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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. 

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. 

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. 

The extent and ecological significance of intraspecific functional diversity within marine microbial populations is still poorly understood, and it remains unclear if such strain-level microdiversity will affect fitness and persistence in a rapidly changing ocean environment. In this study, we cultured 11 sympatric strains of the ubiquitous marine picocyanobacteriumSynechococcusisolated from a Narragansett Bay (RI) phytoplankton community thermal selection experiment. Thermal performance curves revealed selection at cool and warm temperatures had subdivided the initial population into thermotypes with pronounced differences in maximum growth temperatures. Curiously, the genomes of all 11 isolates were almost identical (average nucleotide identities of >99.99%, with >99% of the genome aligning) and no differences in gene content or single nucleotide variants were associated with either cool or warm temperature phenotypes. Despite a very high level of genomic similarity, sequenced epigenomes for two strains showed differences in methylation on genes associated with photosynthesis. These corresponded to measured differences in photophysiology, suggesting a potential pathway for future mechanistic research into thermal microdiversity. Our study demonstrates that present-day marine microbial populations can harbor cryptic but environmentally relevant thermotypes which may increase their resilience to future rising temperatures. 

Abstract Diatoms are among the most abundant phytoplankton that inhabit coastal ecosystems, forming large blooms that fuel coastal food webs. Although diatoms are often large and morphologically distinct, many are small or morphologically cryptic making it difficult to understand the temporal dynamics of whole diatom communities and the environmental factors that drive them. Here, we investigated diatom diversity and its environmental correlates using 6 yr of monthly surface water samples from the Narragansett Bay Plankton Time Series to investigate the seasonal and annual variability of diatom species occurrence. High‐throughput amplicon sequencing of filtered biomass yielded 658 diatom amplicon sequence variants (ASVs), of which 347 were identified to species. Of the 49 diatom genera in the sequencing dataset, 33% had never been observed in the time series using microscopy (1959–2014). We observed a weak quadratic relationship between ASV richness and chlorophyll‐aconcentrations, suggesting that richness decreases during blooms. There was a significant difference in diatom ASV richness by season and we identified distinct assemblages associated with different seasons. These assemblages were remarkably synchronous, exhibiting a sinewave‐like pattern, over 6 yr with an annual periodicity that correlated significantly with seasonal changes in temperature, light, and dissolved inorganic nitrogen. The annual cycle of diatom assemblages suggests stability in a key component of the estuarine food web known to influence ecosystem resilience and function. Deviations from the annual cycle of recurrence could be used to distinguish between changes in community structure driven by annual fluctuations in the environment and those driven by climate‐change stressors. 

In 2016-17, shellfish harvesting closed for the first time in Narragansett Bay, Rhode Island, USA, from domoic acid (DA), a neurotoxin produced by diatoms of the Pseudo-nitzschia genus. Pseudo-nitzschia have occurred frequently for over 60 years in Narragansett Bay’s Long-Term Plankton Time Series (NBPTS), therefore it is surprising that the first closure only recently occurred. Pseudo-nitzschia species are known to vary in their toxin production, thus species identification is critical for understanding the underlying ecological causes of these harmful algal blooms (HABs). DNA in plankton biomass can be preserved for many years, so molecular barcoding of archived samples is useful for delineation of taxa over time. This study used amplification of the Pseudo-nitzschia -specific 18S-5.8S rDNA internal transcribed spacer region 1 (ITS1) in plankton samples and high throughput sequencing to characterize Pseudo-nitzschia species composition over a decade in Narragansett Bay, including eight years before the 2016-17 closures and two years following. This metabarcoding method can discriminate nearly all known Pseudo-nitzschia species. Several species recur as year-round residents in Narragansett Bay ( P. pungens var. pungens, P. americana, P. multiseries , and P. calliantha ). Various other species increased in frequency after 2015, and some appeared for the first time during the closure period. Notably, P. australis , a species prevalent in US West Coast HABs and known for high DA production, was not observed in Narragansett Bay until the 2017 closure but has been present in several years after the closures. Annual differences in Pseudo-nitzschia composition were correlated with physical and chemical conditions, predominantly water temperature. The long-term composition trends of Pseudo-nitzschia in Narragansett Bay serve as a baseline for identifying the introduction of new species, understanding shifting assemblages that contributed to the 2016-17 closures, and monitoring species that may be cause for future concern.