Seasonal change in the abundance of Synechococcus and multiple distinct phylotypes in Monterey Bay determined by rbcL and narB quantitative PCR

Summary Synechococcus is a cosmopolitan marine cyanobacterial genus, and is often the most abundant picocyanobacterial genus in coastal waters. Little is known about Synechococcus seasonal dynamics in coastal zones highly impacted by upwelling. This was investigated by collecting seasonal samples from an upwelling‐impacted Monterey Bay (MB) monitoring station M0, in parallel with measurements of oceanographic conditions during 2006–2008. Synechococcus abundances were determined using quantitative PCR (qPCR) assays and flow cytometry (FCM). A new qPCR assay was designed to target dominant Synechococcus in MB using the rbcL gene, while previously designed assays targeted distinct phylotypes (called narB subgroups) with the narB gene. The rbcL qPCR assay successfully tracked abundant Synechococcus in MB, accounting for on average 89% (± 57%) of FCM‐based counts. Annual spring upwelling caused decreases in Synechococcus and narB subgroup abundances. Differences in narB subgroup abundance maxima and abundance patterns support the view that subgroups differ in their ecologies, including subgroup D_C1, which seems to specifically thrive in coastal waters. Correlations between narB subgroup abundances and measured environmental variables were similar among the subgroups. Therefore, non‐measured environmental factors (e.g. metals, mortality) likely had different influences on subgroups, which led to their distinct abundance patterns at M0.