Environmental Genome Shotgun Sequencing of the Sargasso Sea

J. Craig Venter; Karin Remington; John F. Heidelberg; Aaron L. Halpern; Doug Rusch; Jonathan A. Eisen; Dongying Wu; Ian T. Paulsen; William Nelson; William Nelson; Derrick E. Fouts; Samuel Lévy; Anthony H. Knap; Michael W. Lomas; K. Nealson; Owen White; Jeremy Peterson; Jeff Hoffman; Rachel Parsons; Holly Baden-Tillson; Cynthia Pfannkoch; Yu-Hui Rogers; Hamilton O. Smith

doi:10.1126/science.1093857

Abstract

We have applied âwhole-genome shotgun sequencingâ to microbial populations collected en masse on tangential flow and impact filters from seawater samples collected from the Sargasso Sea near Bermuda. A total of 1.045 billion base pairs of nonredundant sequence was generated, annotated, and analyzed to elucidate the gene content, diversity, and relative abundance of the organisms within these environmental samples. These data are estimated to derive from at least 1800 genomic species based on sequence relatedness, including 148 previously unknown bacterial phylotypes. We have identified over 1.2 million previously unknown genes represented in these samples, including more than 782 new rhodopsin-like photoreceptors. Variation in species present and stoichiometry suggests substantial oceanic microbial diversity.

Keywords

Shotgun sequencingBiologySargasso seaMetagenomicsGenomeAbundance (ecology)SeawaterShotgunRelative species abundanceEvolutionary biologyEcologyGeneGeneticsOceanography

MeSH Terms

ArchaeaAtlantic OceanBacteriaBacteriophagesBiodiversityComputational BiologyCyanobacteriaEcosystemEukaryotic CellsGenesArchaealGenesBacterialGenesrRNAGenomeArchaealGenomeBacterialGenomicsMolecular Sequence DataPhotosynthesisPhylogenyPlasmidsRhodopsinRhodopsinsMicrobialSeawaterSequence AnalysisDNAWater Microbiology

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Publication Info

Year: 2004
Type: article
Volume: 304
Issue: 5667
Pages: 66-74
Citations: 4323
Access: Closed

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APA Style

                            
                                
                                    J. Craig Venter, 
                                
                                    Karin Remington, 
                                
                                    John F. Heidelberg
                                
                                et al.
                            
                            (2004). 
                            Environmental Genome Shotgun Sequencing of the Sargasso Sea. 
                            Science
                            , 304
                            (5667)
                            , 66-74.
                            https://doi.org/10.1126/science.1093857
                        

Identifiers

DOI: 10.1126/science.1093857
PMID: 15001713

Data Quality

Data completeness: 81%