Streamlined genomes, not horizontal gene transfer, mark bacterial transitions to unfamiliar environments

Abstract

Bacterial colonization of unfamiliar environments constitutes a drastic evolutionary transition, likely altering the strength and direction of selection. This process is often assumed to increase rates of horizontal gene transfer (HGT), a major driver of bacterial adaptation. Larger genomes are thought to facilitate such adaptations by providing broader functional repertoires and more integration sites for foreign DNA. Here, we systematically test these ideas across a broad bacterial phylogeny linked to environmental transitions inferred from metagenomic data. Contrary to expectation, we find that bacteria entering new environments typically have smaller genomes and experience lower rates of HGT. The reduction in HGT is fully explained by genome size, with no residual effect of environmental transitions once size is controlled for. These findings suggest that successful bacterial colonizers rely less on genomic plasticity through HGT than previously assumed, highlighting gaps in our understanding of microbial evolutionary dynamics.