Long-term succession of Microcystis genotypes is driven by hydrological conditions and anthropogenic nutrient loading in a large shallow lake

Microcystis blooms that are caused by intensified human activities and global warming have become a challenging environmental problem in global lakes and reservoirs. Research has focused on Microcystis genotypes to understand their proliferation and the development of blooms, although knowledge gaps exist regarding how Microcystis genotype succession occurs over long-term time scales. In this study, high-throughput sequencing was used to investigate decade-long successional patterns of Microcystis genotypes in the large shallow Lake Chaohu that has long suffered from Microcystis blooms. Microcystis populations exhibited high overall genetic diversity, with 11,431 genotypes, and these were relatively stable over the last ∼70 years, with 339 shared core genotypes and 1 dominant genotype. Microcystis genotype succession exhibited three distinct historical phases corresponding to 1944–1960, 1964–1973, and 1976–2015. These successional patterns were clearly influenced by dam construction in 1963, and subsequent nutrient enrichment following the 1970 s. After dam construction, increased hydraulic retention times and slowing of hydrodynamic conditions influenced Microcystis genotype diversity by altering population composition and decreasing genotype richness. Populations and dominant genotypes rapidly returned after dam construction, combined with increased inferred interactions among genotypes. Network analysis also indicated that low abundance Microcystis genotypes, rather than dominant genotypes, may be keystone taxa across the decadal-scale co-occurrence network of Microcystis population.