Evolutionary effects of horizontal gene transfer in bacteria, revealed through experimental adaptation.

Living organisms are equipped with various mechanisms to generate genetic diversity both from within the genome (i.e. mutations) or from outside the cell (e.g. sexual recombintion). Unlike sexual organisms, microbes cannot mate; however, they do possess the ability to acquire external DNA, a process known as horizontal gene transfer (HGT). HGT has been shown to play a major role in microbial ecology and evolution. Here we aim to utilize microbes to explore the dynamics and relative contribution of “within” and “outside the cell” genome alterations to the evolution and adaptation processes. We evolved several populations of naturally competent Bacillus subtilis, either with or without foreign DNA from diverse microbial species. Sequencing of evolved populations revealed extensive acquisition of foreign DNA. HGT occurred only from relatively close Bacilli donor DNA but not from more remote microbes. HGT occurred in bursts, whereby a single bacterial cell appears to have acquired dozens of fragments at once. Acquired segments tend to be clustered in integration “hot spots”. In addition to HGT, Bacillus subtilis genomes acquired local mutations. Many of these local mutations occurred within, and seemed to alter, the sequence of flagella proteins. Local mutations tended to occur in close proximity to foreign DNA integration sites. As for dynamics of evolution, we found that clones that appeared earlier in evolution contained only local mutations, but these were typically replaced later by clones that also contained HGT fragments. Finally, we show that while some HGT fragments could be neutral, others were adaptive and accelerated evolution.