Does nutrient scarcity select for Synechococcus clade III in the Mediterranean Sea?

Synechococcus inhabit both nutrient‐rich estuaries and oligotrophic waters, yet exhibit distinct niche segregation across phylogenetic clades. Previous studies indicated clade III predominated in the ultraoligotrophic Mediterranean Sea. However, the mechanisms underlying clade III's dominance over other clades in ultraoligotrophic waters remain unclear. Here, we measured bulk and clade‐specific growth rates of Synechococcus using a dilution approach during a mesocosm experiment in the Eastern Mediterranean Sea. Clade III exhibited higher growth rates than competing clades and competitive superiority for limited nutrients in mesocosms amended with ammonium and phosphate. Genomic analyses revealed clade III possessed more nitrogen/phosphorus transporters than other clades (except clade VIII and S5.2), which may contribute to their competitive advantage in ultraoligotrophic conditions. Compared to clade VIII/S5.2, clade III's lower GC content and smaller genome size are consistent with adaptation to oligotrophic systems. The unique adaptive genomic traits of clade III Synechococcus may facilitate their ecological success in ultraoligotrophic waters.