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Courtesy of Caltech Information Science and Technology Initiative – Wierman Cray 2 Supercomputer

Grants List


Courtesy of Winn Johnson/WHOI- filtering seawater samples

Woods Hole Oceanographic Institution

Identifying and quantifying new markers of microbially mediated nutrient flow in the ocean

In support of developing new protocols to detect the products of microbial metabolism in seawater to understand the influence of marine microbial communities and their activities on the chemical composition of their surroundings.

Title: Identifying and quantifying new markers of microbially mediated nutrient flow in the ocean
Date Awarded: Aug 2012
Amount: $883,441
Term: 36 months
Grant ID: GBMF3304
Funding Area: Science, Marine Microbiology Initiative


Phytoplankton, bacteria and other aquatic single-celled organisms, or microbes, live in the midst of a water-based soup of organic molecules. The soup is complex – the molecules can have many different sources, structures and fates. Nonetheless, the individual interactions of these molecules with the microbes in the ocean add up to the global scale movement of carbon and other nutrients. Given the importance of these interactions, we need to know more about what kinds of molecules are present in this soup, the conditions under which they are present and how long they stay there. Our project focuses on one group of these molecules, the ones that are made by microbes during their lifetimes. Through this work, we will discover new molecules that can be used to track microbes and their individual activities in order to understand the basis for the global carbon cycle.


Microbial communities in seawater are complex and individual members interact with one another through the heterogeneous pool of organic compounds in their surroundings. Cumulatively, the microbially-mediated production, modification and remineralization of this dissolved organic matter (DOM) drive the short- and long-term carbon cycles in the ocean. Thus the composition of DOM is a fundamental parameter of microbial interactions within consortia and moderates the response of the carbon cycle to large-scale environmental changes. DOM, however, has eluded characterization due to its heterogeneous nature and incompatibility with traditional analytical chemical techniques. Through the advent of electrospray ionization (ESI) coupled to ultrahigh resolution mass spectrometry (FT-MS), characterization of DOM is analytically tractable for the first time and these techniques can be used to examine both environmental DOM mixtures as well as culture-based microbial exudates. The application of ESI MS to marine microbiology will now allow us to explicitly target microbial cellular processes such as production or modification of DOM as the basis of inter- and intra-consortium interactions. Elucidation and identification of the key compounds used as currency in these interactions will facilitate new hypotheses regarding the role of different microbes in the overall carbon cycle. The work proposed here is the fundamental first step towards this goal and, as such, is complementary to other systems biology (i.e., ‘-omics’) studies.


Our goals are to detect, identify and quantify new microbial metabolites that can serve as environmental fingerprints for representative microbial metabolisms. We will conduct culture-based studies with representative phytoplankton, cyanobacteria, heterotrophic bacteria and archaea. Metabolite discovery will be conducted with liquid-chromatography (LC) coupled to ESI-FT-MS and metabolite quantification will be done with LC / triple-quadrupole MS. These data, taken together, will yield a temporal overview of internal and external metabolites for different organisms under known growth conditions. This data will serve as a foundation for a search-able database of organic compounds that will eventually incorporate all our laboratory and complementary field data. The resulting new methods will enable detection of microbial metabolites in seawater in order to assess the impact of key microbial species on the chemical composition of their surroundings. Consequently, these data will help elucidate the basis for interactions within microbial networks and the molecular underpinnings of the global carbon cycle.





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