Please Note: The main page lists projects via BBSRC Research Theme(s) quoted and then relevant Topic(s).
Development of effective phage cocktails for precise crop protection measures
Secondary Supervisor(s): Professor Murray Grant, Dr Andrea Harper (University of York)
University of Registration: University of Warwick
BBSRC Research Themes:
Project Outline
Crop production plays a crucial role in ensuring global food security and maintaining economic stability, especially with the global population projected to reach 9.8 billion by 2050, necessitating a 70% increase in food production. Brassicas such as cabbage, broccoli, cauliflower, Brussels sprouts, and kale are significant contributors to the global diet. However, the presence of bacterial phytopathogens, particularly Xanthomonas species, poses significant threats to crops, leading to substantial economic losses. Black rot in Brassica is caused by the bacteria Xanthomonas campestris pv. campestris (Xcc), which poses substantial threats to marketable yields, economy and food production.The UK's vegetable Brassica industry, faces losses of more than 50% due to this disease. Current control strategies, such as the use of chemicals and antibiotics, face challenges such as environmental impact and the development of antimicrobial resistance. Therefore, it is crucial to develop cost-effective and sustainable strategies to protect these crops from pathogens and boost their productivity and resilience to meet future food demands.
A potential strategy for treating bacterial diseases is the development of phage biopesticides (phage therapy). Phage therapy approaches have been used for the control of both human/animal and plant pathogens. Phages are viruses that infect and kill bacteria. Phages are natural “products” already present in the environment; some phages have very narrow host ranges, thus specifically targeting only the pathogen and not the beneficial microbiome; phages can rapidly evolve, helping with the directed evolution of new genotypes and providing an element of in situ sustainability to potentially overcome bacterial resistance in real time. In plants, phage cocktails have been approved for use in agriculture and proven successful in treating and preventing plant diseases e.g. bacterial fire blight of apple. Moreover, recent advances in our knowledge of the evolutionary ecology of bacteria-phage interactions suggest that phage therapy could be successfully used to treat cherry canker.
We have isolated phages against plant pathogenic bacteria, however, understanding the following questions is instrumental in paving way toward potential use of phages in crop settings, therefore protecting against and preventing antimicrobial resistance in crop disease management strategies.
Project(s)
Project 1
1. How efficient phage therapy is in plants / Do they remain within the plant tissue or disperse? Fluorescence-labelling of phages (green fluorescent protein) and bacteria (Red fluorescent protein) will be applied to leaves via spray. The hypothesis being tested here is that phages remain within plant tissue after reducing the population of their target pathogen. Fluorescence imaging of leaves will be performed with confocal microscopy. Microscopy will be undertaken to visualize the association of phages with both their bacterial host and the plant tissues. These are all established protocols being used at the phage science group at University of Warwick. This will enable visualisation of phage dynamics over time rather than using a culturing method or PCR approach which is only quantitative, but not spatial.
2. Does phage engineering increase their efficacy? By identifying the genetic mutations in phage-bacteria interaction and the phage receptors, phages will be engineered to overcome resistance in bacteria. We will use homologous recombination, followed bymarker-based methods to develop an efficient system of engineering and constructing phage mutants. Phage mutants that target receptors on bacterial cell surface will be generated. This will help to develop phages that bacteria cannot develop resistance to and therefore can be used in phage cocktail design.
Project 2:
1. Does climate change impact phage diversity? The impact of rising temperatures on phage diversity and abundance will be tested by isolating phages from different geographical locations and monitoring their populations through virome extraction and sequencing.
2. Does diversity of microbial community differ under phage application? Impact of phage application on leaf microbial community will be tested by 16S/ITS rRNA amplicon next generation sequencing to catalogue resident bacterial/fungal OTUs and communities and to identify the impact of application of various phage cocktails. This will help with designing phage cocktail for bacterial disease management.
References
1. Greer et al. 2023, Front Microbiol, https://doi.org/10.3389/fmicb.2023.1209258.
2. Greer et al. 2024, JRSNZ, https://doi.org/10.1080/03036758.2024.2345315.
3. Timilsina et al. 2020, Nat Rev Microbiol, doi: 10.1038/s41579-020-0361-8.
4. Vicente et al. 2001, Phytopathol, doi: 10.1094/PHYTO.2001.91.5.4929-LPSN. 2024, https://lpsn.dsmz.de/genus/xanthomonas.
5. Rabiey et al. 2020, Microb Biotechnol, doi: 10.1111/1751-7915.13585.
6. Rabiey et al. 2024, Microb Biotechnol, doi: 10.1111/1751-7915.14489.
7. James et al. 2020, Curr Microbiol, doi: 10.1007/s00284-020-01952-1.
8. Grace et al. 2021, Plant Pathol, https://doi.org/10.1111/ppa.13465.
9. Wagemans et al. 2022, Annu Rev Phytopathol, doi: 10.1146/annurev-phyto-021621-114208.
