The Bermuda Institute for Ocean Sciences Collaboration for Ocean Processes and Ecology (BIOS-SCOPE)
This project, an interdisciplinary scientific study of microbial carbon cycling in the northwestern Sargasso Sea, is funded by Simons Foundation International (SFI). In recent BIOS-SCOPE -supported research we investigated genomes from the SAR202 clade (Landry et al., 2017). These organisms, which we discovered in the 1990's, diversified early in bacterial evolution. By studying genome sequences we were able to reconstruct hypothetical metabolic pathways that we propose evolved in ancient oceans for breaking down and oxidizing recalcitrant carbon molecules. With our BIOS-SCOPE partners we are involved today in laboratory and field research that is testing this hypothesis and elucidating final stages of dissolved organic carbon oxidation by planktonic microbes.
In other work we applied network theory to long term data from BATS and showed that these plankton communities are primarily determined by the environment, but in some phylogenetic domains Hubble's neutral theory may apply (Vergin et al., 2017).
The Sargasso Sea is a natural laboratory for studying how ocean warming influences the movement of carbon from the atmosphere to the deep sea. Here, the ocean rhythmically transitions between cool, productive winter periods when nutrients are mixed to the surface, and warm, summer periods when nutrients are scarce and chlorophyll declines to extreme lows. These seasonal oscillation, which are normal in the northwestern Sargasso Sea, help us understand how ocean biology is changing with the global expansion of thermally stratified oceans. In a recent report we described novel phytoplankton taxa were found in the Sargasso Sea and may prosper in warming oceans (Choi et al., 2017).
The North Atlantic Aerosols and Marine Ecosystems Study (NAAMES)
This project is funded by NASA to study the annual cycle of phytoplankton blooms in the North Atlantic, and their impact on the atmosphere. Our role in NAAMES is to measure plankton diversity by sequencing rRNA gene amplicons, and to analyze the data with bioinformatic methods that will emphasize the achievement of high phylogenetic resolution and placement of sequences in the taxonomic classification schemes that are widely used by plankton experts. We also work with OSU faculty member Dr. Kim Halsey to study the cycling of volatile organic compounds (VOCs) by plankton cells. Dr. Halsey's team focuses on production by phytoplankton, whereas we use the HTCL's unique capabilities to study VOC oxidation by oligotrophic marine microorganisms.
Single Cell Genome Amplification by Optofluidics
This project is the work of OSU graduate student Zach Landry in collaboration with Paul Blainey of the Broad Institute of MIT and Harvard and Stephen Quake of Stanford University. With optofluidics it is possible to sort cells based on their visible morphology and also to work with very small samples. This method has potential advantages in cost, coverage and contamination (Marcy et al., 2007a&b; Blainey et al., 2011; Youssef et al., 2011; Landry et al., 2013). An optical trap is used to sort the individual cells from a concentrated cell suspension inside the microfluidics device. At OSU a workstation of local design is being used to optimize reaction conditions and to sequence the genomes of SAR11 cells and phytoplankton from the North Atlantic. This research was supported by a grant from the Marine Microbiology Initiative of the Gordon and Betty Moore Foundation.
A microfluidics device for optical isolation and single-cell amplification by multiple displacement amplification (MDA). This device has 48 circuits that are loaded individually using the optical trap and processed in parallel. Sequencing is done off-chip.
Dissolved Organic Carbon Cycling by SAR11 Marine Bacteria
This project is focused on the Pelagibacterales, the most abundant group of bacterioplankton in the oceans. Globally, they are estimated to oxidize to CO2 between 5 and 22% of all the organic carbon produced by photosynthesis each day. The activities of bacterioplankton such as SAR11 determine the residence times of different forms of organic carbon, and ultimately shape the composition of dissolved organic pools in the oceans, which rival atmospheric CO2 in mass. Accurate and detailed information about the oceanic carbon cycle is used in models that are valued for their potential to predict and understand future changes in ocean ecosystems. This grant supports analyses of genomic data that predict the carbon oxidation functions of SAR11 cells, and supports experiements with cells in culture, where high-resolution mass spectrometry technology is applied to discover new organic carbon oxidation biochemistry. To assess the importance of SAR11 carbon oxidation functions in ocean ecosystems, this project includes four short oceanographic cruises to the Bermuda Atlantic Time-Series Study Site (BATS), in the western Sargasso Sea. On these cruises, the concentrations and oxidation rates of organic compounds will be measured, and linked to variation in planktonic SAR11 populations. This grant also supports a professional teacher development workshop, "Carbon Cycling by Marine Microorganisms," in OSU's Science and Math Investigative Learning Experiences (SMILE) Program. The SMILE program prepares minority, low income, historically underrepresented, andother educationally underserved students from rural areas to graduate from high school, enroll and succeed in higher education, and pursue STEM careers. This research supported by National Science Foundation Grant OCE-1436865.