ArticleGenome biology2013
Single-cell genomics reveal low recombination frequencies in freshwater bacteria of the SAR11 clade.
Article in Genome biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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44 citing papers in PubMed, 89 citations in OpenAlex.
- Carotenoids bind rhodopsins and act as photocycle-accelerating pigments in marine Bacteroidota.Nature microbiology · 2025Article
- Ecophysiology and global dispersal of the freshwater SAR11-IIIb genus Fontibacterium.Nature microbiology · 2025Article
- Cell type and cell signalling innovations underlying mammalian pregnancy.Nature ecology & evolution · 2025Article
- Polyhydroxybutyrate production by freshwater SAR11 (LD12).The ISME journal · 2025Article
- Integrated genomics provides insights into the evolution of the polyphosphate accumulation trait ofEnvironmental science and ecotechnology · 2024Article
- Freshwater genome-reduced bacteria exhibit pervasive episodes of adaptive stasis.Nature communications · 2024Article
- Tools for microbial single-cell genomics for obtaining uncultured microbial genomes.Biophysical reviews · 2024Review
- Geographic population structure and distinct intra-population dynamics of globally abundant freshwater bacteria.The ISME journal · 2024Article
- Genome reduction occurred in early Prochlorococcus with an unusually low effective population size.The ISME journal · 2024Article
- Origins and Evolution of NovelbioRxiv : the preprint server for biology · 2023Article
- Large-scale phylogenomics of aquatic bacteria reveal molecular mechanisms for adaptation to salinity.Science advances · 2023Article
- Postglacial adaptations enabled colonization and quasi-clonal dispersal of ammonia-oxidizing archaea in modern European large lakes.Science advances · 2023Article
- Uncultured prokaryotic genomes in the spotlight: An examination of publicly available data from metagenomics and single-cell genomics.Computational and structural biotechnology journal · 2023Review
- Long-Read-Resolved, Ecosystem-Wide Exploration of Nucleotide and Structural Microdiversity of Lake Bacterioplankton Genomes.mSystems · 2022Article
- Phylogenetic divergence and adaptation of Nitrososphaeria across lake depths and freshwater ecosystems.The ISME journal · 2022Article
- Dissecting the dominant hot spring microbial populations based on community-wide sampling at single-cell genomic resolution.The ISME journal · 2022Article
- Heterozygous, Polyploid, Giant Bacterium, Achromatium, Possesses an Identical Functional Inventory Worldwide across Drastically Different Ecosystems.Molecular biology and evolution · 2021Article
- Microbial Diversity and Phage-Host Interactions in the Georgian Coastal Area of the Black Sea Revealed by Whole Genome Metagenomic Sequencing.Marine drugs · 2020Article
- The Evolutionary Success of the Marine Bacterium SAR11 Analyzed through a Metagenomic Perspective.mSystems · 2020Article
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Authors and funding
10 authors at 6 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe 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.
resultsWe 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.
conclusionsWe 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.
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