Abstract
The vast majority of surface ocean bacteria are uncultivated. Compared with their cultured relatives, they frequently exhibit a streamlined genome, reduced G+C content and distinct gene repertoire. These genomic traits are relevant to environmental adaptation, and have generally been thought to become fixed in marine bacterial populations through selection. Using single-cell genomics, we sequenced four uncultivated cells affiliated with the ecologically relevant Roseobacter clade and used a composition-heterogeneous Bayesian phylogenomic model to resolve these single-cell genomes into a new clade. This lineage has no representatives in culture, yet accounts for ∼35% of Roseobacters in some surface ocean waters. Analyses of multiple genomic traits, including genome size, G+C content and percentage of noncoding DNA, suggest that these single cells are representative of oceanic Roseobacters but divergent from isolates. Population genetic analyses showed that substitution of physicochemically dissimilar amino acids and replacement of G+C-rich to G+C-poor codons are accelerated in the uncultivated clade, processes that are explained equally well by genetic drift as by the more frequently invoked explanation of natural selection. The relative importance of drift vs selection in this clade, and perhaps in other marine bacterial clades with streamlined G+C-poor genomes, remains unresolved until more evidence is accumulated.
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Acknowledgements
We thank A Rivers, B Satinsky and B Durham for comments on an earlier version of the manuscript, P Foster for advice on P4 phylogenetic analysis, S Sharma and Y Huang for help with bioinformatics, C English for assistance with graphics, three anonymous reviewers for constructive comments and the Georgia Advanced Computing Resource Center at the University of Georgia for computational resources. This research was funded by grants from the Gordon and Betty Moore Foundation and the National Science Foundation (MCB-0702125).
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Luo, H., Swan, B., Stepanauskas, R. et al. Evolutionary analysis of a streamlined lineage of surface ocean Roseobacters. ISME J 8, 1428–1439 (2014). https://doi.org/10.1038/ismej.2013.248
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DOI: https://doi.org/10.1038/ismej.2013.248
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