1] Department of Microbiology, Oregon State University, Corvallis, OR, USA [2] Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA.
Department of Microbiology, Oregon State University, Corvallis, OR, USA.
ISME J. 2014 Jul;8(7):1440-51. doi: 10.1038/ismej.2013.243. Epub 2014 Jan 23.
Bacterioplankton of the SAR11 clade are the most abundant microorganisms in marine systems, usually representing 25% or more of the total bacterial cells in seawater worldwide. SAR11 is divided into subclades with distinct spatiotemporal distributions (ecotypes), some of which appear to be specific to deep water. Here we examine the genomic basis for deep ocean distribution of one SAR11 bathytype (depth-specific ecotype), subclade Ic. Four single-cell Ic genomes, with estimated completeness of 55%-86%, were isolated from 770 m at station ALOHA and compared with eight SAR11 surface genomes and metagenomic datasets. Subclade Ic genomes dominated metagenomic fragment recruitment below the euphotic zone. They had similar COG distributions, high local synteny and shared a large number (69%) of orthologous clusters with SAR11 surface genomes, yet were distinct at the 16S rRNA gene and amino-acid level, and formed a separate, monophyletic group in phylogenetic trees. Subclade Ic genomes were enriched in genes associated with membrane/cell wall/envelope biosynthesis and showed evidence of unique phage defenses. The majority of subclade Ic-specfic genes were hypothetical, and some were highly abundant in deep ocean metagenomic data, potentially masking mechanisms for niche differentiation. However, the evidence suggests these organisms have a similar metabolism to their surface counterparts, and that subclade Ic adaptations to the deep ocean do not involve large variations in gene content, but rather more subtle differences previously observed deep ocean genomic data, like preferential amino-acid substitutions, larger coding regions among SAR11 clade orthologs, larger intergenic regions and larger estimated average genome size.
SAR11 丛的细菌浮游生物是海洋系统中最丰富的微生物，通常代表全球海水中总细菌细胞的 25%或更多。SAR11 分为具有明显时空分布（生态型）的亚群，其中一些似乎是深海特有的。在这里，我们研究了一个 SAR11 深海型（特定深度的生态型）、Ic 亚群的基因组基础，该亚群从 ALOHA 站的 770 米处分离出四个估计完整性为 55%-86%的单细胞 Ic 基因组，并与 8 个 SAR11 表层基因组和宏基因组数据集进行了比较。Ic 亚群的基因组在透光层以下的宏基因组片段招募中占主导地位。它们具有相似的 COG 分布、高局部同线性，并与 SAR11 表层基因组共享大量（69%）的直系同源簇，但在 16S rRNA 基因和氨基酸水平上存在差异，并在系统发育树中形成一个单独的单系群。Ic 亚群的基因组富含与膜/细胞壁/包膜生物合成相关的基因，并显示出独特噬菌体防御的证据。Ic 亚群的大多数特定基因是假设的，并且在深海宏基因组数据中高度丰富，这可能掩盖了生态位分化的机制。然而，有证据表明这些生物具有与它们的表层对应物相似的新陈代谢，并且 Ic 亚群对深海的适应并不涉及基因内容的大变化，而是更多细微的差异，这些差异之前在深海基因组数据中观察到，例如优先氨基酸替换、SAR11 丛的直系同源物中更大的编码区域、更大的基因间区域和更大的估计平均基因组大小。
