Project: Collaborative Research: Linking geochemistry and proteomics to reveal the impact of bacteria on protein cycling in the ocean

Text from NSF award abstract:

Although proteins represent the primary source of new organic nitrogen in the ocean, the identification of individual proteins and mechanisms modulating their preservation has faced analytical and computational challenges in deciphering the vast suite of possible sequences and degradation by-products. Recent efforts to link geochemical cycling, biomedical proteomics and bioinformatics has demonstrated that only a small subset of the suite of proteins produced by marine diatoms appear to survive the degradation process, and those that do are largely protected by physical and enthalpic barriers to microbial attack. Although these discoveries help to explain the survival of individual proteins, they also generate multiple questions regarding bacteria as the dominant recyclers of organic nitrogen and carbon and needs for specific approaches to characterize modified protein products. Bacteria dominate the water column and sedimentary systems in both numbers and diversity, yet their relative contribution to the preserved proteomic pool appears low.

In this project, researchers at Old Dominion Universityand the University of Washington will join forces to decipher the bacterial role in protein recycling and their potential contribution. By integrating high mass accuracy tandem mass spectrometry-based proteomics with stable isotope-based geochemical analysis, they hope to identify those bacterial proteins initially synthesized during organic matter recycling. Three research objectives drive this investigation: (1) to determine the potential contribution of bacteria proteins to marine organic matter; (2) to identify those protein(s) synthesized by heterotrophic marine bacteria during initial stages of organic matter degradation; (3) to determine if glycan (carbohydrate) modifications represent an important component of preserved, yet unidentified, peptides seen in our analysis of oceanic particles and sediments.

Broader Impacts: This project will provide multiple opportunities for interdisciplinary student training in marine chemistry and proteomics as well as address the goal of disseminating results and tools to a broad audience. In the more traditional role, this project will expand the career for a female principal investigator in marine proteomics, support both graduate and undergraduate students at ODU which include opportunities for minority enrichment and provide training for a postdoctoral fellow at UW. On the broader level, the ODU PI participates in high school outreach programs for high achieving students in the local school which provides for summer internships and enrichment programs.

Relevant Links:

Old Dominion University: Marine Organic Geochemistry and Ecology Laboratory (MOGEL) Lab Website
Bering Sea Ecosystem Study: Data Archive
Environmental Proteomics: Bacteria Recyclers in the Ocean
Environmental Proteomics: Proteomics of Colwellia psychretheca at subzero temperatures