Proteins are the metabolic machines of the cell and as such, the study of proteins could illuminate the dominant biological activities that are occurring within cells and reveal how an organism interacts with its environment. Here, we used proteomic techniques to study the abundant marine bacterium SAR11 both as an isolate and in the context of microbial communities.

An accurate mass and time tag library was built to allow quantitative comparison of exponentially growing and stationary phase proteomes of the cultured SAR11 strain Candidatus Pelagibacter ubique HTCC1062. Significant increases in stationary-phase proteins that mitigate oxidative damage; OsmC and thioredoxin reductase were detected. In addition, molecular chaperones, enzymes involved in methionine and cysteine biosynthesis, and regulatory proteins were also up-regulated in stationary phase. The up-regulation of this suite of proteins suggests a system by which Cand. P. ubique cells protect themselves against external stressors when nutrients are scarce without devoting significant resources to proteome remodeling. A mechanism for a global stationary-phase response was not identified.

Metaproteomics is the study of all of the proteins expressed by a microbial community at a given point in time. Metaproteomic analyses were applied to mixed marine microbial communities collected from both oligotrophic and nutrient replete environments. Abundant proteins from SAR11, Prochlorococcus , and Synechococcus cells from the microbial community in the oligotrophic Sargasso Sea were identified using a novel technique for binning organism-specific metagenomic sequences. The SAR11 metaproteome was dominated by periplasmic substrate-binding proteins, specifically for phosphate, amino acids, phosphonate, and polyamines. A large-scale search on an unfiltered database with post-search BLAST annotations allowed for identification of proteins from SAR11 and other dominant bacterioplankton within the microbial community from the nutrient-replete Oregon coast. Here, the SAR11 metaproteome was also dominated by periplasmic substrate-binding proteins, but key substrates were amino acids, taurine, mannitol, and polyamines, suggesting that these substrates may become limiting before phosphorus when nutrients are freely available. The abundance of transport proteins suggests a means by which these cells remain competitive in the microbial community and play a key role in global nutrient cycling.