POM samples were generally obtained at the depths of 10 m and 30 m, or at the subsurface chlorophyll-a maximum (SCM). The vertical profiles of temperature, salinity, and chlorophyll-a fluorescence were monitored in real-time using a conductivity-temperature-depth (CTD) sensor (SBE9plus, Seabird Electronics). Real-time observations were not performed in some specific cases; here, the record-type CTD (SBE19, Seabird Electronics) without a fluorometer was used instead of the SBE9plus. On this basis, we set 30 m as the representative subsurface layer for the spring (March–June) and summer (July–September) seasons as it is below the surface mixed layer in SOJ. During the cruise in September 2020, the POM samples were collected at six depths (0, 10, 30, 50, and 100 m, and SCM) to determine the variations between the sampling layers. In the July and August cruises, photosynthetically active radiation (PAR) was occasionally accessible using a PAR sensor (Seabird Electronics) attached to the CTD. In the summer of SOJ, the mean (± SD) euphotic zone depth—where PAR is 1% of the surface—was 50 (± 14) m (n = 207), and the PAR at a depth of 30 m was 6.8 ± 4.3% of the surface. In May and August 2020, we collected samples at depths of 75 m (n = 3) and 100 m (n = 1), respectively. In spring and summer, considering the mixed layer and the euphotic zone depth, the layers at 0–10 m, 20–65 m, and 75–100 m depths were defined as the surface, subsurface, and deep layers, respectively, to detect the influence of the vertical difference of unevaluated characteristics such as light and phytoplankton community. In winter, all the samples were considered as surface layer samples because the difference in potential density between 10 and 30 m depths was <0.125 at every station, suggesting that they were within the mixed layer.