Horizontal gene transfer rates decrease during transitions to new ecosystems

Horizontal gene transfer (HGT) is a major driver of bacterial evolution, allowing bacteria to acquire new traits from other organisms. It enables the transfer of advantageous traits, such as antibiotic resistance, which can rapidly spread across bacterial populations, affecting public health. Several studies have estimated how widespread HGT can be and suggested that environmental changes are associated with changes in the rate of HGT. It is often considered that environmental changes lead to an increase in HGT rates due to the adaptive benefits of HGT. However, previous studies have been limited to one or a few species and have often focused on specific genes of interest. Here, we systematically investigate the effect of environmental changes on the rate of HGT in a large number of bacterial genomes along a deep phylogeny. We extend the scope of use of existing state-of -the -art methods for HGT inference to infer the transition into new ecosystems and the gain of pathogenicity. Transitions to new environments are associated with a decrease in the rate of HGT, along with the strengthening of purifying selection. This decrease in HGT rates is consistent regardless of genomic relatedness between the donor and recipient. Our results are robust to the use of different methodological frameworks and have implications for understanding the evolution of bacteria and HGT rates in natural microbial communities.