Unifying Paradigms Across the Salinity Divide: Picocyanobacteria in the Laurentian Great Lakes as a Case Study

As a suite of vast inland seas encompassing strong biogeochemical gradients, the Laurentian Great Lakes are a unique freshwater system for exploring fundamental questions about microbial adaptations and evolution across the salinity divide. Here we focus on picocyanobacteria, whose phylogenetic and physiological diversity has been well characterized in marine systems but much less so in freshwater. We used single-cell and metagenome-assembled genomes to construct a genome atlas of picocyanobacteria across the Laurentian Great Lakes. Genome diversity was structured into five distinct clades (GLI-GLV) affiliated with two subclusters: Cyanobium/Synechococcus subcluster 5.2 and Synechococcus subcluster 5.3. These major groups were distinguished by genome properties (e.g. GC content) and gene content; for example, genomes affiliated with subcluster 5.3 lacked genes for nitrate reductase, nitrite reductase, and cyanase. Predicted pigment composition also varied across clades, reflecting a history of lateral gene transfers and gene losses of pigment biosynthesis genes over the course of picocyanobacterial evolution. With respect to spatial distribution, some lineages were cosmopolitan while others showed enrichment in the lower-productivity upper lakes (Superior, Michigan, Huron) or the higher-productivity lower lakes (Erie, Ontario). Notably, genomes with type 2 and type 3 pigments coexisted in each sample, providing evidence for niche complementarity. Our findings, together with the ecotype framework developed for marine picocyanobacteria, highlight common evolutionary and ecological patterns across the salinity divide, as well as features unique to freshwater and marine systems.