High-resolution SAR11 ecotype dynamics at the Bermuda Atlantic Time-series Study site by phylogenetic placement of pyrosequences
High-resolution SAR11 ecotype dynamics at the Bermuda Atlantic Time-series Study site by phylogenetic placement of pyrosequences
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百慕大大西洋时间序列研究地点的高分辨率 SAR11 生态型动态（通过焦磷酸序列的系统发育位置）
DOI：
10.1038/ismej.2013.32
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发表时间：
2013
期刊：
影响因子：
--
通讯作者：
Giovannoni SJ
中科院分区：
文献类型：
--
作者：
Vergin KL;Beszteri B;Monier A;Thrash JC;Temperton B;Treusch AH;Kilpert F;Worden AZ;Giovannoni SJ
下一代测序技术的进步提供了更长的核苷酸序列读数，包含更多关于系统发育关系的信息。我们试图利用这些信息来了解我们在西马尾藻海的长期研究地点浮游细菌的进化和生态。开发了称为PhyloAssigner的生物信息学管道，以将焦磷酸测序读数与16 S核糖体RNA（rRNA）基因的参考多序列比对进行比对，并使用最大似然算法在参考树中分配它们的系统发育位置。在这里，我们使用这个管道来调查生态重要的SAR 11进化枝的Alphaproteobacteria。来自16 S rRNA V1-V2区域的270万个焦磷酸测序读段的组合集（代表百慕大大西洋时间序列研究（BATS）站点的9年）被质量检查并解析成综合细菌树，产生929 036个α变形菌读段。SAR 11进化枝内的系统发育结构与季节性反复出现的时空模式有关。这项分析解决了四个新的SAR 11生态型，除了五个其他已在BATS先前描述。这些数据支持了先前得出的结论，即SAR 11分支通过细分海洋水柱中的生态位空间而多样化，但新的数据揭示了一种更复杂的模式，即分支的深分支在深度地层和季节性制度中反复多样化。新的数据还揭示了在中上层存在一个未被识别的Alphaproteobacteria分支，这里命名为SMA-1（Sargasso Mesopelagic Alphaproteobacteria，第1组）。高分辨率的系统发育分析强调显着的，以前未知的，进化多样化的模式，也许是最广泛分布的异养海洋细菌分支，并强烈联系到生态系统制度。
Advances in next-generation sequencing technologies are providing longer nucleotide sequence reads that contain more information about phylogenetic relationships. We sought to use this information to understand the evolution and ecology of bacterioplankton at our long-term study site in the Western Sargasso Sea. A bioinformatics pipeline called PhyloAssigner was developed to align pyrosequencing reads to a reference multiple sequence alignment of 16S ribosomal RNA (rRNA) genes and assign them phylogenetic positions in a reference tree using a maximum likelihood algorithm. Here, we used this pipeline to investigate the ecologically important SAR11 clade of Alphaproteobacteria. A combined set of 2.7 million pyrosequencing reads from the 16S rRNA V1–V2 regions, representing 9 years at the Bermuda Atlantic Time-series Study (BATS) site, was quality checked and parsed into a comprehensive bacterial tree, yielding 929 036 Alphaproteobacteria reads. Phylogenetic structure within the SAR11 clade was linked to seasonally recurring spatiotemporal patterns. This analysis resolved four new SAR11 ecotypes in addition to five others that had been described previously at BATS. The data support a conclusion reached previously that the SAR11 clade diversified by subdivision of niche space in the ocean water column, but the new data reveal a more complex pattern in which deep branches of the clade diversified repeatedly across depth strata and seasonal regimes. The new data also revealed the presence of an unrecognized clade of Alphaproteobacteria, here named SMA-1 (Sargasso Mesopelagic Alphaproteobacteria, group 1), in the upper mesopelagic zone. The high-resolution phylogenetic analyses performed herein highlight significant, previously unknown, patterns of evolutionary diversification, within perhaps the most widely distributed heterotrophic marine bacterial clade, and strongly links to ecosystem regimes.
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影响因子：
14.9
作者：
Pruesse E;Quast C;Knittel K;Fuchs BM;Ludwig W;Peplies J;Glöckner FO
通讯作者：
Glöckner FO
影响因子：
11
作者：
Carlson, Craig A.;Morris, Robert;Vergin, Kevin
通讯作者：
Vergin, Kevin
影响因子：
64.8
作者：
Margulies, M;Egholm, M;Rothberg, JM
通讯作者：
Rothberg, JM
影响因子：
12.3
作者：
Monier A;Claverie JM;Ogata H
通讯作者：
Ogata H
影响因子：
5.6
作者：
ALTSCHUL, SF;GISH, W;LIPMAN, DJ
通讯作者：
LIPMAN, DJ