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We explored picophytoplankton in the surface (0 m) and bottom (2.3–8.7 m) layers of a shallow (<10 m) eutrophic coastal system (Isahaya Bay, Japan). We found that picophytoplankton (principally Synechococcus) constituted the major phytoplankton in spring and summer. The chlorophyll a (chl. a) concentration in the 0.7–2.0-μm picophytoplankton fraction (hereinafter 'pico-sized chl. a ') and picophytoplankton abundance in Isahaya Bay were higher than those in other eutrophic coastal waters. The pico-sized chl. a concentration and the picophytoplankton abundance counted with an epifluorescence microscope was up to 49.31 μg L−1 and 1.9 × 106 cells mL−1, respectively. Higher contributions of pico-sized chl. a to the total chl. a were evident in summer (up to 63.5%), relative to spring (up to 32.1%), at both depths. Picophytoplankton abundance and the pico-sized chl. a concentration was positively correlated with water temperature and dissolved inorganic phosphorus (DIP) concentrations. Thus, both temperature and DIP may be major controllers of picophytoplankton in Isahaya Bay. The pico-sized chl. a concentration and picophytoplankton cell number at the bottom layer were positively correlated with those in the surface layer, suggesting that picophytoplankton in bottom layers may have sunk from the surface layers. The results imply that the picophytoplankton affects the biogeochemical processes in the bottom of Isahaya Bay more than previously thought. This may be true not only for this estuary but also for other eutrophic coastal seas. • Picophytoplankton contributed considerably to the total phytoplankton biomass in spring and summer of a shallow, eutrophic coastal sea. • Higher contributions of pico-sized chl. a to the total chl. a were evident in summer (up to 63.5%), relative to spring (up to 32.1%), at both depths. • High amount of picophytoplankton may sink from the surface to accumulate in near-bottom layers. [ABSTRACT FROM AUTHOR]

Abstract: Temporal and spatial variations in Synechococcus abundance were investigated over an annual cycle (February'10–January'11) along a salinity gradient (0–35) in the tropical Zuari estuary, influenced by south-west monsoons. Synechococcus exhibited salinity preferences with phycoerythrin-rich cells at salinities >2 (Synechococcus-PEI), >20 (Synechococcus-PEII) and <1 (Synechococcus-PEIII) whereas phycocyanin-rich (Synechococcus-PC) dominant at lower salinities. Downstream stratification during monsoon caused Synechococcus group segregation in the surface and near-bottom waters. During monsoon-break and non-monsoon period stabilized waters, increased salinity, temperature, solar radiation and low rainfall favored high Synechococcus abundance whereas unstable waters, increased turbidity and low solar radiation during active monsoon lowered abundance. SYN-PC positively co-related with nitrate and phosphate and SYN-PEI with phosphate. Synechococcus contribution to phytoplankton carbon biomass ranged from 9 to 29%. In monsoonal estuaries, rainfall intensity regulates freshwater runoff which modulates the estuarine environment, creating temporal–spatial niche segregation of Synechococcus groups thereby serving as indicator organisms of the estuarine hydrodynamics. [Copyright &y& Elsevier]