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Abstract BackgroundDuring the bloom season, the colonial cyanobacteriumMicrocystisforms complex aggregates which include a diverse microbiome within an exopolymer matrix. Early research postulated a simple mutualism existing with bacteria benefitting from the rich source of fixed carbon andMicrocystisreceiving recycled nutrients. Researchers have since hypothesized thatMicrocystisaggregates represent a community of synergistic and interacting species, an interactome, each with unique metabolic capabilities that are critical to the growth, maintenance, and demise ofMicrocystisblooms. Research has also shown that aggregate-associated bacteria are taxonomically different from free-living bacteria in the surrounding water. Moreover, research has identified little overlap in functional potential betweenMicrocystisand members of its microbiome, further supporting the interactome concept. However, we still lack verification of general interaction and know little about the taxa and metabolic pathways supporting nutrient and metabolite cycling withinMicrocystisaggregates. ResultsDuring a 7-month study of bacterial communities comparing free-living and aggregate-associated bacteria in Lake Taihu, China, we found that aerobic anoxygenic phototrophic (AAP) bacteria were significantly more abundant withinMicrocystisaggregates than in free-living samples, suggesting a possible functional role for AAP bacteria in overall aggregate community function. We then analyzed gene composition in 102 high-quality metagenome-assembled genomes (MAGs) of bloom-microbiome bacteria from 10 lakes spanning four continents, compared with 12 completeMicrocystisgenomes which revealed that microbiome bacteria andMicrocystispossessed complementary biochemical pathways that could serve in C, N, S, and P cycling. Mapping published transcripts fromMicrocystisblooms onto a comprehensive AAP and non-AAP bacteria MAG database (226 MAGs) indicated that observed high levels of expression of genes involved in nutrient cycling pathways were in AAP bacteria. ConclusionsOur results provide strong corroboration of the hypothesizedMicrocystisinteractome and the first evidence that AAP bacteria may play an important role in nutrient cycling withinMicrocystisaggregate microbiomes.