Metaproteomic analysis of Chesapeake Bay microbial communities

This study describes the application of proteomic approaches (metaproteomics) to observe expressed protein profiles of natural microbial communities (metaproteomes). The technique was validated using a constructed community and subsequently used to analyze Chesapeake Bay microbial community (0.2 to 3.0 μm) metaproteomes. Chesapeake Bay metaproteomes contained proteins from pI 4–8 with apparent molecular masses between 10–80 kDa. Replicated middle Bay metaproteomes shared ~92% of all detected spots, but only shared 30% and 70% of common protein spots with upper and lower Bay metaproteomes. MALDI-TOF analysis of highly expressed proteins produced no significant matches to known proteins. Three Chesapeake Bay proteins were tentatively identified by LC-MS/MS sequencing coupled with MS-BLAST searching. The proteins identified were of marine microbial origin and correlated with abundant Chesapeake Bay microbial lineages, Bacteroides and α-proteobacteria.Our results represent the first metaproteomic study of aquatic microbial assemblages and demonstrate the potential of metaproteomic approaches to link metagenomic data, taxonomic diversity, functional diversity and biological processes in natural environments.Bacterioplankton contribute significantly to both primary production and biomass in the ocean and coastal water [1,2]. With an average concentration of approximately 106 cells ml-1, bacterioplankton is an important catalyst of biogeochemical processes including oceanic carbon and nitrogen cycles [3,4]. Studying bacterioplankton is challenging because most groups either have never been cultivated [5,6] or grow to very low density in the laboratory [7]. Culture-independent molecular approaches have indicated that environmental bacterial communities are more complex and diverse than previously thought [5,6,8]. Metagenomics is the direct cloning, sequencing, assembly and annotation of DNA from microbial communities and has been applied to waters, soils and extreme environ