Prokaryotic Genomes and Diversity in Surface Ocean Waters: Interrogating the Global Ocean Sampling Metagenome
Prokaryotic Genomes and Diversity in Surface Ocean Waters: Interrogating the Global Ocean Sampling Metagenome
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DOI：
10.1128/aem.02118-08
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发表时间：
2009-04-01
影响因子：
4.4
通讯作者：
Howard, Erinn C.
中科院分区：
文献类型：
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作者：
Biers, Erin J.;Sun, Shulei;Howard, Erinn C.
Magcerer II全球海洋采样(GOS)测序工作极大地扩展了元基因组学的版图，为在全球范围内研究表层海水浮游细菌的遗传潜力提供了机会。在这里，我们描述了每个GOS站点基于栖息地的微生物多样性，包括分类群均匀度和分类群丰富度，并估计了典型的自由生活的表层海水细菌的基因组特征。在0.1-0.8微米大小的表层海水细菌中，甲型变态细菌和特别是SAR11占主导地位(分别为43%和31%)，而其他类群的比例则因海洋生境类型而异。在每种生境类型中，门丰富度的下限估计在18到59个可操作分类单位(OTU)之间。然而，在各个分类水平上，高盐度泻湖群落的OTU丰富度都相对较低，而开阔海洋群落的微生物多样性比其他任何生境都要高得多。基于同一数据集的单拷贝优生细菌基因的丰度，我们估计平均一个自由生活的表层海水细菌(大小在0.1到0.8微米之间)的基因组包含1019个基因和1.8个拷贝的16S rRNA基因，这表明与培养的细菌和来自其他生境(如土壤或酸性矿山废水)的细菌相比，这些细菌的基因组相对精简。
The Sorcerer II Global Ocean Sampling (GOS) sequencing effort has vastly expanded the landscape of metagenomics, providing an opportunity to study the genetic potential of surface ocean water bacterioplankton on a global scale. Here we describe the habitat-based microbial diversity, both taxon evenness and taxon richness, for each GOS site and estimate genome characteristics of a typical free-living, surface ocean water bacterium. While Alphaproteobacteria and particularly SAR11 dominate the 0.1- to 0.8-mu m size fraction of surface ocean water bacteria (43% and 31%, respectively), the proportions of other taxa varied with ocean habitat type. Within each habitat type, lower-bound estimates of phylum richness ranged between 18 and 59 operational taxonomic units (OTUs). However, OTU richness was relatively low in the hypersaline lagoon community at every taxonomic level, and open-ocean communities had much more microdiversity than any other habitat. Based on the abundance of single-copy eubacterial genes from the same data set, we estimate that the genome of an average free-living surface ocean water bacterium (sized between 0.1 and 0.8 mu m) contains similar to 1,019 genes and 1.8 copies of the 16S rRNA gene, suggesting that these bacteria have relatively streamlined genomes in comparison to those of cultured bacteria and bacteria from other habitats (e. g., soil or acid mine drainage).