Single-cell quantification reveals divergent mixotrophic strategies underlying niche partitioning in marine Synechococcus

Marine Synechococcus is among the most widespread and productive autotrophs in the ocean, yet the quantitative role of mixotrophy in different lineages remains poorly constrained. Here, we compared organic nitrogen (urea and leucine) and carbon (glucose) utilization in nutrient-depleted versus nutrient-rich Synechococcus lineages by combining NanoSIMS-based single-cell measurements from field and laboratory incubations with omics analyses. Our findings revealed distinct mixotrophic strategies in different lineages. In nutrient-depleted lineages, elevated urea uptake supplied approximately 40–63% of the estimated total nitrogen demand. This pattern aligned with genomic evidence of enhanced urea transport, particularly the up-regulation of the high-affinity urea transporter DUR3 in low-nitrogen environments. In contrast, nutrient-rich lineages exhibited greater glucose uptake, although the amended organic substrates contributed only 2 to 4% to the estimated cellular carbon demand. These lineage-specific mixotrophic strategies underpinned niche partitioning in marine Synechococcus , refining our understanding of their trophic differentiation and its implications for marine biogeochemical cycling.