Journal
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
Volume 110, Issue 28, Pages 11463-11468Publisher
NATL ACAD SCIENCES
DOI: 10.1073/pnas.1304246110
Keywords
comparative genomics; marine microbiology; microbial ecology; microbial; microevolution; operational taxonomic unit
Categories
Funding
- National Science Foundation [EF-826924, OCE-821374, OCE-1232982]
- US Department of Energy (DOE) [CSP 387]
- Gordon and Betty Moore Foundation
- Spanish Ministry of Science and Innovation [CGL2011-26848/BOS]
- CONSOLIDER-INGENIO Program [CSD2008-00077]
- Natural Sciences and Engineering Research Council of Canada (NSERC)
- Canada Foundation for Innovation
- Canadian Institute for Advanced Research (CIFAR)
- Australian Research Council
- Australian Antarctic Science program
- DOE's Office of Science [DE-AC02-05CH11231]
- Division Of Ocean Sciences
- Directorate For Geosciences [1232982] Funding Source: National Science Foundation
- Div Of Biological Infrastructure
- Direct For Biological Sciences [1226726] Funding Source: National Science Foundation
Ask authors/readers for more resources
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.
Authors
I am an author on this paper
Click your name to claim this paper and add it to your profile.
Reviews
Recommended
No Data Available