SGER (small grant for exploratory research): Sequencing a Pelagibacter (SAR11) genome

该项目的目标是完成海洋细菌Pelagibacter ubique（SAR 11进化枝的成员）的基因组测序和注释。SAR 11进化枝是海水rRNA基因克隆文库中发现的最丰富的细菌进化枝。 它们占回收的细菌16 S rRNA基因的四分之一，并且几乎在调查的每一个海水样本中都发现了它们。 原位杂交数据表明，海洋表层平均35%的细胞是SAR 11，在某些样品中，它们的密度达到450，000个细胞/ml。 它们的生理和生态作用是不确定的，虽然它们被认为是异养生物。 SAR 11最近在俄勒冈州州立大学首次从俄勒冈州沿海海水中分离出来。菌株HTCC 1062（Pelagibacter ubique）是通过应用新开发的高通量培养程序获得的，该程序采用了通过原位杂交筛选细胞阵列的新方法来寻找该生物体的分离株。 用于培养HTCC 1062的培养基是高压灭菌的海水，其中它以30小时的倍增时间呈指数增长，达到约1000的密度。105 - 106细胞ml-1。 HTCC 1062的基因组大小估计为1.54兆碱基。 Diversa公司在没有联邦支持的情况下，将基因组测序的覆盖率提高到2.0- 3.0倍。 该提案将支持完成这一基因组序列的封闭，及其注释和出版。这种微生物的基因组序列将有助于揭示使SAR 11分支成为地球上最成功的微生物群体之一的适应机制。我们预计HTCC 1062将迅速成为研究细菌在海洋碳循环中作用的重要实验模型。因此，完成这一基因组测序将是对基础海洋科学的重要贡献。这是一个微生物基因组测序奖，通过国家科学基金会和农业部之间的合作活动资助。

The goal of this project is to complete sequencing and annotation of the genome of the marine bacterium candidatus Pelagibacter ubique, a member of the SAR11 clade. The SAR11 clade is the most abundant bacterial clade found in rRNA gene clone libraries made from seawater. They account for one quarter of the bacterial 16S rRNA genes recovered and have been found in nearly every seawater sample surveyed. In situ hybridization data demonstrate that on average 35% of the cells in the ocean surface layer are SAR11, and in some samples they reach densities of 450,000 cells/ml. Their physiology and ecological role are uncertain, although they are presumed to be heterotrophs. SAR11 was recently isolated for the first time at Oregon State University from Oregon coastal seawater. Strain HTCC1062 (Pelagibacter ubique) was obtained by the application of newly developed high throughput cultivation procedures which employed novel methods for screening cell arrays by in situ hybridization to search for isolates of this organism. The medium used for cultivation of HTCC1062 is autoclaved seawater, in which it grows exponentially with a doubling time of 30 hours to reach densities of ca. 105 - 106 cells ml-1. The genome size of HTCC1062 is estimated to be 1.54 megabases. Diversa Corporation sequenced the genome to 2.0-3.0x coverage, without federal support. This proposal would support the completion of this genome sequence to closure, and its annotation and publication. The genome sequence of this microorganism will help reveal the adaptive mechanisms that make the SAR11 clade one of the most successful microbial groups on the planet. We anticipate that HTCC1062 will rapidly become an important experimental model for studying the role of bacteria in the oceanic carbon cycle. Therefore, completion of this genome sequence will be an important contribution to basic marine science. This is a Microbial Genome Sequencing Award funded through a collaborative activity between the National Science Foundation and the Department of Agriculture.