Prevalent genome streamlining and latitudinal divergence of planktonic bacteria in the surface ocean

Swan BK, Tupper B, Sczyrba A, Lauro FM, Martinez-Garcia M, González JM, Luo H, Wright JJ, Landry ZC, Hanson NW, Thompson BP, et al. (2013)
Proceedings of the National Academy of Sciences of the United States of America 110(28): 11463-11468.

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Abstract
Planktonic bacteria dominate surface ocean biomass and influence global biogeochemical processes, but remain poorly characterized owing to difficulties in cultivation. Using large-scale single cell genomics, we obtained insight into the genome content and biogeography of many bacterial lineages inhabiting the surface ocean. We found that, compared with existing cultures, natural bacterioplankton have smaller genomes, fewer gene duplications, and are depleted in guanine and cytosine, noncoding nucleotides, and genes encoding transcription, signal transduction, and noncytoplasmic proteins. These findings provide strong evidence that genome streamlining and oligotrophy are prevalent features among diverse, free-living bacterioplankton, whereas existing laboratory cultures consist primarily of copiotrophs. The apparent ubiquity of metabolic specialization and mixotrophy, as predicted from single cell genomes, also may contribute to the difficulty in bacterioplankton cultivation. Using metagenome fragment recruitment against single cell genomes, we show that the global distribution of surface ocean bacterioplankton correlates with temperature and latitude and is not limited by dispersal at the time scales required for nucleotide substitution to exceed the current operational definition of bacterial species. Single cell genomes with highly similar small subunit rRNA gene sequences exhibited significant genomic and biogeographic variability, highlighting challenges in the interpretation of individual gene surveys and metagenome assemblies in environmental microbiology. Our study demonstrates the utility of single cell genomics for gaining an improved understanding of the composition and dynamics of natural microbial assemblages.
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Swan BK, Tupper B, Sczyrba A, et al. Prevalent genome streamlining and latitudinal divergence of planktonic bacteria in the surface ocean. Proceedings of the National Academy of Sciences of the United States of America. 2013;110(28):11463-11468.
Swan, B. K., Tupper, B., Sczyrba, A., Lauro, F. M., Martinez-Garcia, M., González, J. M., Luo, H., et al. (2013). Prevalent genome streamlining and latitudinal divergence of planktonic bacteria in the surface ocean. Proceedings of the National Academy of Sciences of the United States of America, 110(28), 11463-11468.
Swan, B. K., Tupper, B., Sczyrba, A., Lauro, F. M., Martinez-Garcia, M., González, J. M., Luo, H., Wright, J. J., Landry, Z. C., Hanson, N. W., et al. (2013). Prevalent genome streamlining and latitudinal divergence of planktonic bacteria in the surface ocean. Proceedings of the National Academy of Sciences of the United States of America 110, 11463-11468.
Swan, B.K., et al., 2013. Prevalent genome streamlining and latitudinal divergence of planktonic bacteria in the surface ocean. Proceedings of the National Academy of Sciences of the United States of America, 110(28), p 11463-11468.
B.K. Swan, et al., “Prevalent genome streamlining and latitudinal divergence of planktonic bacteria in the surface ocean”, Proceedings of the National Academy of Sciences of the United States of America, vol. 110, 2013, pp. 11463-11468.
Swan, B.K., Tupper, B., Sczyrba, A., Lauro, F.M., Martinez-Garcia, M., González, J.M., Luo, H., Wright, J.J., Landry, Z.C., Hanson, N.W., Thompson, B.P., Poulton, N.J., Schwientek, P., Acinas, S.G., Giovannoni, S.J., Moran, M.A., Hallam, S.J., Cavicchioli, R., Woyke, T., Stepanauskas, R.: Prevalent genome streamlining and latitudinal divergence of planktonic bacteria in the surface ocean. Proceedings of the National Academy of Sciences of the United States of America. 110, 11463-11468 (2013).
Swan, Brandon K., Tupper, Ben, Sczyrba, Alexander, Lauro, Federico M., Martinez-Garcia, Manuel, González, José M., Luo, Haiwei, Wright, Jody J., Landry, Zachary C., Hanson, Niels W., Thompson, Brian P., Poulton, Nicole J., Schwientek, Patrick, Acinas, Silvia G., Giovannoni, Stephen J., Moran, Mary Ann, Hallam, Steven J., Cavicchioli, Ricardo, Woyke, Tanja, and Stepanauskas, Ramunas. “Prevalent genome streamlining and latitudinal divergence of planktonic bacteria in the surface ocean”. Proceedings of the National Academy of Sciences of the United States of America 110.28 (2013): 11463-11468.
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