Abstract
BackgroundRecombination is widespread across the tree of life, because it helps purge deleterious mutations and creates novel adaptive traits. In prokaryotes, it often takes the form of horizontal gene transfer from a donor to a recipient bacterium. While such transfer is widespread in natural communities, its immediate fitness benefits are usually unknown. We asked whether any such benefits depend on the environment, and on the identity of donor and recipient strains. To this end, we adapted Escherichia coli to two novel carbon sources over several hundred generations of laboratory evolution, exposing evolving populations to various DNA donors.ResultsAt the end of these experiments, we measured fitness and sequenced the genomes of 65 clones from 34 replicate populations to study the genetic changes associated with adaptive evolution. Furthermore, we identified candidate de novo beneficial mutations. During adaptive evolution on the first carbon source, 4-Hydroxyphenylacetic acid (HPA), recombining populations adapted better, which was likely mediated by acquiring the hpa operon from the donor. In contrast, recombining populations did not adapt better to the second carbon source, butyric acid, even though they suffered fewer extinctions than non-recombining populations. The amount of DNA transferred, but not its benefit, strongly depended on the donor-recipient strain combination.ConclusionsTo our knowledge, our study is the first to investigate the genomic consequences of prokaryotic recombination and horizontal gene transfer during laboratory evolution. It shows that the benefits of recombination strongly depend on the environment and the foreign DNA donor.
Highlights
Recombination is widespread across the tree of life, because it helps purge deleterious mutations and creates novel adaptive traits
Experimental design Our donors and recipients are derived from E. coli K12, B, and W strains (Additional file 1: Table S1), which originated from different E. coli subspecies
E. coli K12 is unable to grow on this carbon source, but the B and W strain are able to grow in it, probably because they harbor the hpa operon [55]
Summary
Recombination is widespread across the tree of life, because it helps purge deleterious mutations and creates novel adaptive traits In prokaryotes, it often takes the form of horizontal gene transfer from a donor to a recipient bacterium. The recombination of genetic material that leads to the creation of novel and beneficial traits is achieved by different means in different organisms In prokaryotes and their communities, it is achieved through bacterial conjugation, viral transduction, and transformation. All of these processes can lead to horizontal gene transfer, a prominent mode of recombination between bacterial genomes [1,2,3]. Recent comparative studies of 2000 E. coli genomes indicate that the flexible genome may comprise thousands of different gene families, which may help E. coli to occupy a wide range of ecological niches [24]
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