Environmental genome shotgun sequencing of the sargasso sea

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

doi:10.1126/science.1093857

Cited by 4,376Microbial Community Ecology and PhysiologyGenomics and Phylogenetic StudiesEnvironmental DNA in Biodiversity Studies

Environmental genome shotgun sequencing of the sargasso sea

Venter, J. Craig, Remington, Karin, Heidelberg, John F., Halpern, Aaron L., Rusch, Doug, Eisen, Jonathan A., Wu, Dongying, Paulsen, Ian +15 more·2004·Science

DOI 10.1126/science.1093857

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Abstract

We have applied "whole-genome shotgun sequencing" 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.

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Many aspects of intercellular and inter-species signaling, short- and long-term evolution, and regulatory programs are exercised by microbes in their natural settings and are extremely difficult to recapitulate in a controlled setting.
“Since early studies of environmental and host-associated microbial communities (Gill et al., 2006; Tyson et al., 2004; Venter et al., 2004), it has been clear that many aspects of intercellular and inter-species signaling, short- and long-term evolution, and regulatory programs are exercised by microbes in their natural settings and extremely difficult to recapitulate in a controlled setting.”
From Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3 (2021) · cites this paper as Venter et al., 2004

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“…allow the detection of novel sequences and highly diverged regions between the target species and any comparison genome, recent studies indicate that currently available microbial sequence data are too incomplete to detect the full diversity naturally occurring in microbial communities [14,32].”
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Authors: Venter, J. C., Remington, K., Heidelberg, J. F., Halpern, A. L., Rusch, D., Eisen, J. A., Wu, D., Paulsen, I., Nelson, K. E., Nelson, W., Fouts, D. E., Levy, S., Knap, A. H., Lomas, M. W., Nealson, K., White, O., Peterson, J., Hoffman, J., Parsons, R., Baden-Tillson, H., Pfannkoch, C., Rogers, Y.-H., & Smith, H. O.
Affiliations: University of Southern California (US)
The Institute for Biological Energy Alternatives, 1901 Research Boulevard, Rockville, MD 20850, USA.
Corresponding author: Venter, J. Craig
ORCID: Venter, J. Craig
Heidelberg, John F.
Halpern, Aaron L.
Eisen, Jonathan A.
Wu, Dongying
Paulsen, Ian
Nelson, William
Fouts, Derrick E.
Knap, Anthony H.
Lomas, Michael W.
White, Owen
Parsons, Rachel
Venue: Science
Publisher: American Association for the Advancement of Science (AAAS)
Published: 2004-04-02
Volume: 304
Issue: 5667
Pages: 66-74
ISSN: 0036-8075 (ISSN-L)
1095-9203
DOI: 10.1126/science.1093857
OpenAlex: W2113601822
Cited by: 4,376
References: 38
Citations by year: 2026: 61 · 2025: 64 · 2024: 89 · 2023: 82 · 2022: 109 · 2021: 146 · 2020: 139 · 2019: 127 · 2018: 192 · 2017: 160 · 2016: 165 · 2015: 219 · 2014: 246 · 2013: 215 · 2012: 262
FWCI: 274.99
Type: journal article
Language: en
Open access: closed
Locations: Science (publishedVersion)
PubMed (publishedVersion)
Topics: Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Physical Sciences › Environmental Science › Ecology › Environmental DNA in Biodiversity Studies
Keywords: Sargasso Sea, marine microbial diversity, metagenomics, whole genome shotgun sequencing, bacterial phylotypes, novel genes, gene content, microbial community composition
MeSH terms: Cyanobacteria, Archaea, Atlantic Ocean, Bacteria, Bacteriophages, Eukaryotic Cells, Genes, Bacterial, Molecular Sequence Data, Photosynthesis, Phylogeny, Plasmids, Rhodopsin, Seawater, Water Microbiology, Genome, Bacterial, Sequence Analysis, DNA, Ecosystem, Computational Biology, Genes, Archaeal, Genes, rRNA, Genome, Archaeal, Genomics, Rhodopsins, Microbial, Biodiversity

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Environmental genome shotgun sequencing of the sargasso sea

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