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Background  The decomposition of  Microcystis  can dramatically change the physicochemical properties of freshwater ecosystems. Bacteria play an important role in decomposing organic matters and accelerating the cycling of materials within freshwater lakes. However, actions of the bacterial community are greatly influenced by temperature and the amount of organic matter available to decompose during a bloom. Therefore, it is vital to understand how different temperatures and biomass levels affect the bacterial community during the decomposition of  Microcystis .    Results   Microcystis  addition reduced the diversity of bacterial community. The composition of bacterial community differed markedly between samples with different biomass of  Microcystis  (no addition, low biomass addition: 0.17 g/L, and high biomass addition: 0.33 g/L). In contrast, temperature factor did not contribute much to the different bacterial community composition. Total nitrogen (TN), total phosphorus (TP), total organic carbon (TOC), ammonia nitrogen (NH 4  + -N) and oxidation-reduction potential (ORP) were the key measured environmental variables shaping the composition of bacterial community.    Conclusions  Decomposition of  Microcystis  changed the physicochemical characteristics of the water and controlled the diversity and composition of the bacterial community.  Microcystis  biomass rather than temperature was the dominant factor affecting the diversity and composition of the bacterial community.    Electronic supplementary material  The online version of this article (10.1186/s12866-019-1585-5) contains supplementary material, which is available to authorized users.

Variations of bacterial community during the decomposition of Microcystis under different temperatures and biomass