Marine Synechococcus are ubiquitous picocyanobacteria which play a key role in global biogeochemical cycles. They exhibit highly diverse pigment types (PTs) and phylogenetic lineages (three subclusters and more than 20 clades) with distinct ecological traits and niche adaptations. Light, nutrients, temperature and other factors play vital roles in shaping the biogeography and niche segregation of different Synechococcus PTs and phylogenetic lineages. Synechococcus of different PTs contain different phycobiliproteins that absorb different light spectrum. Previous studies mainly focused on the pigment composition and ecophysiology of isolated strains, while knowledge gaps exist on how physical dynamics, such as mixing and stratification may affect the vertical distributions of different PTs in water columns. 
In this thesis, we investigated the dynamics of different Synechococcus PTs across hydrographically distinct systems. First, we analyzed the PT composition of Synechococcus in the eastern Indian Ocean (EIO) and revealed clear niche partitioning: Low-PUB PT 3a and partial-acclimator PT 3eA dominated in shallow coastal waters, while high-PUB acclimators PT 3dA and PT 3c/3dB prevailed in open ocean. Novel PT 3f was abundant throughout, particularly in upper euphotic zone of the oceanic water. Subsequently, we explored the vertical PT/lineage distributions within mesoscale eddies (cyclonic/CE; anticyclonic/ACE) in western South China Sea. Chromatic acclimating PTs dominated in both eddies, due to the great advantages over PTs with fixed pigmentation in eddies where ambient light intensity and spectrum change rapidly due to vertical mixing of upwelling and downwelling. PT 3dA dominated CE, while PT 3dB prevailed in ACE. Phylogenetically, Clade CRD1 dominated CE versus Clade II/III in ACE. Our results showed how physicochemical properties (light, nutrients, temperature) in mesoscale eddies shape the Synechococcus communities. 
Since nutrient availability is another vital factor in determining the niche of different Synechococcus lineages, we further tried to link the nutrient acquisition capability of different phylogenetic clades with their niche adaptation, with the focus on Clade III which are exclusively dominant in ultraoligotrophic Mediterranean waters. Combining dilution assays, nutrient-amended mesocosms, and genomics study, we found that Clade III displayed superior growth rates over others under ammonium/phosphate limitation. Genomic analyses revealed Clade III’s competitive advantage in adapting to extremely oligotrphic environment: more N/P transporters than most clades (except VIII/S5.2), reduced GC content, small genome, elevated pstS copy number, and heightened pstS expression relative to other transporters.