Genetic characterization of strains of Cyanobacteria using PCR-RFLP of the cpcBA intergenic spacer and flanking regions

Oligonucleotide primers, specific for conserved regions of the genes encoding the β- and α-phycocyanin subunits of phycobilisomes (<em>cpcB</em> and <em>cpcA</em>) of cyanobacteria, were used to amplify a DNA fragment containing the intervening intergenic spacer region (<em>cpcBA</em>-IGS) of 19 strains of three morphospecies of cyanobacteria. Six Australian strains were identified as <em>Anabaena circinalis</em> Rabenhorst, six strains were identified as <em>Microcystis aeruginosa</em> Kützing, and seven strains were identified as <em>Nodularia spumigena</em> Mertens. Restriction enzyme digestion of the amplification products from the strains revealed restriction fragment length polymorphism (RFLP) within all three morphospecies. Strains corresponding to <em>M. aeruginosa</em> were highly polymorphic: 11 of the 14 restriction enzymes used displayed RFLPs. The <em>A. circinalis</em> and <em>N. spumigena</em> strains were less variable: three of 14 enzymes and seven of 14 enzymes, respectively, showed RFLPs. The presence of genetic variation between strains within these three divergent morphospecies, which span two orders of cyanobacteria <em>(Chroococcales Wettstein and Nostocales (Borzi) Geitler)</em>, show that the <em>cpcBA-</em> IGS fragment has broad application as a molecular marker for intrageneric studies of cyanobacteria systematics and genetics.