Seasonal and spatial dynamics of the phytoplankton community in the Salish Sea, 2015–2019

•Four phytoplankton functional types were identified by HPLC in the Canadian Salish Sea.•Phytoplankton composition defined three regions within the Canadian Salish Sea.•Phytoplankton composition differed between 2015 (warm year) and 2017 (cool year).•Strong vertical mixing favored centric diatoms; high temperatures and low nutrients favored haptophytes.•The pigment violaxanthin was diagnostic for Heterosigma akashiwo. A chemotaxonomic approach (HPLC) was used to determine the phytoplankton composition for the Salish Sea (coastal NE Pacific Ocean). The method was applied to 721 samples collected between 2015 and 2019. Microscopy was used to build then verify the CHEMTAX matrix and CHEMTAX outputs. Statistical methods were used to describe the patterns of phytoplankton composition over space and time. HPLC produced a more complete picture of the phytoplankton community than previous studies relying on microscopy. Nine taxonomic groups and four phytoplankton functional types were identified: (1) centric diatoms were present year round and were dominant during the spring bloom; (2) small flagellates (cryptophytes, haptophytes, prasinophytes) and pennate diatoms were ubiquitous but generally not bloom-forming; (3) large flagellates (dinoflagellates, dictyochophytes, raphidophytes) were mostly absent but with occasional very large blooms; and (4) cyanobacteria were rare. The pigment violaxanthin was diagnostic for Heterosigma akashiwo, which formed the largest bloom observed in our study (75 μg/L Tchl a). Cluster and network analyses identified three regions based on similarities in phytoplankton composition: (1) Juan de Fuca Strait and tidally mixed areas, (2) central Strait of Georgia, and (3) northern Strait of Georgia. Seasonally, significant differences in taxonomic composition occurred between winter and spring, and interannually between 2015 (a warmer year) and 2017 (a cooler year). Centric diatoms were associated with stronger vertical mixing, whereas haptophytes were associated with higher temperatures, reduced vertical mixing and lower nutrients. The CHEMTAX matrix we present is robust and useful for future studies in this area.