description
- Food producers face the global challenge of sustainably enhancing agricultural production. Increased production of nutrient dense crops is needed to feed the growing global population. However, chemical inputs must be reduced, and valuable resources, such as water, must be better managed to minimise adverse environmental impacts, including climate pollution, while restoring soil fertility. Microbes in the soil are essential for soil health and function. Plant growth promoting rhizobia (PGPR) grow in the rhizosphere and make nutrients available for plants, and produce molecules that stimulate root development, to enhance growth and resilience. In return, plants secrete molecules through their roots that are used by bacteria, hence forming a mutualistic relationship. The ubiquitous PGPR, Azospirillum, adapted to plant association by acquiring traits from soil microbes on mobile genetic elements (MGEs), which are pieces of DNA that move horizontally between bacteria. MGE acquisition can accelerate bacterial evolution, but they can also be costly to the host, so bacteria carry defence systems to limit MGE uptake. Azospirillum strains vary in the number and type of defence systems, but the role of defences in azospirilla genome evolution and crucially, how they affect plant growth promotion, has not been studied. My proposed research will use bioinformatics, molecular biology and plant experiments to determine how bacterial defence systems affect Azospirillum genome evolution. Since wheat is an important crop in the UK, I will isolate azospirilla from the rhizosphere of wheat grown in diverse UK soils. I will sequence the genomes and use bioinformatics pipelines and dedicated predictor tools to assess the abundance and diversity of MGEs present in my isolates and other related Azospirillum. To predict how defence systems may influence MGE uptake, I will quantify the number and types of defences present and perform statistical modelling to test for associations between defence system and MGE abundance. Systems associated with low MGE loads will be experimentally tested by creating mutants lacking the systems and I will perform infection assays using diverse MGEs and a range of delivery mechanisms to understand which types of MGEs are restricted by each system. It is not clear whether defences, by limiting MGE uptake, constrain the evolutionary potential of the host, or protect the genome against costly elements. To gain insight into the role systems play in azospirilla, and crucially, how the defence-MGE dynamics affect the plant growth promotion, I will perform in vitro assays for plant associated traits and plant growth experiments. I will compare the performance of the defence system knockout mutants, mutants that have acquired new MGEs and the ancestral strain. From these experiments, I will have a greater understanding of how defences shape azospirilla evolution. The proposed project will be carried out at the University of Exeter, where I will work with world-leading experts in microbial evolution, ecology and soil microbiology. Excellent mentorship, and valuable training in scientific skills and leadership, will ensure my success throughout the Fellowship and enable me to launch my independent research career. I will work with three project partners to ensure excellence in all aspects of this interdisciplinary project, including Mauchline, an expert in the wheat rhizosphere and the soil microbiome, Wisniewski-Dyé, who has vast experience in azospirilla manipulation and genomics, and Syngenta, who will perform further analysis and development of beneficial strains. Ending global hunger using sustainable agriculture is a major goal of the UN and the proposed project, to characterise azospirilla to be used for wheat growth promotion, will be a valuable contribution. Further, harnessing the soil microbiome will be a critical component of improving the success of crops, while protecting the environment for future generations.