Seasonal Variations of Community Structure and Functional Genes of Synechococcus in the Subtropical Coastal Waters: Insights from FACS and High-Throughput Sequencing

<i>Synechococcus</i> plays a pivotal role in the marine biogeochemical cycle. Advances in isolation techniques and high-throughput sequencing have expanded our understanding of the diversity of the <i>Synechococcus</i> community. However, their genomic diversity, functional dynamics and seasonal variations in the coastal waters are still not well known. Here, seawater samples were collected seasonally (March, June, August, December) from three stations in the coastal waters of Xiamen. Using fluorescence-activated cell sorting (FACS), we isolated 1000 <i>Synechococcus</i> cells per sample and performed ITS amplicon sequencing and metagenomic sequencing to analyze the seasonal variations in community structure and functional genes of <i>Synechococcus</i>. Firstly, we conducted a comparative analysis of in situ data and FACS data from three sampling sites in August. FACS samples revealed low-abundance <i>Synechococcus</i> strains underdetected by in situ samples. In addition, 24 clades representing <i>Synechococcus</i> subclusters S5.1, S5.2, and S5.3 were detected from three in situ samples and twelve FACS samples, suggesting the high diversity of <i>Synechococcus</i> in the coastal waters of Xiamen. Furthermore, the <i>Synechococcus</i> community displayed pronounced seasonal variations, and temperature significantly influenced the variations in <i>Synechococcus</i> community composition. Additionally, <i>Synechococcus</i> populations exhibit seasonal functional dynamics, with enhanced metabolic activity in summer characterized by higher numbers of functional genes associated with metabolic pathways compared to winter samples. Altogether, this study underscored the significance of FACS and high-throughput sequencing to reveal the diversity and functional dynamics of <i>Synechococcus</i>.