How does plasmid-chromosome crosstalk influence the spread of genes through complex microbial communities?

Context Horizontal gene transfer (HGT) is a fundamental evolutionary process whereby genetic information is transferred between different microbes on mobile genetic elements, including circular stretches of DNA known as plasmids. This process enables bacteria to gain new functions, such as virulence, antibiotic resistance and metabolism. We recently discovered that in addition to the genes that encode these functions, plasmids contain a diverse group of regulatory genes that manipulate the behaviour of the host bacterium for the plasmid’s benefit, a process known as plasmid-chromosome crosstalk (PCC). These regulatory genes act to increase host (and therefore plasmid) fitness, and dramatically increase the rate of HGT between different bacteria. Challenge Our research suggests that PCCs are widespread and important drivers of HGT that shape microbial communities in many different environments. However, despite this our current understanding of PCCs is limited. We have a poor understanding of how many PCC regulators function, or how they work together to control bacterial behaviour. The global diversity and conservation of PCC regulators, and whether they co-occur in different plasmids is currently unknown. Finally, we do not understand how PCC-driven changes in bacterial and plasmid fitness affect HGT, and the spread of plasmid-encoded functions, in complex microbial communities. Aims and objectives Our central aim is to understand how PCC influences HGT, and the consequences of this for the spread of important ecological functions through microbiomes. We will build on our extensive prior research with the soil bacterium Pseudomonas fluorescens SBW25 and the large plasmid pQBR103, to address the following interlinked objectives: 1: Using a combination of molecular microbiology and biochemistry, we will characterise the PCC regulators encoded by pQBR103, and determine how they work together to control bacterial metabolism, behaviour and HGT. 2: We will use bioinformatics to map the diversity, conservation and co-occurrence of PCC regulators on existing and newly-sequenced plasmids. 3: We will examine how PCCs control the spread of metabolic genes through complex microbial communities, by tracking an engineered plasmid with the ability to degrade plastic breakdown products. Potential applications and benefits In addition to the employed scientists, who will receive advanced technical and general training that will benefit their future careers, this project will benefit multiple areas of science, including synthetic biology, bioremediation, molecular and environmental microbiology, plasmid biology and evolutionary biology. PCC regulators are present in plasmids found in a diverse range of bacteria including human and plant pathogens. Thus, our findings will be broadly relevant to many different fields. For example, by understanding PCC, we will be better equipped to limit the spread of antimicrobial resistance genes in clinical and environmental settings. Conversely, PCC regulators may be used to drive beneficial traits, such as plastic metabolism genes, into microbiomes in contaminated environments, enabling new approaches to bioremediation. Relevance to BBSRC long-term priorities The proposal builds on our extensive recent research and momentum in this area. By generating fundamental scientific knowledge about a poorly understood area of microbiology, this work is highly relevant to the Understanding the Rules of Life BBSRC priority area. In addition, our research will improve our understanding of how important traits, such as antibiotic resistance and metabolic potential, spread through bacterial populations. As such, our findings will ultimately contribute to the development of new bioremediation processes (Renewable Resources & Clean Growth) and the Combatting Antimicrobial Resistance research priority area.