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Abstract Phytoplankton community size structure influences the production and fate of organic carbon in marine food webs and can undergo strong seasonal shifts in temperate regions. As part of the Northeast US Shelf (NES) Long‐Term Ecological Research program, we measured net primary production (NPP) rates and chlorophylla(Chla) concentrations in three phytoplankton size classes (< 5, 5–20, and > 20 μm) during winter and summer for 3 yr along a coastal‐to‐offshore transect. Mean depth‐integrated NPP was 37% higher in summer than winter, with limited cross‐shelf differences because of significant interannual variability. When averaged across the shelf, depth‐integrated NPP was dominated by the > 20 μm size class in winter and generated equally by the three size fractions in summer because of substantial contributions from cells > 20 μm at the Chlamaximum depth. Furthermore, the relationship between Chlaand NPP, in terms of relative contributions, varied by size class. Variations in this relationship have implications for models of primary productivity on the NES and beyond. In comparison to historical NPP data, we identified equivalent levels of winter NPP but observed a 25% decrease in summer NPP, suggesting a potential reduction in the seasonality of NPP on the NES. Together, our results highlight seasonal shifts in NPP rates of different phytoplankton size classes, with implications for food web structure and export production. These data emphasize the importance of quantifying size‐fractionated NPP over time to constrain its variability and better predict the fate of organic carbon in coastal systems under environmental change. 

Abstract In aquatic ecosystems, allochthonous nutrient transport to the euphotic zone is an important process that fuels new production. Here, we use high‐resolution physical and biogeochemical observations from five summers to estimate the mean vertical nitrate flux, and thus new production over the Northeast U.S. Shelf (NES). We find that the summertime nitrate field is primarily controlled by biological uptake and physical advection–diffusion processes, above and below the 1% light level depth, respectively. We estimate the vertical nitrate flux to be 8.2 ± 5.3 × 10⁻⁶ mmol N m⁻² s⁻¹for the mid‐shelf and 12.6 ± 8.6 × 10⁻⁶ mmol N m⁻² s⁻¹for the outer shelf. Furthermore, we show that the new production to total primary production ratio (i.e., the f‐ratio), consistently ranges between 10% and 15% under summer conditions on the NES. Two independent approaches—nitrate flux‐based new production and O₂/Ar‐based net community production—corroborate the robustness of the f‐ratio estimation. Since ~ 85% of the total primary production is fueled by recycled nutrients over sufficiently broad spatial and temporal scales, less than 15% of the organic matter produced in summer is available for export from the NES euphotic zone. Our direct quantification of new production not only provides more precise details about key processes for NES food webs and ecosystem function, but also demonstrates the potential of this approach to be applied to other similar datasets to understand nutrient and carbon cycling in the global ocean. 

Pseudo-nitzschia harmful algal blooms have recently caused elevated domoic acid in coastal environments of the Northeast United States. In 2017, the toxigenic species P. australis was observed in Narragansett Bay, Rhode Island, a temperate estuarine ecosystem, for the first time since 2009 when DNA monitoring for Pseudo-nitzschia species began. This highly toxic species likely contributed to toxin-related shellfish harvest closures and is hypothesized to have been introduced by an offshore source. Little is known about offshore Pseudo-nitzschia spp. populations in the Northeast Continental Shelf marine ecosystem or how often toxigenic species enter Narragansett Bay through physical processes. Here, we collected filtered biomass samples from multiple time series sites within Narragansett Bay and along the Northeast U.S. Shelf Long-Term Ecological Research transect in winter and summer to investigate the frequency and seasonality of potential Pseudo-nitzschia spp. inflow from the continental shelf to the estuary. Species were taxonomically identified using DNA sequencing of the ITS1 region and domoic acid concentrations were quantified by liquid chromatography with tandem mass spectrometry and multiple reaction monitoring. During six years of sampling, Pseudo-nitzschia species assemblages were more similar between Narragansett Bay and the Northeast shelf in winter than summer, suggesting greater ecosystem connectivity in winter. These winter assemblages were often accompanied by higher domoic acid. Several Pseudo-nitzschia species co-occurred most often with domoic acid and were likely responsible for toxin production in this region, including P. pungens var. pungens, P. multiseries, P. calliantha, P. plurisecta, P. australis, and P. fraudulenta. Domoic acid was detected during periods of relatively low macronutrient concentrations in both seasons, warmer sea surface temperatures in winter, and colder temperatures in summer within this dataset. This study represents some of the first domoic acid measurements on the offshore Northeast U.S. Continental Shelf, a region that supplies water to other coastal environments and could seed future harmful algal blooms. The elevated domoic acid and frequency of hypothesized inflow of toxigenic Pseudo-nitzschia spp. from the Northeast continental shelf to Narragansett Bay in winter indicate the need to monitor coastal and offshore environments for toxins and harmful algal bloom taxa during colder months. 

Long-term ecological time series provide a unique perspective on the emergent properties of ecosystems. In aquatic systems, phytoplankton form the base of the food web and their biomass, measured as the concentration of the photosynthetic pigment chlorophylla(chla), is an indicator of ecosystem quality. We analyzed temporal trends in chlafrom the Long-Term Plankton Time Series in Narragansett Bay, Rhode Island, USA, a temperate estuary experiencing long-term warming and changing anthropogenic nutrient inputs. Dynamic linear models were used to impute and model environmental variables (1959 to 2019) and chlaconcentrations (1968 to 2019). A long-term chladecrease was observed with an average decline in the cumulative annual chlaconcentration of 49% and a marked decline of 57% in winter-spring bloom magnitude. The long-term decline in chlaconcentration was directly and indirectly associated with multiple environmental factors that are impacted by climate change (e.g., warming temperatures, water column stratification, reduced nutrient concentrations) indicating the importance of accounting for regional climate change effects in ecosystem-based management. Analysis of seasonal phenology revealed that the winter–spring bloom occurred earlier, at a rate of 4.9 ± 2.8 d decade⁻¹. Finally, the high degree of temporal variation in phytoplankton biomass observed in Narragansett Bay appears common among estuaries, coasts, and open oceans. The commonality among these marine ecosystems highlights the need to maintain a robust set of phytoplankton time series in the coming decades to improve signal-to-noise ratios and identify trends in these highly variable environments. 

Abstract Diatoms are important components of the marine food web and one of the most species‐rich groups of phytoplankton. The diversity and composition of diatoms in eutrophic nearshore habitats have been well documented due to the outsized influence of diatoms on coastal ecosystem functioning. In contrast, patterns of both diatom diversity and community composition in offshore oligotrophic regions where diatom biomass is low have been poorly resolved. To compare the diatom diversity and community composition in oligotrophic and eutrophic waters, diatom communities were sampled along a 1,250 km transect from the oligotrophic Sargasso Sea to the coastal waters of the northeast US shelf. Diatom community composition was determined by amplifying and sequencing the 18S rDNA V4 region. Of the 301 amplicon sequence variants (ASVs) identified along the transect, the majority (70%) were sampled exclusively from oligotrophic waters of the Gulf Stream and Sargasso Sea and included the generaBacteriastrum,Haslea,Hemiaulus,Pseudo‐nitzschia, andNitzschia. Diatom ASV richness did not vary along the transect, indicating that the oligotrophic Sargasso Sea and Gulf Stream are occupied by a diverse diatom community. Although ASV richness was similar between oligotrophic and coastal waters, diatom community composition in these regions differed significantly and was correlated with temperature and phosphate, two environmental variables known to influence diatom metabolism and geographic distribution. In sum, oligotrophic waters of the western North Atlantic harbor diverse diatom assemblages that are distinct from coastal regions, and these open ocean diatoms warrant additional study, as they may play critical roles in oligotrophic ecosystems. 

Eukaryotic microalgae play critical roles in the structure and function of marine food webs. The contribution of microalgae to food webs can be tracked using compound-specific isotope analysis of amino acids (CSIA-AA). Previous CSIA-AA studies have defined eukaryotic microalgae as a single functional group in food web mixing models, despite their vast taxonomic and ecological diversity. Using controlled cultures, this work characterizes the amino acid δ13C (δ13CAA) fingerprints—a multivariate metric of amino acid carbon isotope values—of four major groups of eukaryotic microalgae: diatoms, dinoflagellates, raphidophytes, and prasinophytes. We found excellent separation of essential amino acid δ13C (δ13CEAA) fingerprints among four microalgal groups (mean posterior probability reclassification of 99.2 ± 2.9%). We also quantified temperature effects, a primary driver of microalgal bulk carbon isotope variability, on the fidelity of δ13CAA fingerprints. A 10°C range in temperature conditions did not have significant impacts on variance in δ13CAA values or the diagnostic microalgal δ13CEAA fingerprints. These δ13CEAA fingerprints were used to identify primary producers at the base of food webs supporting consumers in two contrasting systems: (1) penguins feeding in a diatom-based food web and (2) mixotrophic corals receiving amino acids directly from autotrophic endosymbiotic dinoflagellates and indirectly from water column diatoms, prasinophytes, and cyanobacteria, likely via heterotrophic feeding on zooplankton. The increased taxonomic specificity of CSIA-AA fingerprints developed here will greatly improve future efforts to reconstruct the contribution of diverse eukaryotic microalgae to the sources and cycling of organic matter in food web dynamics and biogeochemical cycling studies. 

This dataset consists of primary production measurements based on uptake of carbon-13 added as 13C-bicarbonate during 24-h deckboard incubations of seawater. Sampling occurred on cruises along the Northeast U.S. Shelf Long Term Ecological Research (NES-LTER) Transect during summer, fall, and winter, starting in summer 2019. Net primary production (NPP) was determined from particulate organic carbon (POC) content and associated stable isotope enrichment. Three data tables are included: 1. Depth-specific primary productivity based on fractional light levels of the surface irradiance with reference to the profile of photosynthetically active radiation (PAR). 2. Integrated primary productivity. 3. Natural abundance POC. The tables derive from the raw data included as other entities. 

These data include diatom composition information from a fixed sampling site in Narragansett, Bay, RI, USA over six years between dates 2008-12-09 and 2014-12-30. Sampling occurred monthly from 2008 to 2013 and twice per month in 2014. Diatom composition data, in the form of amplicon sequencing variants, were obtained via high throughput sequencing of filtered biomass samples. Diatoms are important contributors to marine primary production; however, their vast diversity makes species-level identification challenging. This dataset, collected over many years, includes diatom composition data at a more detailed level than ever before observed in Narragansett Bay and highlights the importance of time series for understanding phytoplankton dynamics in coastal systems. These data were collected by various students over the years with supervision from Dr. Tatiana Rynearson of URI's Graduate School of Oceanography. Diana Fontaine processed these data and together, Dr. Rynearson and her student Ms. Fontaine published their results in Limnology and Oceanography.