Abstract
BackgroundNatural 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.ResultsThis 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.ConclusionOur 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.
Highlights
Natural microbial communities are extremely complex and dynamic systems in terms of their population structure and functions
We developed a metaproteomic approach to document microbial community protein profiles along a transect of the Chesapeake Bay
This study demonstrates that metaproteomic approaches can be successfully applied to naturally occurring and complex microbial communities in their native habitats
Summary
Natural microbial communities are extremely complex and dynamic systems in terms of their population structure and functions. Bacterioplankton contribute significantly to both primary production and biomass in the ocean and coastal water [1,2]. 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 environments [9,10,11,12]. A recent metagenomic study of the Sargasso Sea revealed that substantial complex microbial diversity exists in the ocean: 148 novel bacterial phylotypes and more than a million of previously unknown genes were discovered and annotated [12]
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