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

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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.