Harmful cyanobacterial blooms (CyanoHABs) are linked to increasing anthropogenic nitrogen (N) and phosphorus (P) inputs. However, CyanoHABs in many large lakes continue despite extensive abatement efforts, mostly focused on external P loading. Internal nutrient cycling can modify nutrient availability and limitation; thus, understanding the relative importance of external vs. internal nutrient loading is essential for developing effective mitigation strategies for CyanoHABs. We estimated long‐term nutrient budgets for Lake Taihu, China, from mass balance models using extensive monitoring of input and output nutrient data from 2005 to 2018 to quantify contributions from internal nutrient loading. The nutrient mass balance showed that 9% and 63% of annual external N and P inputs, respectively, were retained in the lake. Denitrification removed 54% of external N loading and can thus help explain rapid decreases in lake N concentrations and summer N limitation. Water columnregeneration can help sustain CyanoHABs over the short term and contributed 38–58% of potentialdemand for summer‐fall,Microcystis‐dominated blooms. Internal P release contributed 23–90% of CyanoHABs P demand, although Taihu was a net P sink on an annual scale. Our results show that internal nutrient cycling helps sustain CyanoHABs in Taihu, despite reductions in external nutrient inputs. Furthermore, N is leaving the lake faster than P, thereby creating persistent N limitation. Therefore, parallel reductions in external N loading, along with P, will be most effective in reducing CyanoHABs and accelerate the recovery process in this and other large, shallow lakes.

Bacteria play key roles in the function and diversity of aquatic systems, but aside from study of specific bloom systems, little is known about the diversity or biogeography of bacteria associated with harmful cyanobacterial blooms (cyanoHABs). CyanoHAB species are known to shape bacterial community composition and to rely on functions provided by the associated bacteria, leading to the hypothesized cyanoHAB interactome, a coevolved community of synergistic and interacting bacteria species, each necessary for the success of the others. Here, we surveyed the microbiome associated with Microcystis aeruginosa during blooms in 12 lakes spanning four continents as an initial test of the hypothesized Microcystis interactome. We predicted that microbiome composition and functional potential would be similar across blooms globally. Our results, as revealed by 16S rRNA sequence similarity, indicate that M. aeruginosa is cosmopolitan in lakes across a 280° longitudinal and 90° latitudinal gradient. The microbiome communities were represented by a wide range of operational taxonomic units and relative abundances. Highly abundant taxa were more related and shared across most sites and did not vary with geographic distance, thus, like Microcystis, revealing no evidence for dispersal limitation. High phylogenetic relatedness, both within and across lakes, indicates that microbiome bacteria with similar functional potential were associated with all blooms. While Microcystis and the microbiome bacteria shared many genes, whole‐community metagenomic analysis revealed a suite of biochemical pathways that could be considered complementary. Our results demonstrate a high degree of similarity across global Microcystis blooms, thereby providing initial support for the hypothesized Microcystis interactome.