Towards engineering the plant microbiome: A molecular dissection of plant-bacteria-fungi interactions

Unsustainable farming practices, such as excessive fertiliser application, have caused environmental damage and led to a food system reliant on fossil fuel intensive processes. Reshaping our global food production system is central to combatting climate change and reducing global inequality.

Plant-associated microorganisms provide numerous functions for crop plants, including augmenting nutrition and suppressing plant pathogens. Understanding the mechanisms favouring proliferation of beneficial microbes and increased plant health is central to developing sustainable agriculture through microbiome engineering. These concepts can be applied to improve both pre- and post-harvest processes that will collectively reduce our requirement for unsustainable fertilisers and harmful pesticides.

Our recent work has revealed an abundant but poorly characterised group of plant bacteria possess extraordinary potential for recycling organic phosphorus back into a plant-available form, inorganic phosphate. Furthermore, these same bacteria also play a key role in helping plants fight off fungal and bacterial pathogens. Hence, they are an agronomically important group of beneficial bacteria. However, due to their highly distinct genomes, we lack understanding of the mechanisms driving their recruitment and subsequent proliferation in the plant microbiome.

Building on our recent research and funding from The Royal Society, this PhD will test the hypothesis that these plant bacteria occupy a distinct ecological niche in the plant microbiome through specialising in plant and microbial glycan (polysaccharide) utilisation, enabling their cooccurrence with other beneficial microbes and providing a synergistic benefit to the plant. The student will combine bacterial genetics, transcriptomics, proteomics, synthetic communities, high-resolution fluorescence microscopy and glycomics to build a holistic understanding of plant-microbe-microbe interactions. In addition to pushing frontiers science, these advances will enable future efforts into engineering microbiome to improve plant health and reduce agriculture’s environmental impact.