Genetic biodiversity among freshwater isolates of pleomorphic cyanobacteria

Cyanobacteria are ubiquitous prokaryotic microalgae, causing thick blooms and capable of producing lethal toxins and undesired malodorous metabolites. In aquatic systems used for recreation, tourism, aquaculture, or drinking purposes, proper identification of environmental isolates is essential to reconcile public– and ecosystem–health, social function, and business strategy. Objective. To isolate cyanobacteria from various sources, collect genetic information, identify novel genotypes, reconstruct phylogenetic relationships, and compare morphology– and DNA–based typing, to improve classification and identification. Method. Cyanobacteria were isolated by serial dilutions, micromanipulation, sequential centrifugation, differential filtration, agar plate streaking. Microscopic identifications based on morphology, were compared to molecular results based on partial fragments of the small ribosomal subunit RNA gene (16S rDNA), the DNA-dependent RNA polymerase gene (rpoC1), and the phycocyanin operon (Cpc). Results. Isolates belonged to the Nostocales (n=22), Chroococcales (n=7), and Oscillatoriales (n=6) subgroups. Morphological and molecular data were in agreement to the species– and genus–level for 26% and 37% of the isolates, respectively. For the remaining 40.0% of the strains, the consensus was at order–level or less. Of the 16S rDNA (n=31) and rpoC1 (n=19) sequences obtained, 32% were novel genotypes at each locus, showing respectively >1.2% or >5% genetic distance from previously known sequences. Conclusions. This study confirms the extraordinary genetic diversity and morphological plasticity of cyanobacteria. Spontaneous or culture-induced pleomorphism, scarcity of reference sequences, and/or lateral gene transfer can hamper confident identification. This highlights the need for further collection of sequence data, improvement of classification, and combined microscopic/molecular approaches for management purposes or research.