Spatial and Temporal Variations in Synechococcus Microdiversity in the Southern California Coastal Ecosystem

The Synechococcus population at the Scripps Institution of Oceanography (SIO) pier in La Jolla, CA shows large increases in abundance, termed “blooms”, that are typically observed in the spring and summer and decline within weeks. Amplicon sequencing of the ITS (internal transcribed spacer) region was used to examine the microdiversity of this cyanobacterial genus during blooms at the SIO pier as well as further offshore in the Southern California coastal ecosystem (CCE). These analyses revealed numerous amplicon sequence variants (ASVs). We found that the ratio between the typically dominant clades at our site (clades I:IV) was different during each bloom and shifted over the course of some, but not all, blooms. We also found that in 2016 there was a highly anomalous bloom, both in its overall Synechococcus abundance and in terms of the Synechococcus clades present, with the generally oligotrophic Synechococcus clade II comprising an unexpectedly large proportion of this bloom. The dominant ASVs found further offshore and in the California Current were the same as those at the pier, but some ASVs showed distinct spatial variation indicating niche boundaries. We also observed that the dominant sequence variant switched during the peak of multiple Synechococcus blooms, with this switch occurring in multiple clades. Some evidence shows this apparent ASV switch to be a physiological response rather than a change in the dominant population. Combining flow cytometry with amplicon sequencing ASV analysis indicates that there are hidden dynamics of Synechococcus microdiversity with distinct spatial and temporal patterns.