Overview

Project Highlights:

  • Novel mechanisms of biocontrol
  • Plant microbiome studies
  • New peptide chemistry


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.

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.

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.

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.

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: e.m.h.wellington@warwick.ac.uk
http://www2.warwick.ac.uk/fac/sci/lifesci/people/ewellington/

Nikki Glover
Deputy Student and Academic Services Manager
School of Life Sciences
Ext. 23502