Taihu, the third-largest lake in China, endured cyanobacterial blooms with increasing frequency, which brought risks to public health and the environment in the surrounding area. To investigate effective and sustainable solutions methods to control blooms, various factors related to bloom-forming have been analyzed. However, colony-associated microbiomes revealed to influence bloom’s rapid growth and accumulation, have not been well studied in structure and compositional perspectives. In this research, we aimed to explore the organizing principles of microbiome assembly in the Taihu ecosystem, using biochemical and bioinformatic techniques. We started by quantifying the number of bacteria of either free-living or symbiotic lifestyles using metagenomics, identifying the bacterium-alga pairs of symbiosis, isolating axenic free-living, symbiotic bacteria, and algal hosts using metagenomics and genomics. With these obtained strains, growth rates of symbiotic bacteria and their hosts alone and together and those of free-living bacteria alone and with randomly picked algae were measured to determine the interspecific relationships: mutualism, commensalism, or parasitism. Metagenome sequencing on obtained samples provided further information about specific genes and pathways involved in the co-existing relationships.