Summary: Lake Taihu in China has suffered serious harmful cyanobacterial blooms for decades. The algal blooms threaten the ecological sustainability, drinking water safety, and human health. Although the roles of abiotic factors (such as water temperature and nutrient loading) in promoting Microcystis blooms have been well studied, the importance of biotic factors (e.g. bacterial community) in promoting and meditating Microcystis blooms remains unclear. In this study, we investigated the ecological dynamics of bacterial community, the ratio of toxic Microcystis , as well as microcystin in Lake Taihu. High‐throughput 16S rRNA sequencing and principal component analysis (PCA) revealed that the bacteria community compositions (BCCs) clustered into three groups, the partitioning of which corresponded to that of groups according to the toxic profiles (the ratio of toxic Microcystis to total Microcystis , and the microcystin concentrations) of the samples. Further Spearman's correlation network showed that the α‐proteobacteria Phenylobacterium strongly positively correlated with the toxic profiles. Subsequent laboratory chemostats experiments demonstrated that three Phenylobacterium strains promoted the dominance of the toxic Microcystis aeruginosa PCC7806 when co‐culturing with the non‐toxic PCC7806 mcyB ⁻ mutant. Taken together, our data suggested that the α‐proteobacteria Phenylobacterium may play a vital role in the maintenance of toxic Microcystis dominance in Lake Taihu.

Freshwater cyanobacterial blooms (e.g., Microcystis blooms) constitute a major global environmental problem because of their risks to public health and aquatic ecological systems. Current physicochemical treatments of toxic cyanobacteria cause the significant release of cyanotoxin microcystins from damaged cells. Biological control is a promising eco-friendly technology to manage harmful cyanobacteria and cyanotoxins. Here, we demonstrated an efficient biological control strategy at the laboratory scale to simultaneously remove Microcystis and microcystins via the combined use of the algicidal bacterial filtrate and the microcystin-degrading enzymatic agent. The algicidal indigenous bacterium Paenibacillus sp. SJ-73 was isolated from the sediment of northern Lake Taihu, China, and the microcystin-degrading enzymatic agent (MlrA) was prepared via the heterologous expression of the mlrA gene in the indigenous microcystin-degrading bacterium Sphingopyxis sp. HW isolated from Lake Taihu. The single use of a fermentation filtrate (5%, v/v) of Paenibacillus sp. SJ-73 for seven days removed the unicellular Microcystis aeruginosa PCC 7806 and the native colonial Microcystis strain TH1701 in Lake Taihu by 84% and 92%, respectively, whereas the single use of MlrA removed 85% of microcystins. Used in combination, the fermentation filtrate and MlrA removed Microcystis TH1701 and microcystins by 92% and 79%, respectively. The present biological control thus provides an important technical basis for the further development of safe, efficient, and effective measures to manage Microcystis blooms and microcystins in natural waterbodies.