ena-STUDY-Department of Evolutionary Biology and Environmental Studies-28-06-2017-15:20:36:983-339
We evolved E. coli populations conjugating to DNA donors of different E. coli strains to novel nutrients to investigate the effects of horizontal gene transfer in adaptation.
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. 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 E. coli to two novel carbon sources over several hundred generations of laboratory evolution, exposing evolving populations to various DNA donors. At 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. During adaptive evolution on the first carbon source, 4-Hydroxyphenylacetic acid (HPA), recombining populations had a clear fitness benefit, which was likely mediated by acquiring the hpa operon from the donor. In contrast, recombining populations had no such benefit during adaptive evolution on the second carbon source, butyric acid, even though they suffered fewer extinctions than non-recombining populations. Furthermore, we identified candidate de novo beneficial mutations.  The amount of DNA transferred, but not its benefit, strongly depended on the donor-recipient strain combination. To 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.
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. 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 E. coli to two novel carbon sources over several hundred generations of laboratory evolution, exposing evolving populations to various DNA donors. At 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. During adaptive evolution on the first carbon source, 4-Hydroxyphenylacetic acid (HPA), recombining populations had a clear fitness benefit, which was likely mediated by acquiring the hpa operon from the donor. In contrast, recombining populations had no such benefit during adaptive evolution on the second carbon source, butyric acid, even though they suffered fewer extinctions than non-recombining populations. Furthermore, we identified candidate de novo beneficial mutations.  The amount of DNA transferred, but not its benefit, strongly depended on the donor-recipient strain combination. To 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.