Characterization of particulate organic matters in the water column of the South China Sea using a shotgun proteomic approach

We characterized particulate organic matter (POM) collected from both the surface (41 m and 200 m) and mesopelagic layers (500 m and 1000 m) in the western South China Sea. By using a shotgun proteomic approach, a total of 3035 proteins matching one or more peptides were detected from four POM samples, 505 of which were identified as high-confidence proteins matching two or more peptides. Cyanobacteria was the largest contributor throughout the water column, while crustaceans and dinophytes were the two major groups contributing to the particulate proteins in the POM collected from 200 m. Subcellular locations and biological processes of particulate proteins varied significantly between the 41-m and 200-m layers: photosynthesis-associated proteins were highly abundant in the 41-m layer while tubulins and actins accumulated in the midwaters, especially at the 200-m layer. Porins, adenosine triphosphate synthases, nutrient transporters, molecular chaperones, and ectoenzymes were frequently detected in the POM samples and presented different distribution patterns within the water column, revealing complex biological processes at the different water layers and/or during the sinking of POM. The sources of surface and midwater particulate proteins are different, and the cellular metabolism, generation of energy, and transport processes in POM are attenuated rapidly down ocean water column. Zooplankton fecal pellet packages and membrane encapsulation might play important roles in protecting particulate proteins from degradation.