Single-cell genomics reveal low recombination frequencies in freshwater bacteria of the SAR11 clade
1 Department of Molecular Evolution and Science for Life Laboratory, Uppsala University, 751 24 Uppsala, Sweden
2 Computational Metagenomics, Center for Biotechnology, Bielefeld University, 335 01 Bielefeld, Germany
3 DOE Joint Genome Institute, Walnut Creek, CA 94598, USA
4 Departments of Civil and Environmental Engineering and Bacteriology, University of Wisconsin, Madison, WI 53706-1691, USA
5 Department of Ecology and Genetics, Limnology and Science for Life Laboratory, Uppsala University, 752 36 Uppsala, Sweden
6 Bigelow Laboratory for Ocean Sciences, East Boothbay, ME 04544-0380, USA
Genome Biology 2013, 14:R130 doi:10.1186/gb-2013-14-11-r130Published: 28 November 2013
The SAR11 group of Alphaproteobacteria is highly abundant in the oceans. It contains a recently diverged freshwater clade, which offers the opportunity to compare adaptations to salt- and freshwaters in a monophyletic bacterial group. However, there are no cultivated members of the freshwater SAR11 group and no genomes have been sequenced yet.
We isolated ten single SAR11 cells from three freshwater lakes and sequenced and assembled their genomes. A phylogeny based on 57 proteins indicates that the cells are organized into distinct microclusters. We show that the freshwater genomes have evolved primarily by the accumulation of nucleotide substitutions and that they have among the lowest ratio of recombination to mutation estimated for bacteria. In contrast, members of the marine SAR11 clade have one of the highest ratios. Additional metagenome reads from six lakes confirm low recombination frequencies for the genome overall and reveal lake-specific variations in microcluster abundances. We identify hypervariable regions with gene contents broadly similar to those in the hypervariable regions of the marine isolates, containing genes putatively coding for cell surface molecules.
We conclude that recombination rates differ dramatically in phylogenetic sister groups of the SAR11 clade adapted to freshwater and marine ecosystems. The results suggest that the transition from marine to freshwater systems has purged diversity and resulted in reduced opportunities for recombination with divergent members of the clade. The low recombination frequencies of the LD12 clade resemble the low genetic divergence of host-restricted pathogens that have recently shifted to a new host.