Xanthomonas plants diseases: mitigating existing, emerging and future threats to UK agriculture

Lead Research Organisation: Fera Science (United Kingdom)
Department Name: Plant Pest & Disease

Abstract

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Technical Summary

X. campestris pv. campestris, one of the most important brassica diseases worldwide, causes black rot, particularly on B. oleracea, where resistance is rare. This multidisciplinary project draws upon risk assessment, pathology, bioinformatic, molecular, imaging in a detailed analysis of Xc genomics, Xcc infection dynamics and screens for new Xcc resistance that can be ultimately be deployed in the field. There are two notable strengths to this proposal. The unique Warwick HRI collection of ~1,000 Xanthomonas isolates, curated and largely collected by Joana Vincente who spearheads the pathology component and who described the first six races of Xcc and Warwicks unique collection of brassica diversity fixed foundation sets (DFFs).
To address specific biological questions outlined in the proposal we will sequence ~960 Xc isolates, including 771 Xcc isolates and multiple isolates of the apoplastic pathogen Xc. raphani. Candidate genes, variants and other genetic elements that are associated with race and infection lifestyle will be used in a variety of assays including generating diagnostic markers, with in field utility, including identification of potential threats such as X. fragariae, X. nasturtii and th X. vasicola pv. vasculorum, supporting our pathogen risk work programme.
Core and variant genes will be delivered in planta, singly and in combination via Xc or P. syringae using chlorophyll imaging to quantify their contribution to virulence, resistance, or as our preliminary data suggests, masking other effector activity. We will also image Xc infections undertaken using new bioluminescence and fluorescent reporters whose emission sits between the Xanthamonadin and chlorophyll emission spectra.
In parallel, we will screen Brassica oleracea, Brassica napus DFFs and also the interfertile C genome crop wild relatives DFF as well as revisiting informative historical mapping lines to identify loci showing race specific or broad spectrum resistance to Xcc.

Planned Impact

Who will benefit from this research?
This project targets UK brassica growers as the ultimate beneficiaries by providing the genetic and genomic knowledge to facilitate new understanding of Xanthomonas virulence mechanisms, how virulence emerges and to identify new sources of Xanthomonas resistance to incentivize breeding companies to use these resources.

The work targets, black rot of crucifers caused by Xanthomonas campestris pv. campestris, a disease that regularly causes loses in brassica UK production, and comparisons with related pathovars, will have impact in the UK producers and related industry including seed and transplant producers. Strategies for using new sources of resistance will lead to the development of new cultivars and the work on Xanthomonas genomics should lead to improved methods of diagnostics that will be available to growers and industry in general.

Additional potential benefits to UK growers.
One of the real concerns of UK growers is incursions of pathogens. Xanthomas disease of maize, a devastating disease in US is also a major concern of UK maize growers. In addition to the diagnostic work proposed which will monitor the spread of the disease in maize fields around the country, we will also undertake a detailed risk assessment which will help maize growers prepare for a future disease outbreak. The knowledge on Xanthomonas diseases of strawberry, watercress and maize, will be important to avoid the introduction and spread of these pathogens in UK crop production. The findings will specifically inform the Defra Plant Health Risk Register and if phytosanitary measures are justified against X. vasicola pv. vasculorum.
Training:

The project will help train the next generation of phytobacterial workers. The UK expertise in plant pathology and in particular bacterial plant diseases has been reduced in the past 10-20 years and the work proposed here will contribute to strengthen teams working at mainly at three institutions (University of Exeter, Fera and University of Warwick) and, critically, will provide training for new students and researchers.

The combination of skills in Plant Pathology, genetics, plant-pathogen interactions and bioinformatics will be essential to provide new knowledge on Xanthomonas pathogens and their hosts. We will use resources available at Warwick and Fera including bacterial collections and plant selections. We will also add to these invaluable collections.

Implementation: The PIs have excellent track records in presenting in scientific conferences and are very well connected within relevant UK and worldwide academic communities. Our track record and extensive network of colleagues and collaborators, in different disciplines of plant biology, will ensure the effective communication of our research output. We will publish our findings in high impact open access journals and we will present our findings at national and international meetings. We will also disseminate our research findings through our project website, social media, news-and-view style articles podcasts.

Genomic data: Sequencing data generated will be made publicly available in relevant databases. This proposal will also contribute to maintain and invest in facilities and new equipment that is necessary for keeping large collections of bacterial isolates and for imaging. These will also be available for other researchers to develop additional studies.

Outreach: We will engage with producers, agronomists and industry groups through site visits and through attendance of meetings and events as described in pathways to impact. In addition, we will also attend events aimed at the general public and will raise awareness on the importance of crop production in the UK and importance of putting in place strategies to reduce the impact of plant bacterial diseases - in particular, the introduction of new diseases should be avoided through testing of seeds and planting materials.
 
Description - Xanthomonas fragariae, a regulated non-quarantine pest, is considered to be absent in the UK, but has occasionally been detected in this country over several years. Isolation of this pathogen is very difficult and we are planning experiments to improve our method of isolation.
- We have assembled isolates of Xanthomonas fragariae and X. arboricola pv. fragariae from the NCPPB collection and confirmed their identity through gyrB sequencing.
- Xanthomonas vasicola pv. vasculorum has never been detected in the UK and constitutes a threat to maize production worldwide. We are developing pest risk analysis to evaluate the threat posed by this pathogen to the UK.
- We have selected appropriate media for isolation of Xanthomonas fragariae of strawberry and we have characterised and selected pathogenic isolates for future testing of varieties grown in the UK.
- We have selected pathogenic isolates of Xanthomonas vasicola pv. vasculorum of maize. We have obtained data on areas grown in the UK and varieties and found that more than 200 different varieties have been grown in the past 10 years.
- We confirmed the identification of Xanthomonas nasturtii isolates from Spain, Portugal and Hawaii, characterised pathogenicity and completed the Koch's postulates to support reports that identify black rot of watercress for the first time in these countries/states. These isolates are being whole genome sequenced at Exeter University.
- We have found that wallflowers are frequently infected with Xanthomonas campestris, collected samples and obtained isolates for further studies.
Exploitation Route - The work on Xanthomonas fragariae and Xanthomonas vasicola pv. vasculorum will be communicated to Defra, producers, agronomists and industry groups.
- In addition, the work at Fera will help train new diagnosticians
Sectors Agriculture

Food and Drink

 
Description Pest risk analysis of bacterial leaf streak of maize to inform Defra
Geographic Reach National 
Policy Influence Type Contribution to a national consultation/review
 
Description Future Proofing in Plant Health - Identification of Xanthomonas diseases of ornamentals
Amount £37,579 (GBP)
Organisation Department For Environment, Food And Rural Affairs (DEFRA) 
Sector Public
Country United Kingdom
Start 04/2022 
End 01/2024
 
Title Improvements in the method used to isolate Xanthomonas fragariae from strawberries 
Description Different media were tested for isolating and growing Xanthomonas fragariae as this is a relatively difficult pathogen to isolate. We will include the methods selected in future publications on Xanthomonas fragariae 
Type Of Material Technology assay or reagent 
Year Produced 2023 
Provided To Others? No  
Impact The laboratory at Fera is now prepared to try to isolate Xanthomonas fragariae from strawberry plants. Before this project, all attempts had failed even with samples that appeared to be positive. Recently, an isolate was obtained from a sample of imported plants from Bulgaria. 
 
Title Increasing the Fera and NCPPB collection of Xanthomonas spp. isolates 
Description We have identified that Fera and the National Collection of Plant Pathogenic Bacteria would benefit from having additional bacterial isolates of Xanthomonas spp. to support research projects and obtain more information related to the diversity of these pathogens. 
Type Of Material Biological samples 
Year Produced 2024 
Provided To Others? Yes  
Impact We have added isolates of Xanthomonas campestris from Brazil, Xanthomonas vasicola pv. vasculorum from the US, Argentina and Brazil and Xanthomonas fragariae from US, Italy, Portugal and Bulgaria. Some (but not all) of these new strains are now available through the NCPPB collection. The genome comparison of these strains will be included in future publications from our project. 
 
Title Selection of diagnostic assays for Xanthomonas vasicola pv. vasculorum of maize 
Description We have tested existing diagnostic methods including PCR and qPCR assays for detection of Xanthomonas vasicola pv. vasculorum, the cause of bacterial leaf streak of maize. We have selected the best methods and we also asked the biotechnicians to design new assays for some particular pathovars or groups of isolates. The existing assays are publish and the newer assays are not available yet. 
Type Of Material Technology assay or reagent 
Year Produced 2024 
Provided To Others? No  
Impact The selection of assays will have a positive impact in the work done at the Fera laboratory to detect Xanthomonas vasicola pv. vasculorum especially from maize seeds. The new assays that are being developed will have a potential wider impact after publication. 
 
Description Conversation with Defra's Pest Risk Analyst 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Policymakers/politicians
Results and Impact Meeting with Helen Anderson, Pest Risk Analyst and Sharon Matthews-Berry, Plant Health Consultant at Defra.
Purpose was to discuss priorities for diagnostics of Xanthomonas spp. diseases.
We have agreed that developing suitable diagnostic assays for species and pathovars of Xanthomonas that are on the risk register will be a priority.
Year(s) Of Engagement Activity 2024
 
Description Conversation with plant breeders and pathologists from Brassica seed company (Sakata) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact After several changes of messages, two members of the XanthThreats project met online with two plant breeders and a plant pathologist from Japan, France and the UK.
We discussed how Xanthomonas isolates can be characterized in order to provide useful information for future breeding.
We agreed to characterize a collection of up to 20 isolates of Xanthomonas campestris from Japan and possibly Europe. We will also provide seeds of brassica differentials and control isolates to the seed company. The paperwork (MTAs) will be prepared to exchange materials during 2024.
Year(s) Of Engagement Activity 2024
 
Description Conversations with Elsoms Seeds about a visit, maize varieties and brassica breeding and bacterial diseases caused by Xanthomonas spp. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Industry/Business
Results and Impact We have been talking with Elsoms Seeds to organise a visit, to obtain maize varieties for screening in this project and to discuss brassica breeding for disease resistance (especially resistance to black rot, Xanthomonas campestris pv. campestris.
Year(s) Of Engagement Activity 2022,2023
 
Description Conversations with strawberry producers and breeders regarding the status of Angular Leaf Spot (caused by Xanthomonas fragariae) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Industry/Business
Results and Impact We have been in contact woth stwaberry producers and breeders. We have asked them if they thought Angular Leaf Spot was present or absent in the UK and if they would like its status to change (from RNPQ to Quarantine or non-regulated) - these questions are difficult as growers fear that plants will be destroyed if the disease is found. Some think that the disease comes regularly in imported plants, whislt others think that the disease is not present and the modern conditions used for growing plants (tunnels with controlled irrigation) limit spread, so the disease is not a problem.
We will visit strawberry breeders. We have obtained plants from two growers and we have tested them and used them in our experiments.
We hope to continue our dialogue and collaboration to obtain more plants to test and to use in experiments.
Year(s) Of Engagement Activity 2021,2022,2023
 
Description Engagement with wallflower growers and seed company regarding bacterial wilt (caused by Xanthomonas campestris) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact Emails were exchanged and phone conversations took place regarding an outbreak of bacterial wilt of wallflowers - we have been in contact with the council, the company that bought the plants, the intermediaries and the seed company that imported seeds. We have obtained seeds from the seed company and have performed seed testing (and found one seed lot infected with the pathogen). We have highlighted the importance of using clean seed lots to avoid outbreaks of bacterial wilt of wallflowers. People involved thought that adverse weather conditions had caused rot of plants, but hopefully we have contributed to raise awareness of the impact that bacterial plant diseases can have.
Year(s) Of Engagement Activity 2022,2023
 
Description Presentation at the APHA Plant Health Symposium 2nd March 2022 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Edward Haynes gave a talk at the APHA Plant Health Symposium 2022 (2nd of March) 'Plant Health in a Changing World'. This was mainly aimed at Plant Health Inspectors.
The talk focused on Xanthomonas arboricola pv. pruni but also introduced the BPD Xanthomonas Threats project and what is being done on other Xanthomonas plant diseases.
Year(s) Of Engagement Activity 2022
 
Description Presentation at the APHA Plant Health Symposium 2nd March 2022 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Adam Bryning and Sarah Carroll gave talks at the APHA Plant Health Symposium 2022 (2nd of March) 'Plant Health in a Changing World'. This was mainly aimed at Plant Health Inspectors. The talk was on 'Recent Findings of Xanthomonas spp. in ornamental plants' and this included work done under this project on Xanthomonas campestris of wallflowers.
Year(s) Of Engagement Activity 2022
 
Description Presentation at the APHA Plant Health and Seed Inspectorate Technical Refresher course 14th September 2023 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Joana Vicente presented an update to the Plant Health inspectors on the Xanthomonas Threats project, in particular focusing on Xanthomonas fragariae and the need for awareness of this pathogen during inspections.
Year(s) Of Engagement Activity 2023
 
Description Twitter #XanthomonasThreats 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact We have started a Twitter # to engage with interested groups.
Year(s) Of Engagement Activity 2020
 
Description Visit to Brassica breeders in Lincolnshire 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Trip for three Fera staff (Joana Vicente, Jennifer Cole, Adam Bryning) to Lincolnshire to visit two seed specialists/breeders; Elsoms Seed and Sakata. Elsoms is a family-run UK seed specialist and breeder, with nearly 180 years of history and over 120 staff. Elsoms specialises in Brassicas, Lettuce, Alliums, Parsnip, Carrots, Beetroot, Herbs, Legumes, Asparagus, Radicchio, Squashes, soft fruits (strawberry grown from seeds) and sweetcorn. Sakata are a Sutterton-based subsidiary of the Japanese flower and vegetable breeding Sakata Seed Corporation based in Yokohama, Japan. Sakata breed several brassica crops, including cauliflower, cabbage, Chinese cabbage, and Pak Choi. They are world leaders in broccoli, and are the breeders of Tenderstem® Broccoli. At Elsoms the team gave a presentation on the Xanthomonas Threats project, we discussed how we could ensure that our research not only improves our knowledge of Xanthomonas pathogens, but perhaps also lead to new diagnostic assays for a range of stakeholders. Seeds for testing in the project were also received. At Sakata the team discussed the possibility of selected lines being screened by the Sakata pathologists. Another valuable project output would be suitable diagnostics for detecting Xcc in seeds and our conversations will carry on with the UK and Japanese Sakata specialists. We also discussed difficulties in exporting and importing materials, which can be especially complicated when infected material is to be exchanged, with frequent delays in paperwork or samples being retained at airports.
Year(s) Of Engagement Activity 2023
 
Description Visit to NIAB East Malling 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Industry/Business
Results and Impact Three members of the Fera team (Joana Vicente, Jenny Cole and Andy Aspin) visited NIAB East Malling. This was particularly useful as East Malling has been responsible for breeding many important strawberry varieties, and the visit enabled an understanding of the drivers of strawberry breeding, and the risk posed by one of the Xanthomonas threats pathogens, Xanthomonas fragariae. The visit to East Malling was extremely valuable as the links with the strawberry breeders and the fruit and wine industry are important for diagnostic and research projects that are run at Fera including the Xanthomonas Threats project.
Year(s) Of Engagement Activity 2023
 
Description Website development 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact We have been developing website page(s) that introduce the Xanthomonas Threats project.
Year(s) Of Engagement Activity 2020,2021,2022
URL https://bacterialplantdiseases.uk/xanthomonas-threats/