The ratios of nitrogen to phosphorus are the key fraction Doramapimod of the Redfield ratio. PC1 represented nutrient limitation to phytoplankton growth in the study area. PC2, explaining 18.80% of the total variance, had positive loadings on DP, and negative loadings on DO and Chl a, which illustrated the similar features of the original data that DO and Chl a are high in coastal shallow stations and low in deep stations offshore ( Figures 2f–g). PC3, explaining 12.97% of the total variance, had positive loadings on PO4-P and negative loadings on pH. pH is determined mainly by biological activities,

and PO4-P comes mainly from the upwelling areas and the estuary in the northern SCS. PC3 therefore represented the impact of macronutrients on biological activities in the upwelling areas and the estuary. PC4, explaining

PARP activation 11.44% of the total variance, had negative loadings on SiO3-Si. SiO3-Si is replenished mainly by the upwelling from the deep sea in the northern SCS ( Chen et al. 2001). PC4 represented the features of upwelling. PC5, explaining 7.81% of the total variance, had strong positive loadings on NH4-N and represented the anthropogenic pollution near the Pearl River Estuary. The massive economic growth and urban development in the Pearl River Delta have resulted in excessive discharges of wastewater in the Pearl River Estuary. NH4-N is an important indicator of anthropogenic pollution in the Pearl River Estuary. Figure 4 shows the horizontal distribution

patterns of silicate at different depths, including the surface, 50 m , 75 m , 100 m , 150 m  and 200 m . At the surface, the concentration of silicate is low (< 3 μmol dm−3) in most of the northern SCS ( Figure 4a). Three high concentration zones can be clearly distinguished: (1) the Taiwan Shoals upwelling in the north-east of the PIS showed a high concentration of ~ 16.46 μmol dm−3; (2) the northern perennial cold cyclonic eddy in the south-west of the PIS had a relatively lower concentration of ~ 5.29 μmol Sclareol dm−3 at the centre; (3) the upwelling region in the west of the PIS was ~ 11.96 μmol dm−3 ( Figure 4a). The spatial distribution of silicate clearly shows three upwelling regions. In Figures 4a–f, the Taiwan Shoals upwelling has been formed at 200 m  depth and is moving to the north-east, and its central concentration of silicate is decreasing from 65.3 μmol dm−3 to 16.46 μmol dm−3. These results illustrate that the Taiwan Shoals upwelling is formed by the deep-sea current climbing up the continental shelf near the PIS in a north-easterly direction. The northern part of the perennial cold cyclonic eddy is steady and stays at the same position in every layer, which is formed by the vertical uplifting current. The upwelling in the west of the PIS is detected at 100 m  depth, and the horizontal distribution traces its process of formation. The upwelling in TSLS ( Han 1998, Shen & Shi 2006) and in the perennial cold cyclonic eddy ( Wu 1991, Huang et al.