Metaproteomic characterization of high molecular weight dissolved organic matter in surface seawaters in the South China Sea

Dissolved organic matter (DOM) is an important reservoir of carbon and energy in the marine environment and plays a key role in regulating the global carbon cycle. This study characterized proteins of high-molecular-weight DOM (size between 5 kDa and <0.2 μm, HMW-DOM) collected from the surface seawaters in the South China Sea using a shotgun proteomic approach in combination with the global ocean sampling combined assembly protein database. A total of 367 protein groups matched by 993 unique peptides from 1991 spectra were identified from four surface HMW-DOM samples. Proteins with unknown taxonomic classification and function dominated the dissolved protein pool (43–53%) while the remaining proteins presented close similarity in biological origin among the four sampling sites. Rhodospirillaceae, Prochlorococcus, SAR11 clade and viruses were the major contributors to dissolved proteins in the HMW-DOM from surface seawaters while very few proteins were from the eukaryotic phytoplankton and no archaeal proteins were detected. Transporters with substrate specificities for nitrogen- and carbon-containing compounds (1.5% of the total spectra for each) were highly detected while no phosphate transporters were found, suggesting that carbon and nitrogen might be more limiting than phosphorus in the surface seawater. Viral proteins were assigned into three families: Myoviridae, Podoviridae and Siphoviridae, and the Myoviridae proteins were the most abundant. Among them, structure proteins were the most abundant viral proteins. This study indicated that the dissolved proteins of HMW-DOM presented compositional and biologically original homogeneity in the surface seawaters of the South China Sea, and bacteria and viruses dominated the dissolved protein pool.