Abstract
Toxic cyanobacterial blooms have persisted in freshwater systems around the world for centuries and appear to be globally
increasing in frequency and severity. Toxins produced by bloom-associated cyanobacteria can have drastic impacts on the
ecosystem and surrounding communities, and bloom biomass can disrupt aquatic food webs and act as a driver for
hypoxia. Little is currently known regarding the genomic content of the Microcystis strains that form blooms or the
companion heterotrophic community associated with bloom events. To address these issues, we examined the bloomassociated
microbial communities in single samples from Lake Erie (North America), Lake Tai (Taihu, China), and Grand Lakes
St. Marys (OH, USA) using comparative metagenomics. Together the Cyanobacteria and Proteobacteria comprised .90% of
each bloom bacterial community sample, although the dominant phylum varied between systems. Relative to the existing
Microcystis aeruginosa NIES 843 genome, sequences from Lake Erie and Taihu revealed a number of metagenomic islands
that were absent in the environmental samples. Moreover, despite variation in the phylogenetic assignments of bloomassociated
organisms, the functional potential of bloom members remained relatively constant between systems. This
pattern was particularly noticeable in the genomic contribution of nitrogen assimilation genes. In Taihu, the genetic
elements associated with the assimilation and metabolism of nitrogen were predominantly associated with Proteobacteria,
while these functions in the North American lakes were primarily contributed to by the Cyanobacteria. Our observations
build on an emerging body of metagenomic surveys describing the functional potential of microbial communities as more
highly conserved than that of their phylogenetic makeup within natural systems.