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      The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific

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      1 , * , 1 , 1 , 1 , 2 , 1 , 1 , 1 , 3 ,   1 , 3 , 1 , 1 , 4 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 2 , 1 , 1 , 5 , 5 , 5 , 5 , 6 , 7 , 7 , 8 , 9 , 10 , 11 , 1 , 1 , 12 , 1 , 1 , 1
      PLoS Biology
      Public Library of Science
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          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          The world's oceans contain a complex mixture of micro-organisms that are for the most part, uncharacterized both genetically and biochemically. We report here a metagenomic study of the marine planktonic microbiota in which surface (mostly marine) water samples were analyzed as part of the Sorcerer II Global Ocean Sampling expedition. These samples, collected across a several-thousand km transect from the North Atlantic through the Panama Canal and ending in the South Pacific yielded an extensive dataset consisting of 7.7 million sequencing reads (6.3 billion bp). Though a few major microbial clades dominate the planktonic marine niche, the dataset contains great diversity with 85% of the assembled sequence and 57% of the unassembled data being unique at a 98% sequence identity cutoff. Using the metadata associated with each sample and sequencing library, we developed new comparative genomic and assembly methods. One comparative genomic method, termed “fragment recruitment,” addressed questions of genome structure, evolution, and taxonomic or phylogenetic diversity, as well as the biochemical diversity of genes and gene families. A second method, termed “extreme assembly,” made possible the assembly and reconstruction of large segments of abundant but clearly nonclonal organisms. Within all abundant populations analyzed, we found extensive intra-ribotype diversity in several forms: (1) extensive sequence variation within orthologous regions throughout a given genome; despite coverage of individual ribotypes approaching 500-fold, most individual sequencing reads are unique; (2) numerous changes in gene content some with direct adaptive implications; and (3) hypervariable genomic islands that are too variable to assemble. The intra-ribotype diversity is organized into genetically isolated populations that have overlapping but independent distributions, implying distinct environmental preference. We present novel methods for measuring the genomic similarity between metagenomic samples and show how they may be grouped into several community types. Specific functional adaptations can be identified both within individual ribotypes and across the entire community, including proteorhodopsin spectral tuning and the presence or absence of the phosphate-binding gene PstS.

          Author Summary

          Marine microbes remain elusive and mysterious, even though they are the most abundant life form in the ocean, form the base of the marine food web, and drive energy and nutrient cycling. We know so little about the vast majority of microbes because only a small percentage can be cultivated and studied in the lab. Here we report on the Global Ocean Sampling expedition, an environmental metagenomics project that aims to shed light on the role of marine microbes by sequencing their DNA without first needing to isolate individual organisms. A total of 41 different samples were taken from a wide variety of aquatic habitats collected over 8,000 km. The resulting 7.7 million sequencing reads provide an unprecedented look at the incredible diversity and heterogeneity in naturally occurring microbial populations. We have developed new bioinformatic methods to reconstitute large portions of both cultured and uncultured microbial genomes. Organism diversity is analyzed in relation to sampling locations and environmental pressures. Taken together, these data and analyses serve as a foundation for greatly expanding our understanding of individual microbial lineages and their evolution, the nature of marine microbial communities, and how they are impacted by and impact our world.

          Abstract

          The Sorcerer II GOS expedition, data sampling, and analysis is described. The immense diversity in the sequence data required novel comparative genomic assembly methods, which uncovered genomic differences that marker-based methods could not.

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          The Paradox of the Plankton

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            The genome sequence of the malaria mosquito Anopheles gambiae.

            Anopheles gambiae is the principal vector of malaria, a disease that afflicts more than 500 million people and causes more than 1 million deaths each year. Tenfold shotgun sequence coverage was obtained from the PEST strain of A. gambiae and assembled into scaffolds that span 278 million base pairs. A total of 91% of the genome was organized in 303 scaffolds; the largest scaffold was 23.1 million base pairs. There was substantial genetic variation within this strain, and the apparent existence of two haplotypes of approximately equal frequency ("dual haplotypes") in a substantial fraction of the genome likely reflects the outbred nature of the PEST strain. The sequence produced a conservative inference of more than 400,000 single-nucleotide polymorphisms that showed a markedly bimodal density distribution. Analysis of the genome sequence revealed strong evidence for about 14,000 protein-encoding transcripts. Prominent expansions in specific families of proteins likely involved in cell adhesion and immunity were noted. An expressed sequence tag analysis of genes regulated by blood feeding provided insights into the physiological adaptations of a hematophagous insect.
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              Comparative metagenomics of microbial communities.

              The species complexity of microbial communities and challenges in culturing representative isolates make it difficult to obtain assembled genomes. Here we characterize and compare the metabolic capabilities of terrestrial and marine microbial communities using largely unassembled sequence data obtained by shotgun sequencing DNA isolated from the various environments. Quantitative gene content analysis reveals habitat-specific fingerprints that reflect known characteristics of the sampled environments. The identification of environment-specific genes through a gene-centric comparative analysis presents new opportunities for interpreting and diagnosing environments.
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                Author and article information

                Contributors
                Role: Academic Editor
                Journal
                PLoS Biol
                pbio
                PLoS Biology
                Public Library of Science (San Francisco, USA )
                1544-9173
                1545-7885
                March 2007
                13 March 2007
                : 5
                : 3
                : e77
                Affiliations
                [1 ] J. Craig Venter Institute, Rockville, Maryland, United States of America
                [2 ] Department of Biological Sciences, University of Southern California, Avalon, California, United States of America
                [3 ] Genome Center, University of California Davis, Davis, California, United States of America
                [4 ] Your Genome, Your World, Rockville, Maryland, United States of America
                [5 ] Departmento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
                [6 ] Department of Oceanography, University of Hawaii, Honolulu, Hawaii, United States of America
                [7 ] Bedford Institute of Oceanography, Dartmouth, Nova Scotia, Canada
                [8 ] Smithsonian Tropical Research Institute, Balboa, Ancon, Republic of Panama
                [9 ] Departamento de Oceanografía, Universidad de Concepción, Concepción, Chile
                [10 ] Escuela de Química, Universidad de Costa Rica, San Pedro, Costa Rica
                [11 ] Department of Environmental Sciences, Rutgers University, New Brunswick, New Jersey, United States of America
                [12 ] Department of Earth Sciences, University of Southern California, Los Angles, California, United States of America
                University of Arizona, United States of America
                Author notes
                * To whom correspondence should be addressed. E-mail: DRusch@ 123456venterinstitute.org
                Article
                06-PLBI-RA-1263R2 plbi-05-03-22
                10.1371/journal.pbio.0050077
                1821060
                17355176
                b363f2b2-89c2-485a-9787-6a59c820082c
                Copyright: © 2007 Rusch et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
                History
                : 14 July 2006
                : 16 January 2007
                Page count
                Pages: 34
                Categories
                Research Article
                Computational Biology
                Computational Biology
                Computational Biology
                Ecology
                Evolutionary Biology
                Genetics and Genomics
                Genetics and Genomics
                Genetics and Genomics
                Genetics and Genomics
                Genetics and Genomics
                Microbiology
                Microbiology
                Microbiology
                Virology
                Eubacteria
                Archaea
                Viruses
                Oceanic Metagenomics
                Custom metadata
                Rusch DB, Halpern AL, Sutton G, Heidelberg KB, Williamson S, et al. (2007) The Sorcerer II Global Ocean Sampling expedition: Northwest Atlantic through eastern tropical Pacific. PLoS Biol 5(3): e77. doi: 10.1371/journal.pbio.0050077
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                Life sciences
                Life sciences

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