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•The relationship between EPS content and Microcystis colony size in Lake Taihu was analyzed.•Relation between EPS content and colony size of Microcystis is colonial morphology dependent.•The maximum EPS content of Microcystis wesenbergii and Microcystis aeruginosa appeared in the size class 100–150 μm.•The EPS content of Microcystis flos-aquae increased along with an increase in colony size.
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