | 2020 |
Description | 'Shared Dialogue Workshops in Multidisciplinary Research' at Scottish Graduate School of Social Science (summer school) |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Postgraduate students |
Results and Impact | Instructional lecture, workshop, and discussion hosted by the Scottish Graduate School of Social Science as part of their postgraduate research methods summer school. Focus on the use of shared dialogue/consultation workshops as a research method. |
Year(s) Of Engagement Activity | 2021,2022 |
Description | Action Oak report article |
Form Of Engagement Activity | A magazine, newsletter or online publication |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Supporters |
Results and Impact | An update on our research projects which we hope will have a positive impact on our work. |
Year(s) Of Engagement Activity | 2023 |
URL | https://www.actionoak.org/action-oak-resources |
Description | Acute Oak Decline (AOD) Interactive Awareness Stakeholder Webinar 23/06/21 |
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 | This webinar will introduce the Bacterial Plant Diseases Research Programme and explain its oak tree health research projects - BACSTOP and Future Oak - both have a focus on using cutting edge science to progress understanding and management of acute oak decline (AOD). The BACSTOP project is developing understanding to guide how we may stop the spread of pathogenic bacteria that are causing the damage and death of many native British oak trees. This includes resolving the controversy of the role of the native beetle Agrilus biguttatus in the spread of AOD and testing the effects of drought stress on the disease. The Future Oak project is characterising the oak tree microbial component to see if it can be manipulated to improve oak tree fitness and disease suppression. This includes comparing the micro-organisms in AOD symptomatic trees vs healthy trees, discovering what key microorganisms' functions are and investigating their potential to protect, remediate and promote the health of oak trees. As well as presenting information about this and previous research it will give participants the opportunity to ask questions to its leading researchers, and will provide participants with an opportunity to discuss how they would like to interact with the projects, and help researchers understand the type of information practitioners want about the management of oak trees for resilience, and how that information should be presented. The webinar is aimed at forest/tree managers and practitioners concerned with oak tree health. It is open to those working in the public forestry sector in England, Scotland, Wales and Northern Ireland as the number of participants is restricted by the Teams limitations (separate webinars to the wider sector community will be available more widely at a later date). |
Year(s) Of Engagement Activity | 2021 |
Description | Bangor University undergraduate research seminar - February 2022 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Undergraduate students |
Results and Impact | Lecture discussing research funded by this project |
Year(s) Of Engagement Activity | 2022 |
Description | First year PhD talk |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Postgraduate students |
Results and Impact | Participation in the Online Year One PhD and MSc by Research Talks organized by the School of Natural Sciences at Bangor University. Research activities regarding method development and sample collection and processing were reported and debated with other academics and postgraduate students. |
Year(s) Of Engagement Activity | 2021 |
Description | Flash presentation at Molecular Microbial Ecology Group |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Postgraduate students |
Results and Impact | Delivered a 4 minute talk briefly describing the rationale and methods behind the MWAS part of the Future Oak project. |
Year(s) Of Engagement Activity | 2021 |
Description | Forest Research oak stakeholder meeting |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Online workshop seminar presentation at a stakeholder reporitng meeting. I presented a research update on the Future Oak project |
Year(s) Of Engagement Activity | 2022 |
Description | Invited guest seminar at Nottingham Trent University |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Invisted research seminar on tree health |
Year(s) Of Engagement Activity | 2021,2022 |
Description | Invited guest seminar at University of Birmingham |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Other audiences |
Results and Impact | Invited research seminar focussing on research associated with enviro mental and host-associated microbiomes |
Year(s) Of Engagement Activity | 2022 |
Description | Popular publication - Woodland Heritage Journal |
Form Of Engagement Activity | A magazine, newsletter or online publication |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Supporters |
Results and Impact | Journal article aimed at a wide readership. An update on our Oak research, including the Bac-Stop and Future Oak project work. acknowledges funding support BBSRC, SG, NERC and DEFRA. Purpose to raise awareness and elicit volunteer support for participation in the project. Outcomes: 1. Impact: awareness and support. |
Year(s) Of Engagement Activity | 2022 |
URL | http://www.woodlandheritage.org/wh-journal |
Description | Presentation at the Forest Research Stakeholder event |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Gave an update presentation on the future oak project to stakeholders at the 2023 Forest Research Oak stakeholder meeting |
Year(s) Of Engagement Activity | 2023 |
Description | Presentation for mini-symposium organized for undergraduate students |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Undergraduate students |
Results and Impact | 3rd year undergraduate students attended to a mini-symposium organized in the module of Molecular ecology and evolution at Bangor University. The aim of the symposium was to show undergraduate students the active research carried out by the early careers researchers at Bangor University, and give them the opportunity to ask questions about it. |
Year(s) Of Engagement Activity | 2022 |
Description | Stakeholder knowledge exchange, field and workshop event |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Supporters |
Results and Impact | A 2 day hybrid event (online and in person) was held where powerpoint and poster presentations were given, a workshop involving break out group and question led discussions, and a survey was carried out; and a field day comprising seeing AOD in the field, open air presentations, and hands on swab testing and lfd testing were carried out. |
Year(s) Of Engagement Activity | 2023 |
Description | The Arboricultural Association news article |
Form Of Engagement Activity | A magazine, newsletter or online publication |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | An article highlighting the importance of British oak trees, the threat of oak decline and the research that is ongoing to monitor and understand these threats. |
Year(s) Of Engagement Activity | 2022 |
URL | https://www.trees.org.uk/News-Blog/Latest-News/Oaks-and-fungi-in-the-UK |