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Hourly, year‐round flow cytometry has made it possible to relate seasonal environmental variability to the population dynamics of the smallest, most abundant phytoplankton on the Northeast US Shelf. To evaluate whether the insights from these data extend toSynechococcusfarther from shore, we analyze flow cytometry measurements made continuously from the underway systems on 21 cruises traveling between the Martha's Vineyard Coastal Observatory (MVCO) and the continental shelf break. We describe how seasonal patterns inSynechococcus, which have been documented in detail at MVCO, occur across the region with subtle variation. We find that the underlying relationship between temperature and division rate is consistent across the shelf and can explain much of the observed spatial variability in concentration. Connecting individual cell properties to annual and regional patterns in environmental conditions, these results demonstrate the value of autonomous monitoring and create an improved picture of picophytoplankton dynamics within an economically important ecosystem.

Picophytoplankton are the most abundant primary producers in the ocean. Knowledge of their community dynamics is key to understanding their role in marine food webs and global biogeochemical cycles. To this end, we analyzed a 16-y time series of observations of a phytoplankton community at a nearshore site on the Northeast US Shelf. We used a size-structured population model to estimate in situ division rates for the picoeukaryote assemblage and compared the dynamics with those of the picocyanobacteriaSynechococcusat the same location. We found that the picoeukaryotes divide at roughly twice the rate of the more abundantSynechococcusand are subject to greater loss rates (likely from viral lysis and zooplankton grazing). We describe the dynamics of these groups across short and long timescales and conclude that, despite their taxonomic differences, their populations respond similarly to changes in the biotic and abiotic environment. Both groups appear to be temperature limited in the spring and light limited in the fall and to experience greater mortality during the day than at night. Compared withSynechococcus, the picoeukaryotes are subject to greater top-down control and contribute more to the region’s primary productivity than their standing stocks suggest.

Marine microbes often show a high degree of physiological or ecological diversity below the species level. This microdiversity raises questions about the processes that drive diversification and permit coexistence of diverse yet closely related marine microbes, especially given the theoretical efficiency of competitive exclusion. Here, we provide insight with an 8‐year time series of diversity withinSynechococcus, a widespread and important marine picophytoplankter. The population ofSynechococcuson the Northeast U.S. Shelf is comprised of six main types, each of which displays a distinct and consistent seasonal pattern. With compositional data analysis, we show that these patterns can be reproduced with a simple model that couples differential responses to temperature and light with the seasonal cycle of the physical environment. These observations support the hypothesis that temporal variability in environmental factors can maintain microdiversity in marine microbial populations. We also identify how seasonal diversity patterns directly determine overarchingSynechococcuspopulation abundance features.