Environmental Genome Shotgun Sequencing of the Sargasso Sea

American Association for the Advancement of Science (AAAS) - Tập 304 Số 5667 - Trang 66-74 - 2004
J. Craig Venter1,2,3,4,5, Karin Remington1,2,3,4,5, John F. Heidelberg1,2,3,4,5, Daniel L. Halligan1,2,3,4,5, Doug Rusch1,2,3,4,5, Jonathan A. Eisen1,2,3,4,5, Dongying Wu1,2,3,4,5, Ian T. Paulsen1,2,3,4,5, William Nelson1,2,3,4,5, Derrick E. Fouts1,2,3,4,5, Samuel Lévy1,2,3,4,5, Anthony H. Knap1,2,3,4,5, Michael W. Lomas1,2,3,4,5, K. Nealson1,2,3,4,5, Owen White1,2,3,4,5, Jeremy Peterson1,2,3,4,5, Jeff Hoffman1,2,3,4,5, Rachel Parsons1,2,3,4,5, Holly Baden-Tillson1,2,3,4,5, Cynthia Pfannkoch1,2,3,4,5, Yu-Hui Rogers1,2,3,4,5, Hamilton O. Smith1,2,3,4,5
1The Center for the Advancement of Genomics, 1901 Research Boulevard, Rockville, MD 20850, USA.
2The Institute for Biological Energy Alternatives, 1901 Research Boulevard, Rockville, MD 20850, USA.
3The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA
4The J. Craig Venter Science Foundation Joint Technology Center, 5 Research Place, Rockville, MD 20850, USA.
5University of Southern California, 223 Science Hall, Los Angeles, CA 90089–0740, USA.

Tóm tắt

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.

Từ khóa


Tài liệu tham khảo

10.1126/science.289.5486.1902

10.1128/AEM.66.6.2541-2547.2000

M. H. Conte, Oceanus40, 15 (1998).

10.1016/S0967-0645(00)00148-X

Materials and Methods are available as supporting online material (SOM) on Science Online.

10.1126/science.287.5461.2196

10.1016/S0168-9525(00)89076-9

10.1038/nbt749

For example Burkholderia may be the only well-represented genus of β-Proteobacteria with highly distinctive GC content whereas there may be many different γ-Proteobacteria.

These putative strains can be easily separated posthoc by reassembly with more stringent overlap criteria. See SOM for details.

10.1038/nature01947

10.1128/aem.60.9.3212-3219.1994

Searches were performed on the sequences longer than 40 bp with BLASTx against the entire nraa data set archived at GenBank.

10.1093/nar/gkg095

10.2216/i0031-8884-34-4-285.1

10.1046/j.1529-8817.1999.3520368.x

10.1093/nar/gkg039

10.3354/ame030019

10.1128/AEM.66.4.1328-1333.2000

A. Chao, Scand. J. Stat.11, 265 (1984).

10.1073/pnas.142680199

S. Giovanonni, M. S. Rappe, in Microbial Ecology of the Oceans, D. L. Kirchman, Ed. (Wiley, New York, 2000), pp. 47–84.

10.1038/nature00917

J. Raymont Plankton and Productivity in the Oceans (William Clowes Limited London ed. 2 1980).

T. Parsons M. Takahashi B. Hargrave Biological Oceanographic Processes (BPCC Wheatons Ltd. Exeter UK ed. 3 1984).

10.1128/aem.33.5.1225-1228.1977

10.1007/s002489900044

10.1126/science.235.4789.689

10.4319/lo.1993.38.5.0924

10.1016/S0079-6611(02)00138-6

K. H. Nealson J. Scott in The Prokaryotes: An Evolving Electronic Resource for the Microbiological Community E. A. Dworkin Ed. (Springer-Verlag NY 2003).

10.1111/j.1751-0813.2000.tb10593.x

The criteria for this filtering were that more than 50% of the assembly had a database hit and more than 30% of the sequence had the best hit to archaeal gene sequences.

10.1128/jb.178.3.591-599.1996

10.1073/pnas.202488399

10.1038/343060a0

10.1016/S0967-0637(01)00027-9

10.1126/science.289.5486.1902

10.1073/pnas.2133554100

10.1038/35081051

10.1046/j.1462-2920.2003.00493.x

10.3354/meps141193

10.3354/meps141183

10.1038/nature01943

10.1128/aem.63.6.2411-2420.1997

10.1023/A:1003742528262

The authors would like to acknowledge P. Lethaby M. Roadman D. Clougherty N. Buck J. Selengut A. Delcher M. Pop H. Koo R. Doering M. Wu J. Badger K. Moffat S. Yooseph E. Kirkness D. Karl K. Heidelberg B. Friedman H. Kowalski and the staff of the J. Craig Venter Science Foundation Joint Technology Center. We also acknowledge the help of N. Nelson at UCSB-ICESS for assistance in acquiring the satellite image in Fig. 1 Further we acknowledge the NSF Division of Ocean Sciences for its ongoing support of the BATS Program and the RV Weatherbird II and the Department of Energy Genomes to Life program for its support of K. Nealson. This research was supported by the Office of Science (B.E.R.) U.S. Department of Energy grant no. DE-FG02-02ER63453 and the J. Craig Venter Science Foundation. This is contribution No. 1646 of the Bermuda Biological Station for Research Inc.

Thông tin
Thông tin xuất bản

American Association for the Advancement of Science (AAAS)

Tập 304 Số 5667

66-74

Thông tin tác giả