Temporal and spatial dynamics of Synechococcus clade II and other microbes in the eutrophic subtropical San Diego Bay

This data set comprises amplicon sequence variants (ASVs) from the nutrient-replete waters of San Diego Bay (SDB). Using 16S and 18S rRNA gene and internal transcribed spacer (ITS) region sequencing for Synechococcus, we analyzed multiple locations in San Diego Bay monthly for over a year (2021-2022) with additional samples dating back to 2015. San Diego Bay ITS region sequences were compared to nearby coastal samples collected from the Scripps Pier at Scripps Institution of Oceanography.