Microdiversity Shapes the Seasonal Niche of Prokaryotic Plankton Inhabiting Surface Waters in a Coastal Upwelling System.

Seasonality of prokaryotic abundance, diversity and community composition was investigated over a 2-year period in a coastal upwelling time-series station. A marked seasonality was found for prokaryotic abundance, peaking during upwelling and upwelling-to-downwelling transition, and decreasing during downwelling. The latter included a deeper mixed layer and a homogeneous water column favouring higher abundance of archaea (i.e., Marine Group II, Candiadatus nitrosopelagicus), SAR406 clade and the group Bacteria_Others including > 400 rare taxa. Upwelling and transition conditions, characterised by enhanced vertical stratification and a marked hydrographic variability, included a community less diverse with core-phylotypes proliferating, i.e., Flavobacteriaceae, Amylibacter and Planktomarina. Physical and biogeochemical variables collectively explained > 40% of the seasonal changes in prokaryotic assemblages. Additionally, fine-tune bacterial features evidenced 'closely related taxa' within particular bacterial phylotypes such as SAR116 clade; certain Flavobacteria belonging to NS2b, NS4 or NS9; members of the family Cryomorphaceae and Marine Group II, displaying seasonal microdiversity patterns. Taken together, seasonal hydrographic forcing induces a shift in the upwelling-driven microbiome providing new insights into the barely explored seasonal niche partitioning of surface prokaryotic communities in such highly productive upwelling systems. These results are of broad interest for understanding ecosystem functioning and forecast the impacts of current environmental change.