Multiannual variations in Microcystis bloom episodes – Temperature drives shift in species composition

•In Lake Kinneret (Sea of Galilee, Israel), the annual winter-spring bloom of Microcystis is composed of several species/strains of different geno- and chemo-types.•Over two decades, the Microcystis community structure has been changed from dominant toxic species to less or non-toxic species.•Long-term records of biotic and abiotic parameters suggest that minor increase in water temperature supported the dominance of less toxic phycoerythrin containing strain.•Laboratory experiments further support the advantage of non-toxic phycoerythrin strain over the toxic strain as the temperature increased in mixed cultures.•The high diversity of Microcystis population during a bloom event emphasize the difficulties in predicting competitive outcome for cyanobacterial populations in natural environments. Cyanobacteria are notorious for producing water blooms and for toxin formation. Toxic cyanobacterial blooms present an ever-increasing serious threat to both the quality of drinking water and recreational uses and severely disrupt aquatic ecosystems, worldwide. In many cases, such blooms are dominated by toxic Microcystis sp. that produce a family of structurally similar hepatotoxins, known as microcystins (MCs). Here we present a retrospective analysis of Microcystis seasonal blooms from Lake Kinneret (Sea of Galilee, Israel) indicating that the population is composed of at least 25 different genotypes and two different chemo-types, whose relative abundance changes over decades. Based on a long-term record of biotic and abiotic parameters and laboratory experiments we propose that minor increase in water temperature, but not in salinity, may affect Microcystis community structure by changing the relative abundance of species/strains from toxic to less or non-toxic species.