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

Lead Research Organisation: UNIVERSITY OF EXETER
Department Name: Biosciences

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

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.

Publications

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Grant M (2022) Culturing Xanthomonas v1

 
Description Through sequencing the genomic DNA of Xanthomonas species, we generated evidence supporting changes in the classification of these important plant-pathogenic bacteria.
Exploitation Route The new names of these pathogens should be adopted by biosecurity authorities when legislating and/or advising plant disease control measures.
Sectors Agriculture

Food and Drink

Environment

 
Title Genome sequencing of 12 taxonomically significant xanthomonads from the NCPPB 
Description Genome sequences for: Xanthomonas campestris pv. esculenti Xanthomonas campestris pv. zinniae Xanthomonas campestris pv. parthenii Xanthomonas campestris pv. cannae Xanthomonas campestris pv. nigromaculans Xanthomonas campestris pv. phormiicola Xanthomonas campestris pv. asclepiadis Xanthomonas cassavae CFBP 4642 Xanthomonas citri Xanthomonas dyei pv. eucalypti Xanthomonas melonis Xanthomonas sp. NCPPB 1067 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? Yes  
Impact These are important for genomics-informed taxonomy of gnus Xanthomonas. They are type strains and pathotype strains of taxa that lack such data. 
URL https://www.ncbi.nlm.nih.gov/bioproject/PRJNA774146
 
Title Genome sequencing of 4 Xanthomonas vasicola 
Description # PRJNA743420 Assembly Details # Assembly Level WGS BioSample Strain Taxonomy GCA_019200945.1 Contig JAHTMX000000000 SAMN20080225 NCPPB 889 Xanthomonas vasicola pv. vasculorum GCA_019209805.1 Contig JAHUTP000000000 SAMN20034691 NCPPB 795 Xanthomonas vasicola pv. vasculorum GCA_019209705.1 Contig JAHUTQ000000000 SAMN20034692 NCPPB 4378 Xanthomonas vasicola pv. musacearum GCA_019209735.1 Contig JAHUTR000000000 SAMN20034693 NCPPB 4390 Xanthomonas vasicola pv. musacearum 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? Yes  
Impact These data replace older poor-quality data for those strains and are important for phylogenomics of Xanthomonas. 
URL https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA743420
 
Title Genome sequencing of Xanthomonas arboricola from strawberry 
Description We sequenced the genomes of bacteria in the WHRI collection, isolated from strawberry plants. 
Type Of Material Database/Collection of data 
Year Produced 2023 
Provided To Others? Yes  
Impact None yet 
URL https://www.ncbi.nlm.nih.gov/bioproject/991941
 
Title Genome sequencing of Xanthomonas arboricola on walnut, hazelnut, peach and apricot in serbia and Montenegro 
Description Xanthomonas arboricola is a bacterial pathogen that causes diseases in various fruit trees, ornamental plants, and other crops. It is divided into different pathovars based on the host plant it infects. One of the pathovars, Xanthomonas arboricola pv. pruni (Xap), specifically affects stone fruit trees such as plums, peaches, and cherries. In Serbia, Xanthomonas arboricola has been reported as a significant concern in stone fruit production. The bacterium can cause a disease known as bacterial spot, characterized by small, water-soaked lesions on leaves, stems, and fruits. As the infection progresses, the lesions may turn necrotic, leading to defoliation and reduced fruit quality and yield. 
Type Of Material Database/Collection of data 
Year Produced 2023 
Provided To Others? Yes  
Impact
URL https://www.ncbi.nlm.nih.gov/bioproject/982436
 
Title Genome sequencing of Xanthomonas campestris from Serbia 
Description Xanthomonas campestris pv. campestris is a gram-negative bacterium that belongs to the family Xanthomonadaceae. It is a plant pathogen that causes black rot disease in a wide range of cruciferous plants, including cabbage, broccoli, cauliflower, and radishes. The bacterium is rod-shaped and motile, and it is characterized by its ability to produce colonies that appear yellow and mucoid on nutrient agar plates. It is a facultative anaerobe, meaning it can grow both in the presence and absence of oxygen. Xanthomonas campestris pv. campestris is primarily transmitted through contaminated seeds, soil, or plant debris. Once it enters the host plant, it colonizes the intercellular spaces and multiplies rapidly. The infection causes characteristic symptoms such as yellow V-shaped lesions on the leaves, wilting, and eventually leads to the development of blackened rot in the vascular tissues. The bacterium possesses various virulence factors that aid in its pathogenicity, including the production of extracellular enzymes and toxins that degrade plant cell walls and suppress the host's defense mechanisms. It also utilizes a type III secretion system to deliver effector proteins into host cells, which manipulate the plant's immune response. Management of Xanthomonas campestris pv. campestris involves employing various strategies such as crop rotation, sanitation practices, and the use of disease-resistant cultivars. Chemical control measures may be employed, although their effectiveness can be limited due to the emergence of resistant strains. Overall, Xanthomonas campestris pv. campestris is an economically significant pathogen that poses a threat to cruciferous crops worldwide and requires integrated management approaches to mitigate its impact 
Type Of Material Database/Collection of data 
Year Produced 2023 
Provided To Others? Yes  
Impact
URL https://www.ncbi.nlm.nih.gov/bioproject/985555
 
Title Genome sequencing of Xanthomonas campestris from ornamentals 
Description Genome sequencing of Xanthomonas campestris from ornamentals 
Type Of Material Database/Collection of data 
Year Produced 2023 
Provided To Others? Yes  
Impact
URL https://www.ncbi.nlm.nih.gov/bioproject/485808
 
Title Genome sequencing of Xanthomonas campestris pv. campestris 
Description Xanthomonas campestris pv. campestris is a gram-negative bacterium that causes black rot disease in cruciferous plants, including cabbage, cauliflower, and broccoli. It is a plant pathogen that affects the vascular system of the host plants, leading to severe damage and economic losses in agricultural settings. 
Type Of Material Database/Collection of data 
Year Produced 2023 
Provided To Others? Yes  
Impact
URL https://www.ncbi.nlm.nih.gov/bioproject/982295
 
Title Genome sequencing of Xanthomonas campestris pv. campestris from WHRI collection 
Description The genus Xanthomonas includes bacterial plant pathogens of more than 350 plant species including many crop plants. For example Xanthomonas campestris pv. campestris (Xcc) causes black rot in brassicas such as cabbage, cauliflower, broccoli, Brussels sprouts, kale, oilseed rape, swede, turnip and mustards. This disease is considered the most important disease of vegetable brassicas worldwide and it occurs annualy in UK brassica growing areas including Lincolnshire and Cornwall. As this disease is more problematic in hot and humid weather, the severity of outbreaks could increase with climate change. 
Type Of Material Database/Collection of data 
Year Produced 2023 
Provided To Others? Yes  
Impact
URL https://www.ncbi.nlm.nih.gov/bioproject/988133
 
Title Genome sequencing of Xanthomonas campestris pv. raphani from WHRI collection 
Description Xanthomonas campestris pv. raphani is a pathovar (pathogenic variant) of the bacterial species Xanthomonas campestris. It specifically affects plants in the Brassicaceae family, including radishes (Raphanus sativus) and other cruciferous vegetables. Xanthomonas campestris pv. raphani causes a disease known as bacterial leaf spot or bacterial blight in radishes and related crops. The bacteria enter the plant through wounds or natural openings and colonize the leaf tissues, leading to the development of characteristic symptoms. The symptoms of bacterial leaf spot caused by Xanthomonas campestris pv. raphani include small, water-soaked lesions on the leaves that may expand and turn brown or black over time. These lesions often have a yellow halo surrounding them. In severe cases, the lesions can coalesce, causing extensive damage to the foliage and reducing the overall quality and marketability of the crop. 
Type Of Material Database/Collection of data 
Year Produced 2023 
Provided To Others? Yes  
Impact
URL https://www.ncbi.nlm.nih.gov/bioproject/991733
 
Title Genome sequencing of Xanthomonas campestris strains from NCPPB 
Description Genome sequencing of 16 Xanthomonas strains. 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? Yes  
Impact Confirms that these strains and pathovars belong to the species Xanthomonas campestris based on phylogenomics. 
URL https://www.ncbi.nlm.nih.gov/bioproject/PRJNA774128
 
Title Genome sequencing of Xanthomonas euvesicatoria from Serbia 
Description Xanthomonas euvesicatoria is a bacterium that causes bacterial spot disease in tomato and pepper plants. It is a pathogenic species within the genus Xanthomonas, which comprises a group of gram-negative bacteria known for causing plant diseases. Bacterial spot, caused by Xanthomonas euvesicatoria, is a common and economically significant disease in tomato and pepper crops worldwide. The bacterium infects the leaves, stems, and fruits of these plants, leading to the development of characteristic symptoms. Infected plants exhibit small, water-soaked lesions on the leaves, which gradually enlarge and turn into dark, necrotic spots. On the fruits, circular, raised lesions with a dark center and a yellow halo can be observed. Xanthomonas euvesicatoria is primarily transmitted through contaminated seeds, but it can also spread through water splashes, wind, and mechanical means. Warm and humid conditions favor the spread and severity of the disease. The bacterium can survive in plant debris and weed hosts, contributing to its persistence between growing seasons. 
Type Of Material Database/Collection of data 
Year Produced 2023 
Provided To Others? Yes  
Impact
URL https://www.ncbi.nlm.nih.gov/bioproject/985260
 
Title Genome sequencing of Xanthomonas floridensis 
Description This species has been isolated from diseased leaves of watercress. 
Type Of Material Database/Collection of data 
Year Produced 2023 
Provided To Others? Yes  
Impact
URL https://www.ncbi.nlm.nih.gov/bioproject/991923
 
Title Genome sequencing of Xanthomonas fragariae 
Description Xanthomonas fragariae is a bacterial pathogen that causes strawberry angular leaf spot disease, which is characterized by the appearance of angular or V-shaped water-soaked lesions on the leaves of strawberry plants. These lesions may turn brown or dark red as the disease progresses. The bacteria are typically spread through splashing water, wind, or contaminated tools and equipment. The infection can lead to reduced plant vigor, stunted growth, and yield losses in strawberry crops. 
Type Of Material Database/Collection of data 
Year Produced 2023 
Provided To Others? Yes  
Impact
URL https://www.ncbi.nlm.nih.gov/bioproject/985246
 
Title Genome sequencing of Xanthomonas nasturtii 
Description Xanthomonas nasturtii is a bacterial pathogen of watercress. 
Type Of Material Database/Collection of data 
Year Produced 2023 
Provided To Others? Yes  
Impact
URL https://www.ncbi.nlm.nih.gov/bioproject/982082
 
Title Genome sequencing of Xanthomonas phaseoli pv. phaseoli from Serbia 
Description Xanthomonas phaseoli pv. phaseoli is a bacterium that causes bacterial blight in common bean plants (Phaseolus vulgaris). It is a pathovar (pathogenic variety) of the Xanthomonas phaseoli species. Bacterial blight is a serious disease that affects the leaves, pods, and stems of common bean plants, leading to significant yield losses in affected crops. The bacterium Xanthomonas phaseoli pv. phaseoli is gram-negative and rod-shaped. It is transmitted primarily through contaminated seed, but it can also be spread through wind, rain, and mechanical means such as farming tools. Once the bacterium enters the plant, it colonizes the vascular system, leading to wilting, leaf necrosis, and the formation of water-soaked lesions. In severe cases, infected pods may display brown streaks or water-soaked spots. 
Type Of Material Database/Collection of data 
Year Produced 2023 
Provided To Others? Yes  
Impact
URL https://www.ncbi.nlm.nih.gov/bioproject/985259
 
Title Genome sequencing of Xanthomonas vasicola 
Description Here we sequence genomes of two further strains of X. vasicola pv. musacearum from Africa plus an additional X. vasicola pv. vasculorum from Madagascar, which is geographically distinct from previously sequenced strains of this pathovar. 
Type Of Material Database/Collection of data 
Year Produced 2023 
Provided To Others? Yes  
Impact
URL https://www.ncbi.nlm.nih.gov/bioproject/743420
 
Title Genome sequencing of miscellaneous Xanthomonas campestris from WHRI collection 
Description Xanthomonas campestris is a Gram-negative bacterial species that encompasses numerous pathovars, each capable of causing disease in different plant species. It is a plant pathogenic bacterium that affects a wide range of economically important crops, including vegetables, fruits, cereals, and ornamental plants. Xanthomonas campestris is characterized by its rod-shaped cells and the ability to move using a single polar flagellum. It is a facultative anaerobe, meaning it can grow both in the presence and absence of oxygen. The bacteria are typically spread through water, wind, insects, contaminated tools, and plant debris. Here we sequence genomes of some miscellaneous strains of X. campestris from the WHRI collection. 
Type Of Material Database/Collection of data 
Year Produced 2023 
Provided To Others? Yes  
Impact None yet. 
URL https://www.ncbi.nlm.nih.gov/bioproject/991952
 
Title Genome sequencing of miscellaneous Xanthomonas from WHRI collection 
Description Genome sequencing of interesting strains from the WHRI collection. 
Type Of Material Database/Collection of data 
Year Produced 2023 
Provided To Others? Yes  
Impact None yet. 
URL https://www.ncbi.nlm.nih.gov/bioproject/991976
 
Title Genome sequencing of miscellaneous plant-associated bacteria 
Description Genome sequencing of bacterial isolates received as Xanthomonas species but revealed by sequencing to be other taxa. 
Type Of Material Database/Collection of data 
Year Produced 2024 
Provided To Others? Yes  
Impact
URL https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1085284
 
Title Genome sequencing of pathotype strains of Xanthomonas 
Description # PRJNA742925 Assembly Details # Assembly Level WGS BioSample Strain Taxonomy GCA_019201075.1 Contig JAHTUK000000000 SAMN19988995 NCPPB 2346 Xanthomonas axonopodis pv. passiflorae GCA_019201065.1 Contig JAHTUQ000000000 SAMN19988989 NCPPB 464 Xanthomonas campestris pv. olitorii GCA_019201545.1 Contig JAHTUM000000000 SAMN19988993 NCPPB 3114 Xanthomonas campestris pv. merremiae GCA_019201525.1 Contig JAHTUL000000000 SAMN19988994 NCPPB 585 Xanthomonas campestris pv. trichodesmae GCA_019201485.1 Contig JAHTVG000000000 SAMN19988973 NCPPB 1757 Xanthomonas campestris pv. blepharidis GCA_019201465.1 Contig JAHTVH000000000 SAMN19988970 NCPPB 1334 Xanthomonas campestris pv. ionidii GCA_019201445.1 Contig JAHTVE000000000 SAMN19988975 NCPPB 1760 Xanthomonas campestris pv. spermacoces GCA_019201425.1 Contig JAHTVC000000000 SAMN19988977 NCPPB 1828 Xanthomonas campestris pv. euphorbiae GCA_019201405.1 Contig JAHTVB000000000 SAMN19988978 NCPPB 2057 Xanthomonas campestris pv. heliotropii GCA_019201375.1 Contig JAHTVA000000000 SAMN19988979 NCPPB 2372 Xanthomonas campestris pv. fici GCA_019201365.1 Contig JAHTUZ000000000 SAMN19988980 NCPPB 2373 Xanthomonas campestris pv. carissae GCA_019201345.1 Contig JAHTVD000000000 SAMN19988976 NCPPB 1787 Xanthomonas campestris pv. veroniae GCA_019201325.1 Contig JAHTUX000000000 SAMN19988982 NCPPB 2932 Xanthomonas campestris pv. daturae GCA_019201305.1 Contig JAHTVF000000000 SAMN19988974 NCPPB 1758 Xanthomonas campestris pv. coriandri GCA_019201285.1 Contig JAHTUW000000000 SAMN19988983 NCPPB 3079 Xanthomonas campestris pv. paulliniae GCA_019201265.1 Contig JAHTUS000000000 SAMN19988987 NCPPB 4351 Xanthomonas campestris pv. viegasii GCA_019201245.1 Contig JAHTUY000000000 SAMN19988981 NCPPB 2498 Xanthomonas campestris pv. convolvuli GCA_019201225.1 Contig JAHTUP000000000 SAMN19988990 NCPPB 575 Xanthomonas campestris pv. clerodendri GCA_019201205.1 Contig JAHTUR000000000 SAMN19988988 NCPPB 4352 Xanthomonas campestris pv. zingibericola GCA_019201185.1 Contig JAHTUO000000000 SAMN19988991 NCPPB 579 Xanthomonas campestris pv. lawsoniae GCA_019201165.1 Contig JAHTUT000000000 SAMN19988986 NCPPB 4349 Xanthomonas campestris pv. pennamericanum GCA_019201145.1 Contig JAHTUU000000000 SAMN19988985 NCPPB 4348 Xanthomonas campestris pv. mirabilis GCA_019201115.1 Contig JAHTUN000000000 SAMN19988992 NCPPB 586 Xanthomonas campestris pv. uppalii GCA_019201105.1 Contig JAHTUV000000000 SAMN19988984 NCPPB 3759 Xanthomonas campestris pv. obscurae GCA_019193005.1 Contig JAHTMP000000000 SAMN19988971 NCPPB 1336 Xanthomonas euvesicatoria pv. alangii GCA_019192985.1 Contig JAHTMO000000000 SAMN19988972 NCPPB 1756 Xanthomonas euvesicatoria pv. physalidis 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? Yes  
Impact These are taxonomically important and allow phylogenomic-based revision of taxonomy. 
URL https://www.ncbi.nlm.nih.gov/bioproject/PRJNA742925
 
Title Re-sequencing of X. vasicola strains at Fera 
Description We performed genome sequencing on strains of Xanthomonas vasicola, most of which had been previously sequenced, for the purposes of verification and quality control and/or to update previous poor-quality genome assemblies. 
Type Of Material Database/Collection of data 
Year Produced 2023 
Provided To Others? Yes  
Impact None yet. 
URL https://www.ncbi.nlm.nih.gov/bioproject/992549