Roots play a vital role in plant nutrition, growth and health, whose potential for crop productivity is not fully utilised. In fact, soil-induced/environmental stress (e.g. salt) and root diseases are the causes of the most devastating losses in crop production. The interface between roots and the soil (rhizosphere) is the habitat of a complex microbiota (rhizo-microbiota) and plays a crucial role for nutrient acquisition and plant stress resistance. The rhizo-microbiota contains billions of beneficial and pathogenic microbes and depending on its composition, can either support or inhibit plant growth and stress adaptation. Despite its impact on agro-ecosystems, little is understood, at the molecular and ecological level, about what controls rhizo-microbiota compositions. Our limited understanding of underlying rhizo-ecological dynamics often limits the success of direct field application of beneficial microbes. Part of the complexity of rhizo-ecological dynamics is based on secondary metabolites released by the microbes in the rhizosphere to restrict competitors or release signalling molecules to communicate and to create a favourable microenvironment. State-of-the-art sequencing and mass spectrometry (MS) techniques enable us now to identify individual members of rhizo-microbiota and analyse their metabolome and transcriptome at high resolution.

In a multidisciplinary approach, this project aims to identify microbial metabolites and genes which selectively disturb pathogenic and support mutualistic communities in the rhizosphere. Our analyses are based on customised tritrophic mutualistic and pathogenic plant root interactions. The aim is to unravel fundamental mechanisms that determine rhizo-ecological dynamics and shape beneficial rhizo-microbiota thereby providing solutions of high relevance for applied agro-science.


The project will include cutting edge liquid chromatography mass spectrometry (LC-MS) and NMR analysis to identify metabolites associated with mutualistic / pathogenic tritrophic interactions and perform RNAseq to obtain microbial transcriptomes in these interactions. For the experiments, Piriformospora indica (Pi; mutualistic fungus), Pseudomonas sp. (mutualistic bacteria) and Agrobacterium sp. (pathogenic bacteria) are used. Within the obtained data sets we will identify the microbial origin of synthesised metabolites in a bioinformatics approach. We will determine the effect of transformed (OE/KD) Pi on plant growth, on its dominance over pathogens and on shaping rhizo-microbiota of soil grown plant roots.

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. 

This work will be carried out through collaborations between the Schäfer (PI, Warwick) plant stress and symbioses lab and the Bending lab (co-I, Warwick), experts in microbiology, and the Ott lab (co-I, Warwick), experts in systems biology and data analyses. The integrated project plan represents an excellent opportunity for the student to work collaboratively and receive training in LC-MS / NMR analyses, RNA seq studies, phenotyping, transcriptome and metabolome data analyses.



Year 1: Usage of model tritrophic Pi-Pseudomonas sp.-plant root (mutualist-mutualist-plant), Pi-Agrobacterium sp.-plant root (mutualist-pathogen-plant) and Pseudomonas sp.-Agrobacterium sp.-plant root (mutualist-pathogen-plant) interaction.

RNA seq and metabolomic analyses using selected tritrophic models to identify metabolites and metabolic genes of Pi and confirm metabolite identities.

Year 2: Overexpression (OE) and knock down (KD) of metabolic genes in Pi and test the synthesis of respective metabolites by mass spectrometry.  

Year 3: Determining the effect of OE/KD in Pi on mutualistic and pathogenic tritrophic interactions and plant growth under biotic and abiotic stress. Determining the effect of OE/KD in Pi on shaping the rhizo-microbiota in Arabidopsis and barley grown in two soils (sandy soil, clay soil) by 454 pyrosequencing.

Partners and collaboration (including CASE)

The project will be embedded in the microbiology, plant-microbe interaction and systems biology community at Warwick to support further collaborations.


Further Details

Potential applicants are invited to contact Patrick Schäfer (p.schafer@warwick.ac.uk)