The cyanobacterium Microcystis occurs as colonies of different sizes with varying abundance of toxic genotypes versus non-toxic genotypes under natural conditions. To investigate the effects of toxic Microcystis genotypes on natural colony formation, samples collected from the mainstream of Haihe River from July to October 2015 were sieved into four colony classes with sizes of <8 μm, 8–20 μm, 20–90 μm and >90 μm. Each colony size class was analyzed for the proportion of toxic Microcystis genotypes, and microcystins (MCs) cellular production of toxic genotypes. The results showed the smallest size class of Microcystis colonies (<8 μm) showed the lowest proportion of toxic genotypes and the highest MC-RR and MC-YR cellular production. With the increasing colony sizes, the proportion of toxic Microcystis genotypes increased but the MC-RR and MC-YR cellular production decreased. A negative correlation between the MCs cellular production and the proportion of toxic genotypes was observed in all four colony size classes, suggesting that the less there were toxic Microcystis cells able to produce MCs, the more each toxic cell needed to produce that molecule. Toxic Microcystis played an important role in the colony formation in natural waters via producing MCs.

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