Genomic and transcriptomic evidence for the diverse adaptations of Synechococcus subclusters 5.2 and 5.3 to mesoscale eddies

Summary Mesoscale eddies are ubiquitous oceanographic features that influence the metabolism and community structure of Synechococcus. However, the metabolic adaptations of this genus to eddy‐associated environmental changes have rarely been studied. We recovered two high‐quality Synechococcus metagenome‐assembled genomes (MAGs) from eddies in the South China Sea and compared their metabolic variations using metatranscriptomic samples obtained at the same time. The two MAGs (syn‐bin1 and syn‐bin2) are affiliated with marine Synechococcus subclusters 5.2 (S5.2) and 5.3 (S5.3), respectively. The former exhibited a higher abundance at the surface layer, whereas the latter was more abundant in the deep euphotic layer. Further analysis indicated that syn‐bin1 had a strong ability to utilize organic nutrients, which could help it to thrive in the nutrient‐deprived surface water. By contrast, syn‐bin2 had the genetic potential to perform chromatic acclimation, which could allow it to capture green or blue light at different depths. Additionally, transcriptomic analysis showed that syn‐bin2 upregulated genes involved in the synthesis of C4 acids, photosystem II proteins, and HCO3‐ transporters in the deep euphotic layer, which might contribute to its predominance in low‐light environments. Overall, this study expands our understanding of oceanic S5.2 and S5.3 Synechococcus by revealing their metabolic adaptations to mesoscale eddies.