Overview

Project Highlights:

  • Prospect for phage infecting globally dominant plant-associated bacteria
  • Characterise novel phage using genomic and metagenomic approaches
  • Assess the potential impact of phage on Methylobacterium spp physiology

Methylobacterium spp are globally significant, Methylobacterium is a genus of pink pigmented, facultative methylotrophs, members of which are able to grow using a limited set of multicarbon compounds as well as one-carbon compounds. They are ubiquitous and abundant bacteria, especially in above ground (phyllosphere) plant-associated microbiota, where they have been shown as dominant component of the microbiome. Phyllosphere populations have been shown to drive degradation of plant derived methanol and methyl halides, thus playing a significant role in cycling of volatiles that affect atmospheric chemistry.

In addition, many plant-associated Methylobacterium spp. are also known to act as plant-growth promoting bacteria due to their widespread ability to synthesise auxins, and therefore have biotechnological potential in an agricultural context. In addition to being associated with plants in the phyllosphere, Methylobacterium have also been found in a wide range of other environments, including soils, plant rhizospheres, activated sludge, freshwater (and sediment), drinking water, for instance.

Bacteriophage are the most abundant biological entity in the biosphere. Phage play a key role in controlling bacterial abundance and diversity as well as affecting bacterial evolution and horizontal gene transfer. In addition, phage have recently been shown to have important effects on bacterial physiology which can significantly influence carbon, sulphur and nitrogen cycling of infected bacteria (Perez Sepulveda 2016; doi: 10.1093/femsle/fnw158).

Given their wide distribution and environmental importance, the fact that not a single phage infecting Methylobacterium spp. has been reported to date is surprising. The prospect of isolating novel phage infecting Methylobacterium spp is therefore likely to provide new, fundamental insights into processes that affect the fitness, survival, and evolution of their hosts. The understanding of processes contributing to the regulation of the Methylobacterium population size is limited, but phages are likely to play a role. Phages infecting Methylobacterium spp. are likely to exist (and indeed prophages are present in some sequenced Methylobacterium genomes; Millard & Schäfer, unpublished), but none have been described previously. The study of Methylobacterium phage would represent a major advance in understanding Methylobacterium evolution, ecology, and such phage would potentially be useful for biotechnological exploitation.

Examples of bacteriophage infecting bacterial strains that were isolated and characterised in a previous PhD project at Warwick (Chan JZ-M, Millard AD, Mann NH and Schäfer H (2014) Comparative genomics defines the core genome of the growing N4-like phage genus and identifies N4-like Roseophage specific genes. Front. Microbiol. 5:506. doi:10.3389/fmicb. 2014.00506.)

Methodology

The main aim of this project is to isolate bacteriophages infecting isolates of Methylobacterium as there is currently not a single report of a Methylobacterium host-phage system in the literature.

Standard agar overlay of a range of existing Methylobacterium isolates already available in the lab or sourced from culture collections and collaborators to screen range of environmental samples (water, soil extracts, leaf washings etc) for presence of phages using plaque assays.

Induction of temperate (prophages) from Methylobacterium strains, e.g. using mitomycin C.

Transmission electron microscope imaging of phage particles.

Phage genome sequencing and analysis.

Virome analysis of phyllosphere/soil samples using metagenomic sequencing and bioinformatics in parallel with characterisation of microbial community diversity

Training and Skills

CENTA students are required to complete 45 days training throughout their PhD including a 10 day placement. In the first year, students will be trained as a single cohort on environmental science, research methods and core skills. Throughout the PhD, training will progress from core skills sets to master classes specific to CENTA research themes.

You will be trained in cultivation of microorganisms, isolation and characterisation of phage, the latest sequencing methodologies including library preparation and bioinformatics analysis of sequence data from high throughput sequence platforms, genome annotation and characterisation of microbial communities using high throughput amplicon sequencing of 16S rRNA genes.

Timeline

Year 1: Isolation and characterisation of Methylobacterium phage

Year 2: Genome sequencing and comparative analysis of phage

Year 3: Explore the abundance and diversity of related phage in phyllosphere and soil systems using metagenomics

Partners and collaboration (including CASE)

We have a network of colleagues in the UK and Europe and overseas with whom we have active research collaborations regarding phage biology.

Further Details

Further details of research in each of the supervisors labs can be obtained from:

Dr Hendrik Schäfer, School of Life sciences, University of Warwick, Coventry, CV4 7AL

http://www2.warwick.ac.uk/fac/sci/lifesci/people/hschaefer/

Dr Andrew Millard, Warwick Medical School, University of Warwick, Coventry, CV4 7AL

http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/millardlab/