Simultaneous Quantification of Cyanobacteria and Microcystis spp. Using Real-Time PCR

  • Oh, Kyoung-Hee (Department of Environmental Engineering, Chungbuk National University) ;
  • Jeong, Dong-Hwan (Water Environmental Chemistry Division, Geum-River Environment Research Center) ;
  • Shin, Seung-Hee (Department of Environmental Engineering, Chungbuk National University) ;
  • Cho, Young-Cheol (Department of Environmental Engineering, Chungbuk National University)
  • Received : 2011.09.21
  • Accepted : 2011.11.14
  • Published : 2012.02.28


In order to develop a protocol to quantify cyanobacteria and Microcystis simultaneously, the primers and probe were designed from the conserved regions of 16S rRNA gene sequences of cyanobacteria and Microcystis, respectively. Probe match analysis of the Ribosomal Database Project showed that the primers matched with over 97% of cyanobacterial 16S rRNA genes, indicating these can be used to amplify cyanobacteria specifically. The TaqMan probe, which is located between two primers, matched with 98.2% of sequences in genus GpXI, in which most Microcystis strains are included. The numbers of cyanobacterial genes were estimated with the emission of SYBR Green from the amplicons with two primers, whereas those of Microcystis spp. were measured from the fluorescence of CAL Fluor Gold 540 emitted by exonuclease activity of Taq DNA polymerase in amplification. It is expected that this method enhances the accuracy and reduces the time to count cyanobacteria and potential toxigenic Microcystis spp. in aquatic environmental samples.


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