Adaptation of an abundant Roseobacter RCA organism to pelagic systems revealed by genomic and transcriptomic analyses
Adaptation of an abundant Roseobacter RCA organism to pelagic systems revealed by genomic and transcriptomic analyses
复制标题
DOI：
10.1038/ismej.2014.134
复制
发表时间：
2015-02-01
期刊：
影响因子：
11
通讯作者：
Simon, Meinhard
中科院分区：
文献类型：
--
作者：
Voget, Sonja;Wemheuer, Bernd;Simon, Meinhard
RCA（Roseophylla clade affiliated）簇，内部16 S rRNA基因序列相似性> 98%，是海洋Roseophylla clade中最大的簇，在温带至（亚）极地海洋中最丰富，占浮游细菌总数的35%。RCA簇的第一个被描述的物种的基因组分析，Planktomarina temperata RCA 23，揭示了这个系统发育谱系是深分支内的Rosebellum进化枝。它与该分支的任何其他生物共享不超过65.7%的同源基因。该基因组是蔷薇属进化枝所有封闭基因组中最小的，表现出基因组流线型的各种特征，并包括有氧无氧光合作用（AAP）和CO氧化的基因。为了评估RCA集群的地球化学意义，我们调查了北海春季浮游植物水华。该集群占总数的5.1%，但占活跃浮游细菌的10-31%（平均18.5%）。元转录组学分析表明，温坦紫菜RCA 23基因组在盛花期转录率高达94%，但在昼夜间存在一定的差异。从挪威峡湾的宏基因组数据集和西北大西洋全球海洋取样考察站的数据集中，温度对虾RCA 23的基因组也被检索到84%和82%。在该区域中，高达6.5%的总读段定位在温带假单胞菌RCA 23的基因组上。这丰富的分类群似乎是一个主要的球员在海洋地球化学。
The RCA (Roseobacter clade affiliated) cluster, with an internal 16S rRNA gene sequence similarity of >98%, is the largest cluster of the marine Roseobacter clade and most abundant in temperate to (sub) polar oceans, constituting up to 35% of total bacterioplankton. The genome analysis of the first described species of the RCA cluster, Planktomarina temperata RCA23, revealed that this phylogenetic lineage is deeply branching within the Roseobacter clade. It shares not >65.7% of homologous genes with any other organism of this clade. The genome is the smallest of all closed genomes of the Roseobacter clade, exhibits various features of genome streamlining and encompasses genes for aerobic anoxygenic photosynthesis (AAP) and CO oxidation. In order to assess the biogeochemical significance of the RCA cluster we investigated a phytoplankton spring bloom in the North Sea. This cluster constituted 5.1% of the total, but 10-31% (mean 18.5%) of the active bacterioplankton. A metatranscriptomic analysis showed that the genome of P. temperata RCA23 was transcribed to 94% in the bloom with some variations during day and night. The genome of P. temperata RCA23 was also retrieved to 84% from metagenomic data sets from a Norwegian fjord and to 82% from stations of the Global Ocean Sampling expedition in the northwestern Atlantic. In this region, up to 6.5% of the total reads mapped on the genome of P. temperata RCA23. This abundant taxon appears to be a major player in ocean biogeochemistry.