New Methods to Explore Mobile Genetic Elements in Bacteria

Abstract

Mobile genetic elements (MGEs) drive horizontal gene transfer, a fundamental process in bacterial evolution. They play a crucial role in the genetic diversity and adaptability of bacteria, and signifi- cantly impact both microbial ecology and human health. Despite their significance, the full extent of their diversity and the complexity of their interactions have remained largely uncharted. This work introduces two novel methods to explore MGEs. The first one, is a strategy for isolating plasmid- dependent phages, a unique set of phages that exploit plasmid-encoded conjugation proteins as re- ceptors for infecting their host bacteria. With this method, we systematically search for new plasmid- dependent phages targeting IncP and IncF plasmids. Our findings show that plasmid-dependent tec- tiviruses are common and abundant in the environment. Using our diverse collection, we showed that these tectiviruses exhibit profound differences in their host range which is associated with variation in the phage holin protein. Additionally, we isolated phages dependent on the IncF plasmid, includ- ing the first plasmid-dependent tailed phage. Finally, we discuss that some of this phage diversity is routinely missed by metaviromic analyses, underscoring the continued importance of culture-based phage discovery. The second one, consists of a computational strategy to identify CRISPR-targeted MGEs within bacterial genomes. Focusing on Salmonella enterica as a model, I investigate the spacer content and diversity within a large collection of high quality genomes. This analysis challenges pre- vious assumptions, demonstrating that the CRISPR spacers in S. enterica are diverse, and commonly target prophage regions. Overall, this work aims to advance our ability to investigate the currently unexplored diversity of MGEs, with an emphasis on leveraging high throughput methods and large data collections, with tractable and concrete systems that can ultimately be experimentally studied.