- Antarctic Permanently Ice-Covered-Lake Microbial Observatory
- Genomics of Oceanic Bacteria
- High Throughput Microbial Cultivation Lab and Collaborative Projects with HTCC Strains
- Marine Microbial Genome Sequencing Project
- Microbial Ecology of Hypoxic Zones in the Northwestern Pacific Ocean
- Ocean Lithosphere
- SAR11 Biology from the Ocean Gyres to the Double Helix
- Sargasso Sea Microbial Observatory
- The Impact of Pelagibacter on DOM Composition Under Light and Dark Conditions
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SAR11 Biology from the Ocean Gyres to the Double Helix
Recently we cultured one of the most abundant organisms on the planet, SAR11, which has been renamed Pelagibacter ubique.
SAR11 is the numerically dominant microorganism in the ocean surface. We have sequenced the 1.3Mb genome of Pelagibacter strain HTCC1062 in collaboration with Diversa Corp. Assembly and annotation were done at OSU. Two additional SAR11 strains have been sequenced by the J. Craig Venter Institute. Future plans include the sequencing of fifteen more strains, including strains isolated by collaborator Dr. Michael Rappé, by the Joint Genome Institute of the Department of Energy.
The data from this NSF, Gordon and Betty Moore Foundation, and Department of Energy sponsored project will be used to understand how SAR11 contributes to geochemical cycles. Also, because SAR11 is one of the smallest cells known, the data will be useful for understanding the basic architecture of cells and genomes.
SAR11, a highly dominant organism, undergoes regular seasonal cycles in abundance. The factors that control SAR11 populations, and other heterotrophic bacterioplankton populations, are largely unknown. Identifying these factors is essential for the formulation of predictive models for planktonic ecosystems.
We have shown that SAR11 cells have sensors for nitrogen, phosphate, and iron limitation, and that they have a very unusual requirement for reduced sulfur compounds. One of our top research priorities is to broadly map SAR11 regulatory networks that control adaptive responses to nutrient limitation. For this purpose, we are using a combination of quantitative proteomics (Accurate Mass and Time tags), microarrays (Affymetrix), and an in silico approach that is being developed by our bioinformatics team. This information will be used to interpret the metabolic status of natural SAR11 populations from environmental transcriptomic and proteomic data.
Multiple genome sequences also allow us to identify the range of natural variation in the SAR11 clade and to identify the physiological adaptations that make each SAR11 ecotype unique. SAR11 and other cosmopolitan clades of marine microorganisms are important models for understanding microbial evolution because of their unusually large population sizes and the background of metagenomic and oceanographic data that are available for their study. Moreover, it is of practical importance to oceanographers to define the properties of ecotypes for the purpose of modeling geochemical processes. We are studying the evolution of the SAR11 clade by sequencing fifteen additional SAR11 genomes using a combination of Sanger sequencing and pyrosequencing (454) technologies in collaboration with Dr. Mike Rappé at the Hawaii Institute for Marine Biology, University of Hawaii, Manoa. Ten of the genomes selected for study are from strains that are closely related to published SAR11 genomes, and five are from phylogenetically diverse SAR11 isolates that represent ecotype variation. Analysis of the data will be used to extend observations recently reported (Wilhelm, et al. (2007), and Vergin, et al. (2007)) showing a high rate of recombination in a coastal Oregon SAR11 population, but the conservation of many genome properties, such as gene order, in SAR11 metagenomic data.