Co-occurrence drives horizontal gene transfer among marine prokaryotes

Understanding the drivers of horizontal gene transfer (HGT) is a key question in microbial evolution. While co-occurring taxa have long been appreciated to undergo HGT more often, this association is confounded with other factors, most notably their phylogenetic distance. To disentangle these factors, we analyzed 15,339 isolate and metagenome-assembled marine genomes. We identified HGT events across these genomes, and identified enrichments for functions previously shown to be prone to HGT. By mapping metagenomic reads from 1,862 ocean samples to these genomes, we also identified co-occurrence patterns and environmental associations. Although we observed an expected negative association between phylogenetic distance and HGT rates, we only detected the association between co-occurrence and phylogenetic distance when restricted to closely related taxa. This observation refines the previously reported trend to closely related taxa, rather than a consistent pattern across all taxonomic levels, at least within marine environments. In addition, we identified a significant association between co-occurrence and HGT, which remains even after controlling for phylogenetic distance and measured environmental variables. Overall, our findings demonstrate the significant influence of ecological associations in shaping marine bacterial evolution through HGT.