Summary: Microcystis is a cosmopolitan genus of cyanobacteria and occurs in many different forms. Large surface blooms of the cyanobacterium are well known in eutrophic lakes throughout the globe. We evaluated the role of microcystins (MCs) in promoting and maintaining bloom‐forming cell aggregates at environmentally relevant MC concentrations (0.25–10 µg l ⁻¹ ). MCs significantly enhanced Microcystis colony sizes. Colonial diameters in microcystin‐RR (MC‐RR)‐treated cultures (at 1 µg l ⁻¹ ) were significantly larger than control colonies, by factors of 1.5, 2.6 and 2.7 in Microcystis wesenbergii DC‐M1, M. ichthyoblabe TH‐M1 and Microcystis sp. FACHB1027 respectively. Depletion of extracellular MC concentrations caused Microcystis colony size to decrease, suggesting that released MCs are intimately involved in the maintenance of Microcystis colonial size. MC‐RR exposure did not influence Microcystis growth rate, but did significantly increase the production of extracellular polysaccharides (EPS). In addition, MC‐RR exposure appeared to trigger upregulation of certain parts of four polysaccharide biosynthesis‐related genes: capD , csaB , tagH and epsL . These results strongly indicate that induction of polysaccharides by MC‐RR was the major mechanism through which MCs enhanced colony formation in Microcystis spp. Cellular release of MCs, therefore, may play a key role in the persistence of algal colonies and the dominance of Microcystis.

Cyanobacteria are photosynthetic prokaryotes that inhabit diverse aquatic and terrestrial environments. However, the evolutionary mechanisms involved in the cyanobacterial habitat adaptation remain poorly understood. Here, based on phylogenetic and comparative genomic analyses of 650 cyanobacterial genomes, we investigated the genetic basis of cyanobacterial habitat adaptation (marine, freshwater, and terrestrial). We show: (1) the expansion of gene families is a common strategy whereby terrestrial cyanobacteria cope with fluctuating environments, whereas the genomes of many marine strains have undergone contraction to adapt to nutrient-poor conditions. (2) Hundreds of genes are strongly associated with specific habitats. Genes that are differentially abundant in genomes of marine, freshwater, and terrestrial cyanobacteria were found to be involved in light sensing and absorption, chemotaxis, nutrient transporters, responses to osmotic stress, etc., indicating the importance of these genes in the survival and adaptation of organisms in specific habitats. (3) A substantial fraction of genes that facilitate the adaptation of Cyanobacteria to specific habitats are contributed by horizontal gene transfer, and such genetic exchanges are more frequent in terrestrial cyanobacteria. Collectively, our results further our understandings of the adaptations of Cyanobacteria to different environments, highlighting the importance of ecological constraints imposed by the environment in shaping the evolution of Cyanobacteria.