Metaproteomics reveals the major microbial players and their biogeochemical functions in a productive coastal system in the northern South China Sea.

We study the metaproteome of the GF/F-prefiltered fraction of a microbial community from Shantou coast summer surface waters using a shotgun proteomic approach. Spectra attributed to the marine Roseobacter clade (MRC), the oligotrophic marine Gammaproteobacteria (OMG) group and Flavobacteria dominated in the microbial community, accounting for 21.0%, 23.2% and 12.7% of all of the detected spectra, respectively, whereas the SAR 92 clade accounted for 50% of the OMG group. The abundance of TonB-dependent receptors (TBDRs) was detected and the majority of TBDRs were attributed to the OMG, whereas a large number of ABC transporters matched to the MRC, which suggests niche separation in the microbial community. Expression of proteorhodopsin and RagB/SusD from Flavobacteria facilitates their attachment and growth on algal-derived organic matter. Taurine and glycine betaine appear to be an important source of carbon and nitrogen for the Rhodobacteraceae and SAR11 cluster. The detection of carbon monoxide dehydrogenase, formate dehydrogenase, O-acetylhomoserine sulfhydrylase and sulfur oxidation protein from the MRC demonstrated that members of the MRC play important roles in coastal ocean biogeochemical cycles. This study provides the first insight into functional processes occurring in microbial communities in coastal waters in the South China Sea.