Analysis of key cyclic-di-GMP signalling systems that control wheat rhizosphere colonisation by Pseudomonas fluorescens

Lead Research Organisation: John Innes Centre
Department Name: Contracts Office

Abstract

Biocontrol agents, soil microorganisms that suppress pathogens and/or promote plant growth, represent an attractive potential alternative to chemical pesticides. Pseudomonas fluorescens functions as an effective biocontrol agent, positively affecting plant health and nutrition and exhibiting antimicrobial capabilities via the production of diverse antibiotics and through direct competition with pathogens in the rhizosphere. The effectiveness of biocontrol is directly related to the effectiveness of bacterial rhizosphere colonisation. However, the intracellular signalling pathways that control rhizosphere colonisation and communication between Pseudomonas, its plant host, and the surrounding soil microbiota are currently poorly defined.

Recent work has identified a key role for cyclic-di-GMP (cdG) signalling in the control of rhizosphere colonisation by P. fluorescens. CdG is a ubiquitous bacterial second messenger that controls processes involved in the switch between sessile, communal and motile, single-celled lifestyles. In-vitro expression technology (IVET) has identified 146 genes in the model P. fluorescens strain SBW25 that are up-regulated in the rhizosphere and phyllosphere. Our analysis of the IVET data suggests that at least seven cdG systems are specifically up-regulated in the SBW25 plant environment. In this project, we aim to functionally characterise those cdG signalling proteins that contribute to SBW25 wheat rhizosphere colonisation using a combination of genetics, molecular microbiology, cell biology and biochemical approaches. We will determine the effects of these cdG systems on global gene expression during colonisation with soil microarrays, and identify the cdG output systems that function during rhizosphere colonisation. Finally, we will analyse the interactions between different cdG-related systems, and how they coordinate their activities to effect an integrated colonisation response.

Publications

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Grenga L (2017) Quick change: post-transcriptional regulation in Pseudomonas in FEMS Microbiology Letters

 
Description We have mapped the expression of several signalling pathways that control colonisation of plants by beneficial microbes. We show how these signalling proteins control plant colonisation and determine their relative importance for the control of different plant-interaction phenotypes.

Based on our fundamental research into how plant bacteria colonise and infect their host plants and animals, we have identified and characterised potential new antimicrobial drug targets in the important human pathogen P. aeruginosa, and the plant pathogenic P. syringae. This research is still at the fundamental stage, but ultimately could lead to the development of new anti-infective drugs, and/or plant protection products that will replace harmful pesticides in the future.

By looking at the population of a key soil microbe and examining how it changes with the environment, we have identified important pathways for plant colonisation, including a number of potentially useful antimicrobial gene clusters. By increasing our understanding of how changes in the plant/soil environment affects important bacterial populaitons, we hope to improve the consistency of farming techniques and enable a reduction in agricultural inputs.
Exploitation Route These findings could be used in the pharma industry to develop new antimicrobials that target pathogen infectivity, rather than killing bacteria outright. This in turn would delay the rise of antibiotic resistance, and prolong the useful lifetime of the drug.

As our findings apply to both plant and human pathogens, there is also potential for this work to be exploited to produce new plant-protection compounds.

Our soil microbiology research is looking promising as a way to identify new, biologically relevant antimicrobial compounds. We also hope to use the findings of this work to improve agronomic advice to farmers, by increasing the consistency of suppressive soil generation and reducing inputs such as water and fertilisers.
Sectors Agriculture, Food and Drink,Environment,Healthcare,Pharmaceuticals and Medical Biotechnology

URL http://jic.ac.uk/directory/jacob-malone/
 
Description BBSRC NProNet Proof of Concept grant
Amount £54,544 (GBP)
Funding ID POC021 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 07/2016 
End 12/2016
 
Description DTP PhD Studentship
Amount £76,000 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 10/2013 
End 09/2017
 
Description DTP PhD Studentship
Amount £76,000 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 10/2017 
End 09/2021
 
Description DTP PhD Studentship
Amount £76,000 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 10/2015 
End 09/2019
 
Description iCASE PhD Studentship
Amount £80,000 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 07/2017 
End 09/2021
 
Description Formal Research collaboration - Rafael Rivilla, Marta Martin and Jacob Malone 
Organisation Autonomous University of Madrid
Country Spain 
Sector Academic/University 
PI Contribution My research group has provided technical advice and support for the biochemistry of cyclic-di-GMP signalling analysis in Pseudomonas, including protein-nucleotide binding assays, ITC, nucleotide quantificaiton by LC/MS. We have hosted two researchers for summer visits to JIC
Collaborator Contribution My research partners are conducting molecular microbiology experiments into Pseudomonas fluorescens plant colonisation, that are informed by the biochemistry from my lab.
Impact One paper has been published so far from this collaboration: Muriel C., Arrebola E., Redondo-Nieto M., Martínez-Granero F., Jalvo B., Pfeilmeier S., Blanco-Romero E., Baena I., Malone J. G., Rivilla R., Martín M. (2018) AmrZ is a major determinant of c-di-GMP levels in Pseudomonas fluorescens F113. Scientific reports 8 p1979
Start Year 2015
 
Description Population genomics of the take-all/wheat/Pseudomonas biosphere 
Organisation Rothamsted Research
Country United Kingdom 
Sector Academic/University 
PI Contribution My team works closely with Dr Tim Mauchline and Prof Kim Hammond Kosack at RR to examine the population structure of Pseudomonas fluorescens isolates in wheat fields that have been infected with the pathogenic fungal disease take-all. We hope to understand the microbiological underpinnings of the phenomenon of take-all suppressive soils.
Collaborator Contribution Prof Hammond-Kosack provides access to her ongoing wheat field trial sites. Dr Mauchline isolates Pseudomonas and other soil microbial samples and does much of the phylogenetic analysis and plant-microbe assays associated with the study.
Impact To date, we have published two research papers (TH Mauchline, et al. Environmental microbiology 17 (11), 4764-4778, and DD Nguyen, et al. Nature Microbiology 2 (1), 16197) and a review (see URL above) based on this collaboration. A PhD student is now working on downstream elements of this project, and we have applied for follow-on research funding.
Start Year 2013
 
Description Educational film (UEA) 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Schools
Results and Impact Contributed to an educational film showing A-level students how mathematics is used in the world of science.
Year(s) Of Engagement Activity 2016