Project proposal form – 2017 entry
Project title: Bacteriophage infecting ubiquitous and abundant plant-associated bacteria
Host institution: Warwick, School of Life Sciences
Theme: Organisms, -Omics, & Biogeochemistry
Key words: Methylobacterium, bacteriophage, phyllosphere, soil
Supervisory team (including institution & email address):
Dr Hendrik Schäfer ([email protected]) School of Life Sciences, University of Warwick
Dr Andrew Millard ([email protected]) Warwick Medical School, University of Warwick
Project Highlights:
& Dr Andrew Millard ([email protected])
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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
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).
Overview:
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.
Figure 1: 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.)
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.
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
sequencing of 16S rRNA genes.
amplicon
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.
Possible 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
.
Further reading:
Kelly et al 2014; The Prokaryotes; DOI 10.1007/978-3642-30197-1_256).
Vorholt
2012,
Nature
doi:10.1038/nrmicro2910.
Rev.
Microbiol;
Schäfer, H. et al. 2007. Bacterial cycling of methyl
halides. In: Ed. Laskin, A.I., Sariaslani, S., and G. Gadd
(eds.), Adv. Appl. Microbiol. 61, 307-346. DOI:
10.1016/S0065-2164(06)61009-5.
Chan, J.Z-M., Millard, A.D., Mann, N.H. and H. Schäfer.
2014. 'Comparative genomics defines the core
genome of the growing N4-like phage genus and
identifies N4-like Roseophage specific genes.'
Frontiers Microbiol. 5, article 506, 1-14. doi:
10.3389/fmicb.2014.00506
Perez Sepulveda et al, 2016. ‘ Marine phage genomics:
the tip of the iceberg’ FEMS letters 365, 5 doi
10.1093/femsle/fnw158
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/hsc
haefer/
Dr Andrew Millard, Warwick Medical School,
University of Warwick, Coventry, CV4 7AL
http://www2.warwick.ac.uk/fac/med/research/tsm/
microinfect/staff/millardlab/