2026-W16 How do bacteriophages shape microbial communities in plant environments?

PROJECT HIGHLIGHTS

  • Explores the ecological role of naturally occurring phages in shaping plant microbial community; 
  • Combines evolutionary experiments, metagenomics, and transcriptomics to study phage–microbe interactions; 
  • Generates knowledge to support sustainable microbiome-based disease management in crops. 

Overview

The plant microbiome, particularly in the phyllosphere (aboveground surfaces) and rhizosphere (rootassociated zone), plays a vital role in plant health, nutrient cycling, and disease resistance [1]. However, little is known about the ecological and evolutionary pressures shaping microbial community dynamics in these environments [2]. Bacteriophages, viruses that infect bacteria, are increasingly recognised as key drivers of microbial diversity and evolution, yet their influence in plantassociated environments remains poorly understood [3]. 

Our recent study showed that applying a phage cocktail to cherry leaves and shoots did not significantly impact microbial diversity (Figure 1) [4]. However, it remains unclear how naturally occurring phages shape microbial community structure and function in planta [5]. 

This project aims to investigate how natural phage populations influence microbial community composition, diversity, and function in the phyllosphere and rhizosphere. Using metagenomic and ampliconbased microbiome sequencing, we will characterise bacterial and viral communities across multiple crop species and environmental conditions [6]. Evolutionary experiments in controlled microcosms will be used to track phage–bacteria coevolution over time [7]. In parallel, metabolomic and transcriptomics will identify bacterial and viral genetic factors that mediate phage susceptibility and resistance in plant pathogenic bacteria, focusing on phage receptors and antiviral defence systems [8]. 

This research will provide new insights into the ecological roles of phages in plant environments and the evolutionary mechanisms that maintain microbial diversity [9]. The findings will inform sustainable plant microbiome management strategies and contribute to a broader understanding of viral ecology, aligning with the NERC remit on biodiversity, microbial resilience, and ecosystem function [10]. 

Figure 1. Alpha diversity indices of bacterial and fungal communities from cherry leaves sampled 3 and 30 days after treatment (DPT). The treatments were Pseudomonas syringae pv. syringae 9097, phage cocktail 5C, Pss combined with phage cocktail 5C, and a control. Diversity was evaluated using three indices: Chao1, estimating the total number of species per sample; Shannon’s index, reflecting community diversity (higher values indicate greater diversity); and Simpson’s index, reflecting community evenness (higher values indicate a more even community). Data adapted from Rabiey et al., 2025 [4]. 

Box plots compare bacterial (16S) and fungal (ITS) diversity across Control, 5C, Pas, and Pas+SC conditions using Chao1, Shannon, and Simpson indices. Red boxes show day 30 samples; blue boxes show DPT samples. Bacterial Chao1 values are higher at day 30 in the Control group. Fungal diversity trends are similar across conditions. The image highlights microbial diversity changes over time and treatment.

Case funding

This project is not suitable for CASE funding

Host

  • University of Warwick

Theme

  • Climate and Environmental Sustainability, Organisms and Ecosystems

Supervisors

Project investigator

Co-investigators

How to apply

Each host has a slightly different application process.
Find out how to apply for this studentship.

All applications must include the CENTA application form.
Choose your application route

  • Does the diversity of microbial communities change under phage pressure?
    Leaf and soil samples will be collected from selected crop species. Phages will be introduced into these samples, and at least six generations of evolution will be conducted. 16S and ITS rRNA amplicon sequencing, along with virome sequencing, will be used to catalogue resident bacterial and fungal ASVs and to identify bacterial and fungal pathogens, as well as phage communities, before and after phage-driven evolution. 
  • Do culturable microbes isolated under phage pressure affect pathogens and plants differently? To investigate the influence of phages on microbial communities and their potential for pathogen suppression, bacteria, fungi, and phages will be isolated from the samples. Their antagonistic activity against pathogens will be tested both individually and as microbial consortia. 
  • How do phages alter leaf chemical composition? Collected leaf samples will be analysed using untargeted metabolomics and transcriptomics to identify unique chemical signatures and gene expression profiles resulting from phage exposure. 

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, metabolomics, transcriptomic, genomics, bioinformatic and data management and statistical analysis and interpretation of large and complex data sets.  

The student will be supported to develop these skills within the SLS at Warwick, allowing the student to excel in these key 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 institution, and will provide comprehensive support for the student across all aspects of the project. The student will also have access to bioinformatic training for sequence analysis.  

Not applicable.

  • Year 1: Field experimental design and training in field data/sample collection will be completed. Samples will be collected from phyllosphere and rhizosphere environments. Evolutionary experiments will be initiated to study phage–microbe interactions. In parallel, microbial isolation and culture-based screening will be conducted to obtain bacterial, fungal, and phage isolates. 
  • Year 2: DNA extraction will be carried out for 16S rRNA and ITS amplicon sequencing to characterise bacterial and fungal communities. Virome extraction will be performed to assess viral and phage diversity. Initial bioinformatic and statistical analyses will begin. 
  • Year 3: The impact of phage evolution on plant metabolite profiles and gene expression will be investigated using untargeted metabolomics and RNA sequencing (transcriptomics). Data integration across experiments will be conducted. 
  • Year 3.5: Final data analysis will be completed. Manuscripts will be prepared for publication, and the PhD thesis will be written and submitted. 
  1. Trivedi P, Leach JE, Tringe SG, Sa T, Singh BK. Plant–microbiome interactions: from community assembly to plant health. Nat Rev Microbiol. 2020;18(11):607–621. DOI: https://doi.org/10.1038/s41579-020-0412-1 
  2. Fitzpatrick CR, Copeland J, Wang PW, et al. Assembly and ecological function of the root microbiome across angiosperm plant species. Proc Natl Acad Sci USA. 2018;115(6):E1157–E1165. DOI: https://doi.org/10.1073/pnas.1717617115 
  3. Koskella B, Brockhurst MA. Bacteria–phage coevolution as a driver of ecological and evolutionary processes in microbial communities. FEMS Microbiol Rev. 2014;38(5):916–931. DOI: https://doi.org/10.1111/1574-6976.12072 
  4. PappRupar M, Grace ER, Korotania N, Ciusa ML, Jackson RW, Rabiey M. Impact of Phage Therapy on Pseudomonas syringae pv. syringae and Plant Microbiome Dynamics Through Coevolution and Field Experiments. Environ Microbiol. 2025 Mar;27(3):e70076. DOI: https://doi.org/10.1111/1462-2920.70076  
  5. Chaturongakul S, Ounjai P, Pholwat S, et al. Phage–host interaction: an ecological perspective. J Bacteriol. 2004 Jun;186(12):3677–3686. doi: 10.1128/JB.186.12.3677-3686.2004 
  6. Mazor Y, Greenberg I, Toporik H, et al. Novel phages of Pseudomonas syringae unveil numerous potential auxiliary metabolic genes. J Gen Virol. 2024;105:001990. DOI: https://doi.org/10.1099/jgv.0.001990  
  7. Morella NM, Gomez AL, Wang G, Leung MS, Koskella B. The impact of bacteriophages on phyllosphere bacterial abundance and composition. Mol Ecol. 2018;27(8):2025–2038. DOI: https://doi.org/10.1111/mec.14542  
  8. Hampton HG, Watson BNJ, Fineran PC. The arms race between bacteria and their phage foes. Nature. 2020;577(7790):327–336. DOI: https://doi.org/10.1038/s41586-019-1894-8  
  9. Warring SL, Sisson HM, Fineran PC, Rabiey M. Strategies for the biocontrol of Pseudomonas infections prefruit harvest. Microb Biotechnol. 2024;17(3):700–712. DOI: https://doi.org/10.1111/1751-7915.70017  
  10. Fems Microbiol Ecol. The role of rhizosphere phages in soil health. FEMS Microbiol Ecol. 2024;100(5):fiae052. DOI: https://doi.org/10.1093/femsec/fiae052

Further details and How to Apply

We are not carrying out experiments on organisms that necessitate ethical or other types of approvals or licenses, other than necessary APHA compliance. There is no genetic or biological risk, as all bacteria are sourced directly from the UK natural environment. There are no plans to release genetically modified organisms during this project. This work is approved by the UoW under existing genetic manipulation and biological safety committee project reference 456. 

For any enquiries related to this project please contact Mojgan Rabiey, [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 7th January 2026.   

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