| Summary: | The standing stock of phytoplankton carbon is a basic and essential property for understanding oceanic ecosystems, biogeochemical cycles, and regional climates. However, current related algorithms mainly focus on remote-sensed application, which cannot describe the vertical profile of phytoplankton carbon throughout the whole euphotic zone. In this study, we modified a previous absorption-based bio-optical algorithm to acquire vertical variabilities of the total and size-partitioned phytoplankton carbon based on field data from the South China Sea (<i>SCS</i>). The mean absolute errors and the biases between estimated and field picophytoplankton carbon were <2.14 and 0.6–2.0, respectively. The results showed that the vertical profile of total phytoplankton carbon displayed a Gaussian distribution in the stratified <i>SCS</i> basin. The picophytoplankton carbon was always the fundamental component of the total phytoplankton carbon within the whole euphotic zone. The dominant picophytoplankton species changed from <i>Synechococcus</i>-like cyanobacteria at the sea surface to pico-sized haptophytes at the phytoplankton carbon maximum layer. The strong covariation between total phytoplankton carbon and chlorophyll-a concentration suggested that they can be converted into each other through an accurate carbon-to-chlorophyll ratio in the open <i>SCS</i>. These results provide essential information that can be used to decipher the three-dimensional structure of total and size-partitioned phytoplankton carbon in the open <i>SCS</i>.
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