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ABSTRACT The diversity of the marine cyanobacteriumSynechococcuscan be broadly separated into clades, with clade II typically present in warm oligotrophic water, and clades I and IV found in cooler coastal water. We found amplicon sequence variants (ASVs) belonging to clade II in the nutrient‐replete waters of San Diego Bay (SDB). Using the 16S rRNA gene, 18S rRNA gene and internal transcribed spacer region sequencing, we analysed multiple locations in SDB monthly for over a year, with additional samples dating back to 2015.Synechococcuscommunity composition differed from the nearby coast into SDB in terms of dominant clade and ASVs. Specific clade II ASVs became relatively more abundant towards the back of the bay and showed seasonality, with higher relative abundance in the warm months. Select ASVs group phylogenetically and show similar seasonal and spatial distribution patterns, indicating these ASVs have adapted to SDB. Isolates matching clade II ASVs from SDB show pigment composition that is better adapted to the green light available in SDB, further supporting our findings. Other microbial taxa also show SDB enrichment, providing evidence that SDB is a chemostat‐like environment where circulation, temperature, light and other environmental conditions create a zone for microbial evolution and diversification. 

Summary TheSynechococcuscyanobacterial population at the Scripps Institution of Oceanography pier in La Jolla, CA, shows large increases in abundance, typically in the spring and summer followed, by rapid declines within weeks. Here we used amplicon sequencing of the ribosomal RNA internal transcribed spacer region to examine the microdiversity within this cyanobacterial genus during these blooms as well as further offshore in the Southern California coastal ecosystem (CCE). These analyses revealed numerousSynechococcusamplicon sequence variants (ASVs) and that clade and ASV composition can change over the course of blooms. We also found that a large bloom in August 2016 was highly anomalous both in its overallSynechococcusabundance and in terms of the presence of normally oligotrophicSynechococcusclade II. The dominant ASVs at the pier were found further offshore and in the California Current, but we did observe more oligotrophic ASVs and clades along with depth variation inSynechococcusdiversity. We also observed that the dominant sequence variant switched during the peak of multipleSynechococcusblooms, with this switch occurring in multiple clades, but we present initial evidence that this apparent ASV switch is a physiological response rather than a change in the dominant population.