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SoCoBio (Universities of Southampton, Kent, Sussex, Portsmouth and NIAB EMR)

What are rhizosphere microbial characteristics associated with healthy plants?

Primary Supervisor:  Prof Xiangming Xu, NIAB EMR
Secondary Supervisor: Dr Marc G Dumont, School of Biological Sciences, University of Southampton

Soil health has been an increasingly important issue for sustainable agriculture, particularly in terms of soil-borne pathogens and nutrient/water availability. The recent withdrawal of several broad-spectrum chemical soil-fumigants leads to increasing crop losses due to soil-borne pathogens. Soil microbial communities include numerous beneficial microbes as well as specific microbial pathogens. However, it is not clear which characteristics of soil microbial communities are related to plant health and what are possible mechanisms underlying such an association. This PhD project attempts to answer these two questions.

Over the last five years, we have collected pairs of diseased-healthy plant rhizosphere samples and used high-throughput (HTP) next-generation DNA sequencing (NGS) of rRNA gene amplicons to characterise the communities of bacteria and fungi on strawberry, beans, oak, cotton and apple. More than 300 samples have been sequenced. From these data, we have already published a number of papers separately for each plant species. For apple and oak, we also have shotgun metagenomics data as well.

The first objective for this PhD studentship is to carry out a meta-analysis of these NGS data to determine whether there are common features in microbial communities that are associated with diseased or healthy plants and, if so, characterise such features. For instance, one aspect of the meta-analysis could be the determination / comparison of microbial network relationships between disease and heathy plants at two different levels (amplicon and metagenomics sequences).

The second objective is concerned with hypothesis testing of those key features identified in the meta-analysis and studying the nature of these key features. The work will involve selectively eliminating relevant microbial groups or adding specific microbes and then studying subsequent plant development and plant-microbe interactions. Stable isotope probe may be used here to study specific plant-microbe interactions. As far as which crop is to be used, it will depend on the meta-analysis results and experimental specific requirements.