The patchy distribution of oligopeptide production abilities in cyanobacterial populations enables the classification of strains into different oligopeptide-based chemotypes. In order to evaluate the ecological significance of chemotypes in natural systems, we tracked the seasonal dynamics and sedimentation losses of Microcystis chemotypes in the eutrophic Valmayor reservoir (Spain). Fifty-three distinct chemotypes were identified throughout the season, six of them only present as benthic colonies. There was no correlation between chemotype affiliation and taxonomic morphospecies or colony size. The succession of chemotypes in the water column occurred synchronically in pelagic and littoral habitats and at different depths. Shifts in chemotype assemblages successfully explained temporal fluctuations in biomass-standardized microcystin contents of the bloom. The dynamics of chemotypes were driven both by asynchronous proliferation in the water column and significantly different sedimentation rates among chemotypes. While differential settling was the most important loss process shaping chemotype succession, the existence of alternative processes selectively inflicting massive losses to individual chemotypes was observed. Together, the significant differences in sedimentation and pelagic net growth rates among chemotypes, their segregation among pelagic and benthic habitats, as well as the existence of chemotype-selective loss processes, show that Microcystis oligopeptide chemotypes interact differently with their environment and represent commonly overlooked ecologically functional intraspecific linages.

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