Download Microbial warfare in the rhizosphere

Project proposal form – 2017 entry
Project title: Microbial warfare in the rhizosphere: the role of secreted peptides in the root zone
Host institution: University of Warwick
Theme: Anthropogenic impact and environmental sustainability
Key words: ecology of antibiotic production, natural microbiomes, plant-microbe interactions, biocontrol
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Supervisory team: Supervisory team (including institution & email address): Professor Elizabeth Wellington,
School of Life Sciences, University of Warwick, [email protected]; Dr Lijiang Song,
Department of Chemistry, University of Warwick, [email protected]; Professor Peter Hawkey,
Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham,
Birmingham Heartlands Hospital, [email protected]
Project Highlights:
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Novel mechanisms of biocontrol
Plant microbiome studies
New peptide chemistry
Overview:
The rhizosphere is an environment of intense
competition between microorganisms providing
beneficial services to the plant and gaining nutrients
from root exudates. Some bacteria have been
reported to produce biologically active metabolites
which have inhibitory effects on competitors and
these can include potential plant pathogens so benefit
the plant. Members of the phylum Bacteroidetes are
found in human, animal and plant microbiomes but
given this prevalence very little is known about their
precise role and physiology. What is clear perhaps is
the fascinating ecology of members of this group
whose gliding motility complex is unique and this is
associated with the novel Type IX Secretion System
thought to be involved in the transport of large
proteins. Members of the group have been implicated
in biological control of pathogens in the human gut
and it is clear that they play a role in controlling soil
borne plant pathogens in soil1. In addition some
biologically active peptides produced by bacteroidetes
could be implicated in beneficial effects in the plant
rhizosphere. Recent work in our group has provided
compelling evidence that nonribosomal peptide
synthetase (NRPS) genes are highly dispersed and
show distinct biogeographic distribution where
detailed analysis has shown that bacteroidetes are an
important group driving this diversity (Fig. 1)2. This
means that peptides produced by bacteroidetes in soil
and the rhizosphere are diverse and must play
important functions. The aim of this project is to study
the colonisation of the rhizosphere by introduced
flavobacterial strains and develop in situ methods to
study their growth and development. In addition we
aim to investigate the production of NRPs in vitro
and in situ to elucidate both their structure and
function.
Figure 1: OTU networks in cytoscape based on
diversity within nonribosomal peptide synthetase
adenylation domains in community DNA extracted
from different soils.
Methodology:
Initial studies will focus on elucidating the conditions
under which NRPs are produced and initiate methods
for extraction and determine approaches to resolve
their chemical structure. Proteomics will be used to
monitor gene expression and allow identification of
key NRPSs involved in biosynthesis in vitro and in
situ3. This will lead to development of methods for
monitoring prevalence and expression in the
rhizosphere. Plant pots will be used initially before
field work is established to determine colonisation of
plant rhizosphere in natural habitats in parallel with
seeding experiments in field trials. The overall
objective is to evaluate how flavobacteria colonise the
rhizosphere and determine their impact on the
natural root microbiomes when introduced at
different stages of plant growth.
Objectives
1. Determine factors regulating expression of NRPs in
flavobacterial strains.
2. Develop methods to monitor NRP expression in soil
3. Elucidate structure of key NRPs and investigate
their mode of action.
Training and skills:
CENTA students will attend 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 the student's projects and themes.
Extensive training in experimental techniques related
to molecular analysis of environmental samples will
be provided in our lab by two post-doctoral research
fellows working on related projects. This includes
developing skills in the field of chemistry and
environmental genomics involving metaproteomics.
This project will provide a unique opportunity to work
with a skilled natural product chemist in the
Chemistry Department. In addition skills in extracting
proteins from soil will be developed and a detailed
understanding of proteomics established with highly
experienced staff and academics running the
proteomics unit.
Partners and collaboration (including CASE):
The experimental expertise in Wellington lab will be
complimented by detailed expert knowledge provided
by Lijiang Song in the Chemistry Department where
there is access to state-of-the-art analytical
equipment for MS and NMR in addition to HPLC in
SLS. In Birmingham at Heartlands Hospital Professor
Hawkeye has spent over 30 years working on
antibiotic therapies for treating infections and is
knowledgible about modes of antibiotic action action.
Additional expertise in biological control will be
gained from collaborating with Syngenta who produce
inocula such a pseudomonad strains for control of
plant pathogens.
Possible timeline:
Year 1: Develop assays for peptides and define
expression in vitro.
Year 2: Study flavobacterial strains in the rhizosphere
and define conditions conducive to survival, growth
and NRP production.
Year 3: Establish interations in vitro and in soil with
rhizosphere bacteria and fungi, and determine impact
on the root microbiome.
Further reading:
1) Kolton M, Frenkel O, Elad Y, Cytryn E (2014).
Potential role of Flavobacterial gliding-motility and
type IX secretion system complex in root colonization
and plant defense. Mol Plant Microbe Interact.
27:1005-13
2) Amos GC, Borsetto C, Laskaris P, Krsek M, Berry AE,
Newsham KK, Calvo-Bado L, Pearce DA, Vallin C,
Wellington EM (2015). Designing and Implementing
an Assay for the Detection of Rare and Divergent
NRPS and PKS Clones in European, Antarctic and
Cuban Soils. PLoS One. 10: E0138327.
3) Johnson-Rollings AS, Wright H, Masciandaro G,
Macci C, Doni S, Calvo-Bado LA, Slade SE, Vallin Plou C,
Wellington EM (2016). Exploring the functional soilmicrobe interface and exoenzymes through soil
metaexoproteomics. ISME J. 8: 2148-50
4) Wilmes, P.; Bond, P. L., (2006). Metaproteomics:
studying functional gene expression in microbial
ecosystems. Trends Microbiol, 14, 92-97.
Further details:
Professor E M H Wellington
School of Life Sciences
The University of Warwick
Coventry CV4 7AL
United Kingdom
Tel: 00442476 523184
Fax: 00442476 523701
Email: [email protected]
http://www2.warwick.ac.uk/fac/sci/lifesci/people/ew
ellington/