Using phages as a precision tool to control pathogen abundance and virulence in the plant rhizosphere microbiome

Plant pathogenic bacteria cause considerable economic losses to food production systems. The main reason for this is that hardly any effective control methods exist to mitigate this damage. In this proposal, we will develop a predictive framework and holistic understanding of how to control plant pathogenic Ralstonia solanacearum bacterium in the plant rhizosphere microbiomes by using bacteria-specific viruses, phages. We will focus on three key aspects that make phages especially useful tools for crop protection. First, we will explore the advantage of phage specificity and test if we can 'precision edit' microbiomes by selectively targeting only the pathogen. This is important not only for the efficacy but also for the safe use of phages as they should not cause collateral damage to the surrounding microbiome in the rhizosphere. Second, we will determine the evolutionary consequences of phage selection for pathogen competitiveness and virulence using metabolic modelling and direct experimentation. While it is likely that pathogens can rapidly evolve resistance to phages, this is often costly to the pathogen. Phages could thus be used as 'evolutionary tools' to weaken the pathogen by selecting resistance adaptations that incur high metabolic burden or impair virulence gene expression. Third, we will explore if phage-mediated changes in pathogen virulence and microbiome composition predictably alter plant immune responses having potential additional beneficial effects on the plant health. Here, we will move beyond pathogen-centric view to build a holistic understanding of community-level feedbacks by systematically exploring responses in plant gene expression when challenged with phage resistant and susceptible pathogens in the absence and presence of natural rhizosphere microbiome. Finally, the most promising phages will be selected for industrial manufacturing and their biocontrol efficacy and safety validated in greenhouse trials using potato. To achieve these goals, we will bring together an interdisciplinary research team consisting of academics and industry partners experienced in ecology and evolution of phage-bacteria-plant interactions, genomics, metabolic modelling and plant transcriptomics. The proposed research is innovative, timely and pushes the boundaries of traditional crop protection to precision control of plant pathogenic bacteria in the plant rhizosphere using phages.

In this proposal, we will develop a predictive framework and holistic understanding of how to control plant pathogenic Ralstonia solanacearum bacterium in the plant rhizosphere microbiomes by using bacteria-specific viruses, phages. The aims of this project are: (A) to better understand the ecology and evolution of pathogen-phage-plant interactions in the plant rhizosphere, and (B) to use this information to develop, manufacture and validate a novel phage biocontrol application in collaboration with industry partners (iMEAN, APS Biocontrol and Fera). First, we will determine if phages can be used to 'precision control' pathogens in complex rhizosphere microbiomes and if phages are safe to the plants and non-pathogenic bacteria in the rhizosphere using lab and plant infection experiments (microbiological co-culture assays; 16S rRNA sequencing, pathogen-specific qPCR and infections using Microtom tomato model in plant growth chambers). Second, we will test if phages can be used as 'evolutionary tools' to select for less competitive and non-virulent pathogen genotypes using experimental evolution, genome-scale metabolic modelling (project partner: iMEAN) and direct validation linking mutations to pathogen competitiveness and virulence (microbiological assays for virulence trait expression; direct virulence measurements using Microtom; catabolism with Biolog assays; direct competition assays against fluorescently labelled ancestral strain). Third, we will explore if phage-mediated changes in pathogen virulence and microbiome composition predictably alter plant immune responses having potential additional beneficial effects on the plant health using plant transcriptomics (and RT-qPCR) and bacterial metatranscriptomics in factorially designed infection experiment. Finally, we will design, manufacture (project partner: APS Biocontrol) and validate phage biocontrol combinations in greenhouse experiments using potato (Project partner: Fera).

Who will benefit and why?

1. General public. Education about plant-microbe interactions is important for the public understanding of how food can be produced and protected from pathogens environmentally friendly and sustainably in the future. To promote knowledge on phage-pathogen-plant interactions, we will deliver an exhibit for the University of York's annual Festival of Ideas (year 2), where we will showcase our research for the public in York city centre. We will focus on explaining what phages are, their role in medical, agricultural and natural microbial communities and their importance for crop protection and food production. We will also present our research at the yearly Pint of Science (https://pintofscience.co.uk/) in York (year 1), an event designed to encourage the public debate of science, and Soapbox Science (year 3), which publicises the work of women in STEMM.

2. Scientific community. We will organise a related research symposium on the topic in a large international scientific conference (ESEB, ISME, SMBE, AEM) during the project. This symposium will also be used as a basis to edit a special issue on the topic in MDPI Open Access Journal Life where Friman is 'Evolution' section Editorial Board member. Findings will also be communicated by all team members at scientific meetings. Target audiences will include biologists, agronomist, mathematical modellers and biotechnologists with interests in applied microbiome research. high impact journals with a cross-disciplinary readership will be targeted to publish findings in an open-access format. Press media releases will be written and discussed with the science communications team at York upon publication. Publication fees will be covered by York Open Access Fund (https://www.york.ac.uk/library/info-for/researchers/open-access/yoaf/).

3. Crop protection and microbial inoculant industry. Friman currently collaborates with two agri-food companies, DLF Trifolium (DK) and Legume Technology (UK), through a large Danish research project, NCHAIN, to improve cattle feed production by matching specific nitrogen-fixing rhizobium bacteria with high-yield clover cultivars (PhD project supervision at York). Commercial Rhizobium inoculants are currently sold in peat carrier mixture that gives the inoculant a shelf life of two months. In the proposed project, we will develop a new approach for storing and disseminating phage products with APS Biocontrol (UK). Specifically, we will trial new lyophilisation methods to turn phages into a powder format, which can be packed in sachets and mixed with water before application. Friman already has a non-disclosure agreement in place with APS Biocontrol and meetings will be set-up with the University of York intellectual property & legal (IPL) team to assess the potential need for patents during the project.

4. The Government and Agriculture policymakers. York is the institutional lead in the N8 AgriFood initiative, an HEI- and government-funded initiative to connect academic research with wider society including businesses, policymakers and NGOs. We will work with N8 AgriFood Knowledge Exchange Fellows who are industry specialists embedded within our research teams. We will also liaise with the head of Agricultural Development at the Soil Association and present our results in one of their knowledge transfer events and develop existing links with Fera, Defra, CHAP and SASA. All activities will be advertised, disseminated and reported through the existing N8 communication mechanisms and dedicated stakeholder engagement events during the project.