Description: The data-sets comes from three locations representative of three different marine ecosystems: Fjord (Chilean Patagonia), Ny-Ålesund (Arctic) and Mediterranean (Crete). It contains chemical and biological data collected in three mesocosm and four microcosm experiments conducted in the spring - summer period, in which the physico-chemical (pH, Carbon) and biological (grazing) conditions were altered to represent potential future climate change scenarios. The data-sets contains measurements in: carbonate chemistry, macro- and micro-nutrients concentrations, primary production, phytoplankton taxonomy, virus abundance, bacterial production, bacterial abundance, Zoo- and microzoo-plankton abundance, grazing rates for different taxonomic groups.

Description: The purpose of the present study was to explore the composition and variation of the pico-, nano- and micro-plankton communities in Norwegian coastal waters and Skagerrak, and the co-occurrence of bacteria and viruses. Samples were collected along three cruise transects from Jaeren, Lista and Oksoy on the south coast of Norway and into the North Sea and Skagerrak. We also followed a drifting buoy for 55 h in Skagerrak in order to observe diel variations. Satellite ocean color images (SeaWiFS) of the chlorophyll a (chl a) distribution compared favorably to in situ measurements in open waters, while closer to the shore remote sensing chl a data was overestimated compared to the in situ data. Using light microscopy, we identified 49 micro- and 15 nanoplankton sized phototrophic forms as well as 40 micro- and 12 nanoplankton sized heterotrophic forms. The only picoeukaryote (0.2-2.0 µm) we identified was Resultor micron (Pedinophyceae). Along the transects a significant variation in the distribution and abundance of different plankton forms were observed, with Synechococcus spp and autotrophic picoeukaryotes as the most notable examples. There was no correlation between viruses and chl a, but between viruses and bacteria, and between viruses and some of the phytoplankton groups, especially the picoeukaryotes. Moreover, there was a negative correlation between nutrients and small viruses (Low Fluorescent Viruses) but a positive correlation between nutrients and large viruses (High Fluorescent Viruses). The abundance of autotrophic picoplankton, bacteria and viruses showed a diel variation in surface waters with higher values around noon and late at night and lower values in the evening. Synechococcus spp were found at 20 m depth 25-45 nautical miles from shore apparently forming a bloom that stretched out for more than 100 nautical miles from Skagerrak and up the south west coast of Norway. The different methods used for assessing abundance, distribution and diversity of microorganisms yielded complementary information about the plankton community. Flow cytometry enabled us to map the distribution of the smaller phytoplankton forms, bacteria and viruses in more detail than has been possible before but detection and quantification of specific forms (genus or species) still requires taxonomic skills, molecular analysis or both.

Description: This dataset is a subset of the abundance of microorganisms (smaller than 20 µm) enumerated using flow cytometry (FCM) during the Multidisciplinary drifting observatory for the study of Arctic Climate (MOSAiC) sampled from first year sea ice (FYI) core bottom 5 cm sections from leg 2 and 3 (February, March, April 2020). For sea ice derived FCM abundance data, subsamples of 15 mL were taken from pooled ice core sections that were melted in filtered sea water and correspondingly a correction factor applied (details provided in the data-file), to enumerate the abundance of microorganisms per mL of melted sea ice. Additional expedition and sampling details can be found in the ECO-overview paper (Fong et al., to be submitted to Elementa). We thank all persons involved in the expedition of the Research Vessel Polarstern during MOSAiC in 2019-2020 (AWI_PS122_00) as listed in Nixdorf et al. (2021). Flow cytometry (FCM) is a fast, high-throughput method to enumerate the abundance of microorganism (smaller than 20 µm). FCM uses the hydrodynamic focusing of a laminar flow to separate and line up microscopic particles. When particles pass a laser beam, the generated light scattering can be used to estimate their cell size, obtain information about cell granularity and surface characteristics and determine fluorescence from inherent pigments or applied stains, such as DNA binding ones. Photosynthetic microorganisms have auto-fluorescent pigments, such as chlorophylls which in combination with the light scattering properties (cell size) or surface properties, can be used to group them into clusters of similar or identical organism types. Heterotrophic microorganisms, including archaea, bacteria and heterotrophic nanoflagellates, and virus do not have fluorescent pigments and require staining, for example using SYBR Green to stain Nucleic Acids (DNA) in order to distinguish these cells from other organic and inorganic particles in the sample. Samples for flow cytometric analysis were taken in triplicates or quadruplicates of 1.8 mL of sample water and fixed with 36 μL 25 % glutaraldehyde (0.5 % final concentration) at 4 °C in the dark for approximately 2 hours, then flash frozen in liquid nitrogen and stored at -80 °C until analysis. The abundance of pico- and nano-sized phytoplankton and heterotrophic nanoflagellates (HNF) were determined using an Attune® NxT, Acoustic Focusing Cytometer (Invitrogen by Thermo Fisher Scientific) with a 20 mW 488 nm (blue) laser. Autotrophic pico-and nano-sized plankton were counted directly after thawing and the various groups discriminated based on their red fluorescence (BL3) vs. orange fluorescence (BL2), red fluorescence (BL3) vs. side scatter (SSC) and orange fluorescence (BL2) vs. side scatter (SSC). For HNF analysis, the samples were stained with SYBR Green I for 2 h in the dark and 1-2 mL were subsequently measured at a flow rate of 500 µl min-1 following the protocol of Zubkov et al. 2007. Following the Zubkov protocol, HNF are enumerated using a fixed gate and in case of sea ice samples, there is an overlap between HNA-bacteria with very high fluorescence and HNF, which is not possible to disentangle with current methodology. The abundance of virus and bacteria was determined using a FACS Calibur (Becton Dickinson) flow cytometer with a 15 mW 480 nm (blue) laser. Prior analysis of virus and bacteria, samples were first thawed, diluted x10 and x100 with 0.2 μm filtered TE buffer (Tris 10 mM, EDTA 1 mM, pH 8), stained with a green fluorescent nucleic acid dye (SYBR Green I ; Molecular Probes, Eugene, Oregon, USA) and then incubated for 10 min at 80°C in a water bath (Marie et al. 1999). Stained samples were counted at a flow rate of around 60 µL min-1 and different groups discriminated on a biparametric plot of green florescence (BL1) vs. side scatter (SSC). This allowed to distinguish virus particles of different sizes, and different bacterial groups including low nuclear acid (LNA) and high nuclear acid (HNA) bacteria. Names of size groups of photosynthetic and heterotrophic organisms are in accordance to "Standards and Best Practices For Reporting Flow Cytometry Observations: a technical manual (Version 1.1)" (Neeley et al., 2023). A short summary is listed here: RedPico = picophytoplankton (1-2 µm); RedNano = Nanophytoplankton (2-20µm), which includes subgroups RedNano_small (2-5 µm), RedNano_large (5-20 µm); OraPico = Nanophytoplankton with more orange fluorescence; OraNano = Cryptophytes; OraPicoProk = Synechococcus; HetNano = heterotrophic nanoflagellates; HetProk = bacteria (and when present archaea); HetLNA = low nucleic acid (LNA) containing bacteria; HetHNA = high nucleic acid (HNA) containing bacteria with the subgroups HetProk_medium = HNA-bacteria subgroup with less fluorescence signal, HetProk_large = HNA-bacteria subgroup with more fluorescence signal and HetProk_verylarge = HNA-bacteria subgroup with very strong fluorescence signal; Virus = virus-like particles, including size refined subgroups: LFV (low fluorescence virus or small virus); MFV (medium fluorescence virus or medium virus); HFV (high fluorescence virus or large virus) according to Larsen et al., 2008. Exemplary plots showing the gating strategies that were followed can be found in "Interoperable vocabulary for marine microbial flow cytometry" (Thyssen et al., 2022).

Description: This dataset gives an overview of the abundance of microorganisms (smaller than 20 µm) enumerated using flow cytometry (FCM) during the Multidisciplinary drifting observatory for the study of Arctic Climate (MOSAiC) sampled from ship-based and on-ice CTD rosettes during leg 1, 2, 3, 4 and 5 (November 2019 – September 2020). Additional expedition and sampling details can be found in the ECO-overview paper (Fong et al., to be submitted to Elementa). We thank all persons involved in the expedition of the Research Vessel Polarstern during MOSAiC in 2019-2020 (AWI_PS122_00) as listed in Nixdorf et al. (2021). Flow cytometry (FCM) is a fast, high-throughput method to enumerate the abundance of microorganism (smaller than 20 µm). FCM uses the hydrodynamic focusing of a laminar flow to separate and line up microscopic particles. When particles pass a laser beam, the generated light scattering can be used to estimate their cell size, obtain information about cell granularity and surface characteristics and determine fluorescence from inherent pigments or applied stains, such as DNA binding ones. Photosynthetic microorganisms have auto-fluorescent pigments, such as chlorophylls which in combination with the light scattering properties (cell size) or surface properties, can be used to group them into clusters of similar or identical organism types. Heterotrophic microorganisms, including archaea, bacteria and heterotrophic nanoflagellates, and virus do not have fluorescent pigments and require staining, for example using SYBR Green to stain Nucleic Acids (DNA/RNA) in order to distinguish these cells from other organic and inorganic particles in the sample. Samples for flow cytometric analysis were taken in triplicates or quadruplicates of 1.8 mL of sample water and fixed with 36 μL 25 % glutaraldehyde (0.5 % final concentration) at 4 °C in the dark for approximately 2 hours, then flash frozen in liquid nitrogen and stored at -80 °C until analysis. The abundance of pico- and nano-sized phytoplankton and heterotrophic nanoflagellates (HNF) were determined using an Attune® NxT, Acoustic Focusing Cytometer (Invitrogen by Thermo Fisher Scientific) with a 20 mW 488 nm (blue) laser. Autotrophic pico-and nano-sized plankton were counted directly after thawing and the various groups discriminated based on their red fluorescence (BL3) vs. orange fluorescence (BL2), red fluorescence (BL3) vs. side scatter (SSC) and orange fluorescence (BL2) vs. side scatter (SSC). For HNF analysis, the samples were stained with SYBR Green I for 2 h in the dark and 1-2 mL were subsequently measured at a flow rate of 500 µl min-1 following the protocol of Zubkov et al. 2007. The abundance of virus and bacteria was determined using a FACS Calibur (Becton Dickinson) flow cytometer with a 15 mW 480 nm (blue) laser. Prior analysis of virus and bacteria, samples were first thawed, diluted x10 and x100 with 0.2 μm filtered TE buffer (Tris 10 mM, EDTA 1 mM, pH 8), stained with a green fluorescent nucleic acid dye (SYBR Green I ; Molecular Probes, Eugene, Oregon, USA) and then incubated for 10 min at 80°C in a water bath (Marie et al. 1999). Stained samples were counted at a flow rate of around 60 µL min-1 and different groups discriminated on a biparametric plot of green florescence (BL1) vs. side scatter (SSC). This allowed to distinguish virus particles of different sizes, and different bacterial groups including low nuclear acid (LNA) and high nuclear acid (HNA) bacteria. Names of size groups of photosynthetic and heterotrophic organisms are in accordance to "Standards and Best Practices For Reporting Flow Cytometry Observations: a technical manual (Version 1.1)" (Neeley et al., 2023). A short summary is listed here: RedPico = picophytoplankton (1-2 µm); RedNano = Nanophytoplankton (2-20µm), which includes subgroups RedNano_small (2-5 µm), RedNano_large (5-20 µm); OraPico = Nanophytoplankton with more orange fluorescence; OraNano = Cryptophytes; OraPicoProk = Synechococcus; HetNano = heterotrophic nanoflagellates; HetProk = bacteria (and when present archaea); HetLNA = low nucleic acid (LNA) containing bacteria; HetHNA = high nucleic acid (HNA) containing bacteria with the subgroups HetProk_medium = HNA-bacteria subgroup with less fluorescence signal, HetProk_large = HNA-bacteria subgroup with more fluorescence signal and HetProk_verylarge = HNA-bacteria subgroup with very strong fluorescence signal; Virus = virus-like particles, including size refined subgroups: LFV (low fluorescence virus or small virus); MFV (medium fluorescence virus or medium virus); HFV (high fluorescence virus or large virus) according to Larsen et al., 2008. Exemplary plots showing the gating strategies that were followed can be found in "Interoperable vocabulary for marine microbial flow cytometry" (Thyssen et al., 2022).

Description: Data were collected on and off the shelf northwest of Svalbard during cruises in January, March, May, August and November 2014. The sampling depths were 1, 5, 10, 20, 30, 50, 100, 200, 500, 750, and 1000 m, as well as at the depth of the Chl a maximum. The sampling concentrated on the core of the northwards drifting warm Atlantic water, which enters the Arctic Ocean north of Svalbard either south or north of the Yermark plateau. Transects were sampled across the core of the Atlantic water inflow at 79N, and additionally at 79.4N in May and August. Heavy drift ice restricted the sampling to the shelf and shelf-break in May and August 2014. During January, March, and November, the area north of Svalbard was largely ice-free, which allowed sampling off the shelf-break into the Arctic Ocean during winter. At all stations, depth profiles of temperature, salinity and fluorescence were taken with a CTD (Seabird SBE 911 plus). Water was sampled with Niskin bottles from discrete depths for analysis of inorganic nutrients, chlorophyll a (Chl a), microbial abundance, bacterial production (BP), as well as DOM and POM. In May and August, three process stations each (in datasheet referred to as P-stations: P1, P3, P4 in May, and P5, P6, P7 in August, at these stations more time-demanding processes were investigated, such as in situ primary production and vertical export of POM. Chl a was determined by filterig 100-500mL water onto Whatmann GF/F glass fiber filters. Chl a was determined fluorometrically (10-AU, Turner Designs) from triplicates of each filter type after extraction in 5 mL methanol at room temperature in the dark for 12 h without grinding. Abundances of microorganisms: picophytoplankton, nanophytoplankton, virus, heterotrophic bacteria, and heterotrophic nanoflagellates were determined on an Attune(R) Focusing Flow Cytometer (Applied Biosystems by Life technologies) with a syringe-based fluidic system and a 20 mW 488 nm (blue) laser. Samples were fixed with glutaraldehyde (0.5% final conc.) at 4°C for minimum 2 h, shock frozen in liquid nitrogen, and stored at -80 °C until analysis. Total organic carbon (TOC) in unfiltered seawater was analyzed by high temperature combustion using a Shimadzu TOC-VCSH. All samples were acidified with HCl (to a pH of around 2) and bubbled with pure N2 gas in order to remove any inorganic carbon. Calibration was performed using deep seawater and low carbon reference waters. A blank consisting of milliQ water was analyzed every eighth sample to assess the day-to-day instrument variability. Concentration of total nitrogen (TN) was determined simultaneously by high temperature combustion using a CPH-TN nitrogen analyzer. Total organic nitrogen (TON) was calculated by subtracting the inorganic nitrogen (NOx = NO3 + NO2 + NH4+) measured from parallel nutrient samples. The instrument was calibrated using a standard series of acetoanilide and the accuracy of the instrument was evaluated using seawater reference material provided by the Hansell CRM (consensus reference material) program. For analysis of particulate organic carbon (POC) and particulate organic nitrogen (PON), triplicate subsamples (100 - 500 mL) were filtered onto precombusted Whatman GF/F glass-fibre filters (450°C for 5 h), dried at 60°C for 24 h and analyzed on-shore with a Leeman Lab CEC 440 CHN analyzer. Prior to analysis, the dried samples were fumed by concentrated HCl in 24 h before re-drying at 60°C for 24 h to remove inorganic carbon. Unfiltered seawater was filled directly from the Niskin bottles into 30 mL acid washed HDPE bottles and stored at -20°C. Nitrite and nitrate (NO-2 + NO- 3 ), phosphate (PO3- 4 ) and silicic acid (H4SiO4) were measured on a Smartchem200 (by AMS Alliance) autoanalyser following procedures as outlined in Wood et al. (1967) for NO-3 + NO-2 , Murphy and Riley (1962) for PO3-4 and Koroleff (1983) for the determination of H4SiO4. The determination of NO-3 was done by reduction to NO-2 on a built-in cadmium column, which was loaded prior to every sample run. Seven-point standard curves were made prior to every run. Two internal standards and one blank were inserted for every 8 samples and these were used to correct for any drift in the measurements. Concentration of NH+4 was determined directly in fresh samples using ortho-phthaladehyde according to Holmes et al. (1999)