| Marine phytoplankton are generally considered to be the main primary producers in marine ecosystems. The community structure of phytoplankton not only reflects the complicated relationships among different trophic levels but also reflects the effects of the environmental factors on the primary production. Being one of the basic scientific researches, the study on the phytoplankton community plays an important role in identifying the roles of all kinds of essential elements in the global biogeochemistry cycle. In the recent years, global climate change has become one of the most important environmental problems human beings faced. Because of the importance of phytoplankton to estimate the global production and carbon cycle, determining phytoplankton functional groups is the key to understanding various global biogeochemical processes.At present HPLC method combined with CHEMTAX factorization program has become one of the main methods to study the phytoplankton community. In this research, HPLC-CHEMTAX method was applied to assess phytoplankton taxonomic composition of northern South China Sea (nSCS) in 2009. The purposes of this study were to (1) study the phytoplankton pigments distribution in nSCS, (2) investigate the phytoplankton community composition in nSCS, (3) investigate how phytoplankton pigments and community composition response to the co-varying environmental factors, (4) offer some basic data for determining the roles of phytoplankton functional groups in various global biogeochemical processes.A total of 22 stations (4 transects) in the northern SCS were surveyed from February 11 to 23 and August 12 to 24,2009.Atotal of 230 samples were analyzed by HPLC-CHEMTAX method. Fourteen marker pigments belong to 9 phytoplankton taxa in the samples were analyzed by HPLC system. We recognized four different vertical distribution patterns of pigments in winter:chlorophyll a (Chl a)-like type, divinyl chlorophyll a (DV Chl a) type, even distribution type, and surface type. The average value of ratios of accessory photo-protective pigments (APP) to accessory photo-synthetic pigments (APS) was 0.89±0.63 in the upper 50 m and 0.16±0.06 below 50 m depth. With depth increasing, APP decreased and photo-synthetically active radiation (PAR) attenuated accordingly. There was an obvious succession of phytoplankton community from inshore to open sea:diatoms were dominant in the inshore region, while chrysophytes, Prochlorococcus, cyanobacteria and prymnesiophytes were dominant in the open sea. Vertical distribution of phytoplankton also showed great differences from inshore to open sea. In the inshore and shelf, diatoms were the most important components in the water column and cyanobacteria were secondary components of the community in the upper water. In slope and open sea, Prochlorococcus and cyanobacteria were important groups above the subsurface chlorophyll a maxima (SCM) while chrysophytes dominated below the SCM. It was proved that the Hong Kong Southeast Anti-Cyclonic Eddy have a great effect on phytoplankton community structure in the survey region.The distribution patterns of pigments in summer were similar to winter. The average value of ratios of APP to APS was 1.11±0.88 in the upper 50m and 0.07±0.15 below 50 m depth. The photo-protective effect was enhanced in summer. The phytoplankton community also showed obvious regional characters like winter. The insore region (depth<50m), continental shelf and continental slope-open sea regions had very different phytoplankton community structures. The abundances of diatoms, Prochlorococcus, cyanobacteria and chrysophytes had great gradients from inshore region to open sea region. Compared with winter, the abundance of Prochlorococcus was higher in summer and Prochlorococcus distributed a larger region. The phytoplankton biomass and community structures of the east of the survey region (transect S1) was very different from the west of the survey region (transect S2) which was less affected by the Pearl River.Influenced by monsoon, the hydrological and chemical environment in winter and summer were quite different in survey region. Phytoplankton biomass and community structure made different responses to the interaction of light, temperature, nutrients and many other environmental factors. The high nutrients and low temperature of the inshore region were flavored by diatoms and other phytoplankton groups which have large cell sizes while pico-phytoplankton like Prochlorococcus tended to dominate in open sea region with low nutrients and high temperature. Chrysophytes favored low-light environment so they dominated below the euphotic layer. The Pearl River had stronger influence on the survey region in summer, in view of salinity, nutrients and temperature and so on. Because of the effect of the fresh water from the Pearl River, the abundance of diatoms was higher in summer and chlorophytes had a larger distribution region.
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