Metaproteomic characterization of dissolved organic matter in the water column of the South China Sea

We characterized dissolved organic matter (DOM; < 0.7 mu m in size) collected from the surface (10-m and 75-m) and bathypelagic (3000-m) layers in the South China Sea using the shotgun proteomic approach. A total of 182 proteins matched by 286 unique peptides were identified from three DOM samples. The number of proteins in the large DOM (LDOM; 0.2-0.7-mu m fraction) was significantly greater than that in the small DOM (SDOM; 5-kD-0.2-mu m fraction). There was no remarkable difference in the number of proteins between the surface and bathypelagic SDOMs. The sources of dissolved proteins were diverse in surface DOM, including various bacterial and phytoplankton groups as well as Oomycetes, whereas the Archaea, Proteobacteria, and some phytoplankton groups were the major contributors to bathypelagic DOM. Proteins involved in cytoskeleton, energy production and conversion, posttranslational modification, protein turnover, and chaperones presented high abundance in surface LDOM, whereas proteins involved in translation, ribosomal structure, and biogenesis were more abundant in bathypelagic LDOM. Proteins involved in transport and metabolism, cell wall or membrane or envelope biogenesis, and photosynthesis were abundant in the 75-m LDOM. A urea ABC transporter assigned to amino acid transport and metabolism was the most abundant protein in the 10-m SDOM, whereas methylenetetrahydromethanopterin reductase involved in energy production and conversion dominated the protein profiles in the 75- and 3000-m SDOMs. The dissolved proteins in the water column are diverse and dynamic, with each layer characterized by unique proteins, and only a very minor amount of proteins from the surface are protected and transferred to the deep sea.