Professor Adam Eyre-Walker – University of Sussex
Dr. Franklin Nobrega – University of Southampton
Bacteria are usually regarded as clonal organisms, however they can undergo a form of sexual reproduction by the exchange of genetic material by various process including those that involve parasitic elements such as bacteriophage.
The exchange of genetic material involves 1) the exchange of genes, or parts of genes, that are already present in the genome, leading to the recombination of these genes into the acceptor genome; or 2) the transfer of genes that are not present in the genome, in a process known Horizontal Gene Transfer (HGT). Both of these processes are known to have profound consequences for bacteria, in particular in the acquisition of antibiotic resistance. Understanding these processes is therefore important for both medical and agricultural science. However, the general prevalence of these sexual processes in bacteria remains unclear. The aim of the project is to investigate the frequency of homologous recombination and HGT in bacteria through a combination of bioinformatic analyses and experiments, and to investigate their role in the adaptation of bacteria to their environment.
The project will be divided into three parts. In the first part, the student will use bioinformatic techniques to assess the frequency of HGT across diverse bacterial species, and investigate whether HGT is largely mediated by parasitic genetic elements such as bacteriophages. In the second part of the project, the student will use population genetic techniques to estimate the frequency of homologous recombination across bacterial species, and to assess how this affects the frequency of adaptative evolution. And in the third, part the student will run a novel selection experiment in which strains of Escherichia coli will be allowed to evolve either with or without phage. We will test whether phage accelerate the rate of evolution, and by sequencing determine whether phage mediated homologous recombination and HGT.