The northwestern Sargasso Sea undergoes annual cycles of productivity with increased production in spring corresponding to periods of upwelling, and oligotrophy in summer and autumn, when the water column becomes highly stratified. The biological productivity of this region is reduced during stratified periods as a result of low concentrations of phosphorus and nitrogen in the euphotic zone. To better understand the mechanisms of microbial survival in this oligotrophic environment, we used capillary liquid chromatography (LC)-tandem mass spectrometry to detect microbial proteins in surface samples collected in September 2005. A total of 2215 peptides that mapped to 236 SAR11 proteins, 1911 peptides that mapped to 402 Prochlorococcus proteins and 2407 peptides that mapped to 404 Synechococcus proteins were detected. Mass spectra from SAR11 periplasmic substrate-binding proteins accounted for a disproportionately large fraction of the peptides detected, consistent with observations that these extremely small cells devote a large proportion of their volume to periplasm. Abundances were highest for periplasmic substrate-binding proteins for phosphate, amino acids, phosphonate, sugars and spermidine. Proteins implicated in the prevention of oxidative damage and protein refolding were also abundant. Our findings support the view that competition for multiple nutrients in oligotrophic systems is extreme, but nutrient flux is sufficient to sustain microbial community activity.

Proteorhodopsins are light-dependent proton pumps that are predicted to have an important role in the ecology of the oceans by supplying energy for microbial metabolism. Proteorhodopsin genes were first discovered through the cloning and sequencing of large genomic DNA fragments from seawater. They were later shown to be widely distributed, phylogenetically diverse, and active in the oceans. Proteorhodopsin genes have not been found in cultured bacteria, and on the basis of environmental sequence data, it has not yet been possible to reconstruct the genomes of uncultured bacterial strains that have proteorhodopsin genes. Although the metabolic effect of proteorhodopsins is uncertain, they are thought to function in cells for which the primary mode of metabolism is the heterotrophic assimilation of dissolved organic carbon. Here we report that SAR11 strain HTCC1062 ('Pelagibacter ubique'), the first cultivated member of the extraordinarily abundant SAR11 clade, expresses a proteorhodopsin gene when cultured in autoclaved seawater and in its natural environment, the ocean. The Pelagibacter proteorhodopsin functions as a light-dependent proton pump. The gene is expressed by cells grown in either diurnal light or in darkness, and there is no difference between the growth rates or cell yields of cultures grown in light or darkness.

Fluorochemicals have widespread applications and are released into municipal wastewater treatment plants via domestic wastewater. A field study was conducted at a full-scale municipal wastewater treatment plant to determine the mass flows of selected fluorochemicals. Flow-proportional, 24-h samples of raw influent, primary effluent, trickling filter effluent, secondary effluent, and final effluent and grab samples of primary, thickened, activated, and anaerobically-digested sludge were collected over ten days and analyzed by liquid chromatography electrospray-ionization tandem mass spectrometry. Significant decreases in the mass flows of perfluorohexane sulfonate and perfluorodecanoate occurred during trickling filtration and primary clarification, while activated sludge treatment decreased the mass flow of perfluorohexanoate. Mass flows of the 6:2 fluorotelomer sulfonate and perfluorooctanoate were unchanged as a result of wastewater treatment, which indicates that conventional wastewater treatment is not effective for removal of these compounds. A net increase in the mass flows for perfluorooctane and perfluorodecane sulfonates occurred from trickling filtration and activated sludge treatment. Mass flows for perfluoroalkylsulfonamides and perfluorononanoate also increased during activated sludge treatment and are attributed to degradation of precursor molecules.

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