Project highlights

  • Climate change impacts on Brassica health 
  • Phage and virome community changes due to climate change  
  • Links between phage, virome community and black rot disease 

Overview

The Gram-negative bacterial genus Xanthomonas causes diseases in over 400 plant species, leading to significant agricultural losses. Xanthomonas campestris pv. campestris (Xcc) affects economically important Brassica crops such as cauliflower, cabbage, and broccoli, as well as other cruciferous crops and the model plant Arabidopsis thaliana. Xcc comprises eleven races, with Race 1 and Race 4 being the most destructive for Brassica crops. Xcc is a vascular pathogen that colonizes plants via hydathodes or wounds, forming biofilms in the vascular system where it releases degradative enzymes and virulence factors.  

Controlling black rot is challenging and currently relies on using pathogen-free planting material and eliminating potential inoculum sources. Bacteriophage biocontrol is a promising alternative method to these approaches. Phages are viruses that infect bacteria and are highly specific to their bacterial hosts, leading to the lysis of the bacterial host without harming plants or animals. Phages have been explored as potential biocontrol agents against Pseudomonas syringae pathovars actinidiae, aesculi, and syringae.  

Climate change is predicted to increase global temperatures by 1.5 to 2°C by 2050. Elevated temperatures affect soil and leaf microbiomes and viromes. Higher temperatures can alter the composition and diversity of soil microbial communities, influencing nutrient cycling, soil structure, and plant health. Similarly, leaf microbiomes can be impacted, affecting plant growth, disease resistance, and overall physiology. These changes influence plant health and productivity.  

The relationship between bacteriophage and virome diversity and plant response to rising temperatures is largely unexplored. Microbial communities are crucial for plant health, enhancing plant tolerance to stresses, including pathogens, by boosting defense responses. We hypothesise that Brassica grown at different temperatures may exhibit lower viral and phage abundance due to heat stress or less favourable conditions for their hosts. Elevated temperatures could alter leaf/root chemistry, impacting microbial diversity and diminishing the capacity to suppress pathogens. We will examine how phage and virome diversity changes over time and how these changes affect phage interactions with key pathogens, such as Xcc.  

Host

University of Warwick

Theme

  • Climate and Environmental Sustainability

Supervisors

Project investigator

Co-investigators

How to apply

Methodology

Collection of soil and leaf samples from Brassica fields: Wellesbourne curates a well-characterized set of Xcc isolates (>600). Soil and leaf samples will be collected from brassica fields over different seasons using the prevalent Xcc strains. Health status of Brassica plants will be recorded. Phages will be isolated using established methods and characterised via electron microscopy and genome sequencing.  

Virome extraction: Viromes from soil and leaf samples will be extracted using established protocols. The quality of extracts will be checked, and the viromes will be sequenced.  

Bioinformatic analysis: Phage genomes and viromes will be analyzed, following established pipelines, to understand their diversity across samples and seasons.  

Testing phage efficacy for disease control: Host specificity of isolated phages will be tested on Xcc diversity set based on whole genomic sequences of 600 Xcc isolates. This will determine whether season impacted phage host range and infectivity.  

Training and skills

DRs will be awarded CENTA Training Credits (CTCs) for participation in CENTA-provided and ‘free choice’ external training. One CTC can be earned per 3 hours training, and DRs must accrue 100 CTCs across the three and a half years of their PhD.  

The student will receive specialist training for this multidisciplinary project, encompassing fieldwork, microbiology, genomics, viromic, data management, bioinformatic, statistical analysis and interpretation of large and complex data sets.  

The student will be supported to develop these skills within the School of Life Sciences at the University of Warwick, and Department of Genetics and Genome Biology at the University of Leicester, allowing the student to excel in all of these aspects of data acquisition, analysis and dissemination and to build important networks.  

The supervisory team is multi-disciplinary and highly experienced, based in excellent, well-equipped institutions, and will provide comprehensive support for the student across all aspects of the project.  

Further details

For any enquiries related to this project please contact Dr Mojgan Rabiey, University of Warwick, [email protected].  

To apply to this project:  

  • You must include a CV with the names of at least two referees (preferably three) who can comment on your academic abilities.  

 Applications must be submitted by 23:59 GMT on Wednesday 8th January 2025.  

Possible timeline

Year 1

Year 1/2: Field experimental design and field data/sample collection training undertaken. Samples will be collected from Brassica fields, 3 times during the year, for two years, from different Brassica species including kale, cauliflower and broccoli. Bacteriophages will be isolated against Xcc dominant strains. DNA will be extracted for phage genome sequencing to assess diversity. Viromes will be extracted from soil and leaf samples, following the established methods. The quality of the extract will be checked. The extracts will be sent for sequencing.  

Year 2

Year 2/3: Bioinformatic analysis of phage genomes and virome seqeunecs will be done to investigate the impact of temperature, time and season on both phage and virome diversity. Phage host range assays will be performed for a large set of Xcc strains to understand their efficacy and if temperature, time and season has any impact on phage efficacy.  

Year 3

Year 3.5: Final analysis of the data, writing up of manuscripts and thesis will be done.  

This project has a built-in resilience in the fieldwork, covering spring/summer/autumn or winter components of data collection over two years. Phage and virome biodiversity assessment will include DNA genome sequencing, metabarcoding, and viromic analysis which will be analysed using multivariate analysis tools in R and Warwick Scientific Computing Research Technology Platform (SCRTP). Additionally, the project involves isolating bacteria and phage for further investigation of culturable microbial community in relation to social and spatial ecology, and assessment of the role of temperature on phage and virome diversity in brassicas under current climate change scenario.  

Further reading

Vicente, J. G. & Holub, E. B. 2013. Xanthomonas campestris pv. campestris (cause of black rot of crucifers) in the genomic era is still a worldwide threat to brassica crops. Molecular Plant Pathology, 14(1), pp.2-18. 

Lu, L., Monakhos, S. G., Lim, Y. P. & Yi, S. Y. 2021. Early defense mechanisms of Brassica oleracea in response to attack by Xanthomonas campestris pv. campestris. Plants, 10(2), pp.123-132. 

Di Lallo, G., Evangelisti, M., Mancuso, F., Ferrante, P., Marcelletti, S., Tinari, A., Superti, F., Migliore, L., D’Addabbo, P., Frezza, D., Scortichini, M. & Thaller, M. C. 2014. Isolation and partial characterization of bacteriophages infecting Pseudomonas syringae pv. actinidiae, causal agent of kiwifruit bacterial canker. Journal of Basic Microbiology, 54(12), pp.1210-1221. 

James, S. L., Rabiey, M., Neuman, B. W., Percival, G. & Jackson, R. W. 2020. Isolation, characterisation and experimental evolution of phage that infect the horse chestnut tree pathogen, Pseudomonas syringae pv. aesculi. Current Microbiology, 77(11), pp.1438-1447. 

Rabiey, M., Roy, S. R., Holtappels, D., Franceschetti, L., Quilty, B. J., Creeth, R., Sundin, G. W., Wagemans, J., Lavigne, R. & Jackson, R. W. 2020. Phage biocontrol to combat Pseudomonas syringae pathogens causing disease in cherry. Microbial Biotechnology, 13(6), pp.1428-1445. 

Classen, A. T., Sundqvist, M. K., Henning, J. A., Newman, G. S., Moore, J. A. M., Cregger, M. A., Moorhead, L. C. & Patterson, C. M. 2015. Direct and indirect effects of climate change on soil microbial and soil microbial-plant interactions: What lies ahead? Ecosphere, 6(8), p.130. Available at: http://dx.doi.org/10.1890/ES15-00217.1  

Durham, D. M., Sieradzki, E. T., ter Horst, A. M., Santos-Medellín, C., Bess, C. W. A., Geonczy, S. E. & Emerson, J. B. 2022. Substantial differences in soil viral community composition within and among four northern California habitats. ISME Communications, 2(100), pp.1-10. Available at: https://doi.org/10.1038/s43705-022-00171-y