BACKGROUND: Natural microbial communities are extremely complex and dynamic 
systems in terms of their population structure and functions. However, little is 
known about the in situ functions of the microbial communities.
RESULTS: 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 microm) metaproteomes. Chesapeake Bay metaproteomes contained 
proteins from pI 4-8 with apparent molecular masses between 10-80 kDa. 
Replicated middle Bay metaproteomes shared approximately 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 
alpha-proteobacteria.
CONCLUSION: 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.