The role of evolutionary refinement in horizontal gene transfer of rhizobial symbiosis genes

Rhizobia are nitrogen-fixing bacteria that form intimate, intracellular symbioses with legume plants. Rhizobia convert atmospheric nitrogen, which is inaccessible to plants, to ammonia which can be used by the plant. This relationship is vital for global nitrogen cycling and will play a key role in the move to sustainable food production as it negates the need for polluting industrial fertilisers. While much attention on rhizobia-legume interactions focuses on the efficacy of single bacterial strains, in reality, natural legumes engage in symbiosis with a large diversity of rhizobia strains. Processes that underlie the diversity within rhizobia populations are poorly understood but will be critical to the functioning of the symbiosis and the capacity for rhizobial populations to adapt to changing environments or new agricultural practices.

The transfer of DNA between individuals - known as horizontal gene transfer (HGT) - is a crucial process in bacterial evolution contributing to genome diversification. Evidence suggests that HGT is fundamental to the rhizobia-legume symbiosis; core symbiosis genes are encoded on mobile genetic elements, often plasmids (known as sym-plasmids), and show patterns of distribution indicative of regular transfer within populations. Reshuffling of sym-plasmids into different bacterial hosts generates genomic diversity within rhizobia populations as different plasmids carry sym genes. While this is likely to be beneficial at a population scale, it is challenging to explain at the individual level; Acquisition of plasmids is often costly for bacteria due to conflicts between existing and incoming DNA and HGT could disrupt beneficial associations between mobile symbiosis genes and other (non-mobile) genes in the chromosome known to be involved in the symbiosis. Such challenges can be overcome by adaptation to ameliorate conflicts or embed new genes into existing gene networks. Understanding the dynamics of sym-plasmid HGT therefore first requires us to have an understanding of what - if any - costs there are to sym-plasmid transfer, and how these can be resolved through evolution.

The aim of this project is to provide key insights into fundamental aspects of this process. We will develop a tractable model system with which to test a. How novel sym-plasmid acquisition impacts the fitness and symbiotic performance of rhizobia and b. What evolutionary processes are required to ameliorate and/or optimise this relationship.

These key insights will allow us to develop these ideas into larger research avenues. Central to this will be the development of a multi sym-plasmid/bacteria model system which will be vital to future work expanding this research field. Future work will include, for example, a detailed analysis of the mechanisms limiting sym-plasmid transfer. The outputs from this project will feed directly into this by identifying targets of selection in resolving barriers to sym-plasmid transfer. Gene knockout/knockdown experiments can then be used to investigate these targets, exploring the mechanistic basis for these barriers. Other major avenues of research will investigate the ecological drivers of sym-plasmid mobility. For example, a key hypothesis for the maintenance of sym-plasmid HGT is that rhizobial diversity is beneficial e.g. in diverse legume populations where the host environment is unpredictable. Future grants would draw on findings from this study to investigate what conditions favour the persistence of sym gene HGT.

Understanding the role of diversity, its barriers and the processes that overcome them will be important for developing strategies for legume crop production. Legumes (e.g. soya) grown outside their native ranges are inoculated with 1-2 strains of rhizobia but alternative strategies - such as increasing inoculant diversity or even 'selective breeding' of local rhizobia populations through sym gene HGT could be more effective.