Microcystins are produced by cyanobacteria carrying microcystin synthetase (mcy) genes in blooms. The present study investigated seasonal variations in concentrations of mcy A and 16S rRNA genes, encoded in the genus Microcystis using real-time PCR, and measured the water quality variables and microcystin concentrations in a hypereutrophic fish pond between June and November 2007. Prior to field survey, the relationship between axenic Microcystis aeruginosa NIES 102 cell abundance and concentrations of mcy A and 16S rRNA genes was determined by real-time PCR in the laboratory. Based on the quantitative relationship, microcystin-producing and total Microcystis cell numbers in the study site were estimated. The average dominance ratio of microcystin-producing strains in the total Microcystis population was approximately 80% and microcystin concentration was highly associated with toxic Microcystis cell numbers equivalent of mcy A gene. It was also observed that total nitrogen concentration was associated with development of Microcystis blooms, and high concentrations of NOx and NH4 increased microcystin production by promoting growth of microcystin-producing Microcystis strains.

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