PIF2025 - Deciphering the role of CNVs in bacterial adaptation - (PID2024-161831NA-I00)

We live in a bacterial world, bacteria have adapted to live in almost every single corner of our planet, even the most remote ones. Given their ubiquity, abundance, key role for important processes such as biogeochemical cycles, and their impact on human health, it is crucial to understand how bacteria adapt. A common mechanism of adaptation is copy number variations (CNVs), which involve the amplification or deletion of one or more genes. The amplification of genes increases the dosage of the affected gene, and therefore, its expression. CNVs are thought to be adaptive in situations where a rapid increase in expression is beneficial. However, CNVs are unstable and usually costly, which increases their chances of being lost. Because CNVs are usually transient, it is likely that their role in adaptation has been underestimated. The aim of CNVs-ADAPT is to deepen our knowledge on bacterial adaptive copy number changes by investigating their impact on adaptation in the short term and long term. To do so we will use experimental evolution to track in real-time how CNVs emerge and evolve in populations adapting to nutrient stress. We will combine experimental evolution to large-scale genome sequencing to investigate the mutations underpinning adaptation and assess the role of CNVs in driving adaptation. CNVs-ADAPT has three specific objectives: 1) Investigate the emergence and frequency of CNVs during adaptation; 2) Investigate the stability and divergence of CNVs; and 3) Study t