The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific.
The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific.
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DOI：
10.1371/journal.pbio.0050077
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发表时间：
2007-03
期刊：
影响因子：
9.8
通讯作者：
Venter JC
中科院分区：
文献类型：
--
作者：
Rusch DB;Halpern AL;Sutton G;Heidelberg KB;Williamson S;Yooseph S;Wu D;Eisen JA;Hoffman JM;Remington K;Beeson K;Tran B;Smith H;Baden-Tillson H;Stewart C;Thorpe J;Freeman J;Andrews-Pfannkoch C;Venter JE;Li K;Kravitz S;Heidelberg JF;Utterback T;Rogers YH;Falcón LI;Souza V;Bonilla-Rosso G;Eguiarte LE;Karl DM;Sathyendranath S;Platt T;Bermingham E;Gallardo V;Tamayo-Castillo G;Ferrari MR;Strausberg RL;Nealson K;Friedman R;Frazier M;Venter JC
世界上的海洋含有复杂的微生物混合物，其中大部分在遗传和生物化学上都没有特征。我们在这里报告的海洋浮游微生物群的宏基因组研究，其中表面（主要是海洋）的水样进行了分析，作为巫师II全球海洋采样探险的一部分。这些样本是从北大西洋通过巴拿马运河并在南太平洋结束的数千公里横断面上收集的，产生了一个由770万个测序读数（63亿bp）组成的广泛数据集。虽然几个主要的微生物分支占主导地位的海洋生态位，数据集包含了巨大的多样性与85%的组装序列和57%的未组装的数据是独特的，在98%的序列同一性截止。使用与每个样品和测序文库相关的元数据，我们开发了新的比较基因组和组装方法。一种比较基因组学方法，称为“片段募集”，解决了基因组结构、进化、分类或系统发育多样性以及基因和基因家族的生物化学多样性的问题。第二种方法被称为“极端组装”，它使得大量非克隆生物的大片段组装和重建成为可能。在分析的所有丰富的群体中，我们发现了几种形式的广泛的核糖体型内多样性：（1）在整个给定基因组的直向区域内的广泛序列变异;尽管单个核糖体型的覆盖率接近500倍，但大多数单个测序读数是独特的;（2）基因内容的许多变化，其中一些具有直接的适应性影响;和（3）高度可变的基因组岛，其变化太大而不能组装。核糖体型内的多样性被组织成遗传上孤立的种群，这些种群具有重叠但独立的分布，这意味着不同的环境偏好。我们提出了新的方法来测量宏基因组样本之间的基因组相似性，并展示了它们如何被分为几个社区类型。特定的功能适应可以在单个核糖体和整个社区中识别，包括蛋白视紫质光谱调谐和磷酸盐结合基因PstS的存在或不存在。海洋微生物仍然难以捉摸和神秘，尽管它们是海洋中最丰富的生命形式，构成海洋食物网的基础，并驱动能量和营养循环。我们对绝大多数微生物知之甚少，因为只有一小部分可以在实验室中培养和研究。在这里，我们报告了全球海洋采样考察，这是一个环境宏基因组学项目，旨在通过对海洋微生物的DNA进行测序，而无需首先分离单个生物体，从而阐明海洋微生物的作用。从8 000公里以外的各种水生生境中共采集了41个不同的样本。由此产生的770万个测序读数提供了前所未有的视角，可以看到天然存在的微生物种群中令人难以置信的多样性和异质性。我们已经开发了新的生物信息学方法来重建大部分培养和未培养的微生物基因组。生物多样性分析与采样地点和环境压力有关。总的来说，这些数据和分析为我们极大地扩展对单个微生物谱系及其进化、海洋微生物群落的性质以及它们如何受到我们世界的影响和影响的理解奠定了基础。魔法师II GOS远征，数据采样和分析进行了说明。序列数据的巨大多样性需要新的比较基因组组装方法，这揭示了基于标记的方法无法揭示的基因组差异。
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. 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. TheSorcerer 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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影响因子：
64.8
作者：
Frigaard, NU;Martinez, A;DeLong, EF
通讯作者：
DeLong, EF
影响因子：
5.1
作者：
Brown, MV;Schwalbach, MS;Fuhrman, JA
通讯作者：
Fuhrman, JA
影响因子：
56.9
作者：
Gill, Steven R.;Pop, Mihai;Nelson, Karen E.
通讯作者：
Nelson, Karen E.
影响因子：
4.5
作者：
Fuller, NJ;West, NJ;Scanlan, DJ
通讯作者：
Scanlan, DJ
影响因子：
56.9
作者：
DeLong, EF;Preston, CM;Karl, DM
通讯作者：
Karl, DM