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

SGER（探索性研究小额资助）：对 Pelagibacter (SAR11) 基因组进行测序

• 批准号: 0307223
• 负责人: Stephen Giovannoni
• 金额: $ 9.96万
• 依托单位: Oregon State University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2003
• 资助国家: 美国
• 起止时间: 2003-03-15 至 2005-02-28
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0307223&HistoricalAwards=false
• 关键词: SGER; small; grant; exploratory; research

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.

本项目的目标是完成SAR11分支的海洋细菌候选Pelagibacter ubique的基因组测序和注释。SAR11进化支是在海水rRNA基因克隆文库中发现的最丰富的细菌进化支。它们占已发现的细菌16S rRNA基因的四分之一，几乎在所有调查的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SAR11，在一些样品中，它们的密度达到45万个细胞/ml。他们的生理和生态作用是不确定的，虽然他们被认为是异养的。最近，俄勒冈州立大学首次从俄勒冈州沿海海水中分离出了SAR11。菌株HTCC1062 （Pelagibacter ubique）是采用新开发的高通量培养方法获得的，该方法采用原位杂交筛选细胞阵列的新方法来寻找该生物的分离株。用于培养HTCC1062的培养基是高压灭菌的海水，在海水中，它以30小时的倍增时间呈指数增长，达到约105 - 106个细胞ml-1的密度。HTCC1062的基因组大小估计为1.54兆碱基。Diversa公司在没有联邦政府支持的情况下对基因组进行了2.0-3.0倍的测序。该提案将支持完成该基因组序列的闭合，并对其进行注释和发表。这种微生物的基因组序列将有助于揭示使SAR11进化支成为地球上最成功的微生物群之一的适应机制。我们预计HTCC1062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，该基因组序列的完成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，由国家科学基金会和农业部合作资助。