Streamlining and core genome conservation among highly divergent members of the SAR11 clade.
Streamlining and core genome conservation among highly divergent members of the SAR11 clade.
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作者：
Grote J;Thrash JC;Huggett MJ;Landry ZC;Carini P;Giovannoni SJ;Rappé MS
SAR11是一个古老而多样的异养细菌分支，在世界各地的海洋中非常丰富，它们在海洋碳循环中发挥着重要作用。系统发育的分支顺序和时空模式的细胞分布从南极海洋环境之间的相关性表明，SAR11已经演变成也许十几个或更多的专门的生态型，跨越进化距离相当于一个细菌的顺序。我们从不同的SAR11文化中分离和测序基因组，代表三个主要的谱系，包括分支的全部宽度。新的数据扩展了以前仅限于SAR11 Ia亚支的基因组进化和基因内容的观察，为该分支的起源，进化和生态学提供了更广泛的视角。我们发现小基因组在整个进化枝和一个非常高的比例的核心基因组基因（48%至56%），表明小基因组大小可能是一个祖先的特征。在其核心基因组保守水平上，SAR11的成员是离群值，是已知最保守的自由生活细菌。进化枝的共同特征包括低GC含量、高基因同线性、由rRNA基因限定的大的高变区和低数量的旁系同源物。基因组之间的差异包括磷代谢，糖酵解，C1代谢的基因，这表明营养资源利用的适应性专业化是重要的生态位划分和生态型分化的分支内。这些数据提供了支持的结论，精简选择有效的细胞复制在南极栖息地发生在整个进化和多样化的这支。SAR11进化枝是世界上最丰富的海洋微生物类群，使它们成为全球碳循环的关键参与者。对它们的生物化学和新陈代谢的了解越来越多，导致对海洋中有机碳的氧化和封存有了更机械的了解。SAR11中小基因组的发现为简化选择可以在低营养环境中驱动基因组减少的理论提供了关键支持。在文化中的分离株的研究揭示了非典型的有机营养需求，可以归因于基因组的减少，如条件营养缺陷型甘氨酸及其前体，减少硫化合物的要求，并在海洋环境中的C1化合物的广泛循环的证据。然而，要了解这些途径的遗传变异和分布以及整个群体的流线型等特征，需要对不同的SAR11代表进行分离和基因组测序，我们在这里提供了分析。
SAR11 is an ancient and diverse clade of heterotrophic bacteria that are abundant throughout the world’s oceans, where they play a major role in the ocean carbon cycle. Correlations between the phylogenetic branching order and spatiotemporal patterns in cell distributions from planktonic ocean environments indicate that SAR11 has evolved into perhaps a dozen or more specialized ecotypes that span evolutionary distances equivalent to a bacterial order. We isolated and sequenced genomes from diverse SAR11 cultures that represent three major lineages and encompass the full breadth of the clade. The new data expand observations about genome evolution and gene content that previously had been restricted to the SAR11 Ia subclade, providing a much broader perspective on the clade’s origins, evolution, and ecology. We found small genomes throughout the clade and a very high proportion of core genome genes (48 to 56%), indicating that small genome size is probably an ancestral characteristic. In their level of core genome conservation, the members of SAR11 are outliers, the most conserved free-living bacteria known. Shared features of the clade include low GC content, high gene synteny, a large hypervariable region bounded by rRNA genes, and low numbers of paralogs. Variation among the genomes included genes for phosphorus metabolism, glycolysis, and C1 metabolism, suggesting that adaptive specialization in nutrient resource utilization is important to niche partitioning and ecotype divergence within the clade. These data provide support for the conclusion that streamlining selection for efficient cell replication in the planktonic habitat has occurred throughout the evolution and diversification of this clade. The SAR11 clade is the most abundant group of marine microorganisms worldwide, making them key players in the global carbon cycle. Growing knowledge about their biochemistry and metabolism is leading to a more mechanistic understanding of organic carbon oxidation and sequestration in the oceans. The discovery of small genomes in SAR11 provided crucial support for the theory that streamlining selection can drive genome reduction in low-nutrient environments. Study of isolates in culture revealed atypical organic nutrient requirements that can be attributed to genome reduction, such as conditional auxotrophy for glycine and its precursors, a requirement for reduced sulfur compounds, and evidence for widespread cycling of C1 compounds in marine environments. However, understanding the genetic variation and distribution of such pathways and characteristics like streamlining throughout the group has required the isolation and genome sequencing of diverse SAR11 representatives, an analysis of which we provide here.