Exploring host-microbiota interactions for improved crop health and food safety

Understanding how multicellular organisms perceive microbial 'friend' or 'foe' is one of the most fascinating questions in biology. This basic concept has widespread implications: for example in agriculture, crop plants interact with a multitude of microorganisms forming a distinct community, the 'plant microbiome', which can modulate plant growth, health and development. In the last decade, advances in experimental and computational approaches have provided unprecedented insights into how plant microbiomes are assembled.

Soil is the principle source of the plant microbiome and its composition is fine-tuned by plant species- and genotype-specific mechanisms, and also impacted by plant developmental age and external factors such as crop management. Plant perception of the microbes occurs via an active series of interactions that are based on immune responses. The outcomes of the interactions can range from symptomatic disease to symbiosis and plant growth. Occasionally 'unwanted' members of the microbiome can become established and cause plant disease, or rarely, human illness. Improving our understanding of the microbiome raises the possibility of biocontrol of unwanted pathogens by the addition of specific members of the microbiome.

Agriculture is undergoing major changes to become more sustainable, for example through strategies to improve soil health and reduce inputs. Our project will contribute to sustainable agriculture and food security by characterising the three-way interaction between the microbiome, host genotype and plant immunity, for improved crop productivity & health. This will be done in a cross-disciplinary approach of microbiology, plant biology, bioinformatics and biotechnology.

The main aim of the project is to determine the interaction of the plant microbiome with plant genotype and the resulting impact on plant immunity, for beneficial outcomes. We will use horticultural species (e.g. spinach and tomato) for which multiple genotypes are available, and for which we have data on the microbiome for tomato, data on the interactions of both species with unwanted members of the microbiome (foodborne pathogens: Salmonella enterica and Escherichia coli O157:H7).

The specific questions to be addressed are:
What constitute the endogenous microbiome of healthy spinach and tomato plants?
How well does a synthetic community establish compared to the endemic microbiome over a normal growth cycle and how does the immune responses compare?
Can inoculation with a synthetic community affect establishment of unwanted pathogens in the microbiome?
To address these questions the student will embark on glasshouse and laboratory work for plant inoculations, microbiota analysis, plant defence responses, and specific microbe quantification. The student will capitalise on state of the art experimental and computational facilities available at SRUC and UoD and benefit from being embedded on existing research networks at the host institutions (UK Plant Microbiome Cryobank BBR and EU microbiome food system project CIRCLES).