Phytoplankton pigments were used to study the community structure and phytoplankton size class in Goa’s estuaries. The study revealed that fucoxanthin and chlorophyll a were the most dominant pigments. The correlation of diagnostic pigments (DP) and chl a correlated positively in both estuaries (Mandovi: R2 = 0.703, P < 0.01; Zuari: R2 = 0.892, P < 0.01), suggesting that DP can serve as a proxy to measure phytoplankton biomass. Results showed that with DP and biomass proportion, phytoplankton size class (picoplankton, nanoplankton and microplankton) can be derived. Picoplankton biomass was highest during pre-monsoon season, while microplankton biomass was high during monsoon season. The high abundance of microplankton may support planktivorous fishery productivity.
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