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Background and aims: The strong clinical association between primary sclerosing cholangitis (PSC) and ulcerative colitis (UC) suggests common factors in their pathogenesis. Smoking, previous appendectomy, and tonsillectomy have been associated [...]

Vertical velocities can be estimated indirectly from in situ observations by theoretical frameworks like the ω‐equation. Direct measures of vertical exchanges are challenging due to their typically ephemeral spatiotemporal scales. In this study we address this problem with an adaptive sampling strategy coupling various biophysical instruments. We analyze the 3‐D organization of a cyclonic mesoscale structure finely sampled during the Observing Submesoscale Coupling At High Resolution cruise in the Ligurian Sea during fall 2015. The observations, acquired with a moving vessel profiler, highlight a subsurface low‐salinity layer (≃50 m), as well as rising isopycnals, generated by geostrophic cyclonic circulation, in the structure's center. Reconstructed 3‐D fields of density and horizontal velocities are used to estimate the vertical velocity field down to 250 m by applying the adiabatic QG ω‐equation, for the first time in this region. The vertical motions are characterized by multipolar patterns of downward and upward velocities on the edges of the structure and significantly smaller vertical velocities in its center. Both the 3‐D distribution of particles (size ≥100 μm), measured with a laser optical plankton counter, and the Synechococcus and Prochlorococcus abundances (cell per cubic meter) measured by flow cytometry are consistent with the 3‐D velocity field. In particular, a secondary vertical recirculation is identified that upwells particles (from 250 to 100 m) along isohalines to the structure's center. Besides demonstrating the effect of vertical patterns on biogeochemical distributions, this case study suggests to use particle matter as a tracer to assess physical dynamics. Key Points: An adaptive sampling strategy allows for fine‐scale observations of biophysical vertical processes inside a cyclonic mesoscale structureMultipolar patterns of intense downward and upward velocities (from adiabatic QG omega‐equation) are identified on the edges of the structureParticle matter appears as a valid tracer of vertical velocities [ABSTRACT FROM AUTHOR]

Phytoplankton observation in the ocean can be a challenge in oceanography. Accurate estimations of their biomass and dynamics will help to understand ocean ecosystems and refine global climate models. This requires relevant datasets of phytoplankton at a functional level and on a daily and sub meso scale. In order to achieve this, an automated, high frequency, dedicated scanning flow cytometer (SFC, Cytobuoy, NL), has been developed to cover the entire size range of phytoplankton cells whilst simultaneously taking pictures of the largest of them. This cytometer was directly connected to the water inlet of a pocket Ferry Box during a cruise in the North Sea, 8-12 May 2011 (DYMAPHY project, INTERREG IV A "2 Seas"), in order to identify the phytoplankton community structure of near surface waters (6m) with a high resolution spacial basis (2.2±1.8 km). Ten groups of cells, distinguished on the basis of their optical pulse shapes, were described (abundance, size estimate, red fluorescence per unit volume). Abundances varied depending on the hydrological status of the traversed waters, reflecting different stages of the North Sea blooming period. Comparisons between several techniques analyzing chlorophyll and the scanning flow cytometer, using the integrated red fluorescence emitted by each counted cell, showed significant correlations. The community structure observed from the automated flow cytometry was compared with the PHYSAT reflectance anomalies over a daily scale. The number of matchups observed between the SFC automated high frequency in situ sampling and the remote sensing was found to be two to three times better than when using traditional water sampling strategies. Significant differences in the phytoplankton community structure within the two days for which matchups were available, suggest that it is possible to label PHYSAT anomalies not only with dominant groups, but at the level of the community structure. [ABSTRACT FROM AUTHOR]

Phytoplankton cells in the size range ∼1-50 μm were analysed in surface waters using an automated flow cytometer, the Cytosub (http://www.cytobuoy.com), from the Azores to the French Brittany during spring 2007. The Cytosub records the pulse shape of the optical signals generated by phytoplankton cells when intercepted by the laser beam. A total of 6 distinct optical groups were resolved during the whole transect, and the high frequency sampling (15 min) provided evidence for the cellular cycle (based on cyclic changes in cell size and fluorescence) and distribution changes linked to the different water characteristics crossed in the north east Atlantic provinces. Nutrient concentrations and mixed layer depth varied from west to east, with a decrease in the mixed layer depth and high nutrient concentrations in the middle of the transect as well as near the French coast. Data provided a link between the sub meso scale processes and phytoplankton patchiness, some abundance variations due to the cellular cycle can be pointed out. The high frequency spatial sampling encompasses temporal variations of the phytoplankton abundance, offering a better insight into phytoplankton distribution. [ABSTRACT FROM AUTHOR]

The ultraphytoplankton composition and dynamics were assessed during a Saharan dust event occurring off the southern Tunisian coasts during the MERITE-HIPPOCAMPE Trans-Mediterranean oceanographic cruise. The composition of atmospheric dust was characterized in terms of nutriments and trace metals. Data-assimilative hydrodynamic model revealed no differences in the hydrological features along the sampling track and almost no water transport occurred during the period of atmospheric deposition. Dust deposition increased the growth rates and the productivity of the major phytoplanktonic cytometric groups, resulting in the highest surface biomass along the Mediterranean transect. One group, distinguished by low fluorescence and nanoplanktonic size, reacted to dust deposition within hours, exhibiting the highest growth rate and net productivity. The dust composition showed a substantial enrichment with organic phosphorous representing (56 % of Total phosphorus) and trace metals mainly Fe, Mn and V., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

This paper looks at experiential feedback and the technical and scientific challenges tied to the MERITE-HIPPOCAMPE cruise that took place in the Mediterranean Sea in spring 2019. This cruise proposes an innovative approach to investigate the accumulation and transfer of inorganic and organic contaminants within the planktonic food webs. We present detailed information on how the cruise worked, including 1) the cruise track and sampling stations, 2) the overall strategy, based mainly on the collection of plankton, suspended particles and water at the deep chlorophyll maximum, and the separation of these particles and planktonic organisms into various size fractions, as well as the collection of atmospheric deposition, 3) the operations performed and material used at each station, and 4) the sequence of operations and main parameters analysed. The paper also provides the main environmental conditions that were prevailing during the campaign. Lastly, we present the types of articles produced based on work completed by the cruise that are part of this special issue., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier Ltd. All rights reserved.)

Here we assessed the subsurface ultraphytoplanktonic (< 10 μm) community along a North-South round-trip Mediterranean transect as part of a MERITE-HIPPOCAMPE cruise campaign in April-May 2019. Temperature, salinity, and nutrient concentrations in subsurface waters (2-5 m depth) were also measured along the transect. The subsurface ultraphytoplankton community structure was resolved with a spatial resolution of few kilometers and temporal resolution of 30-min intervals using automated pulse shape recording flow cytometry. The subsurface waters were clustered into seven areas based on temperature and salinity characteristics. Synechococcus were by far the most abundant group in all prospected zones, and nanoeukaryotes were the main biomass component, representing up to 51 % of ultraphytoplanktonic carbon biomass. Apparent net primary productivity (NPP) followed a decreasing gradient along the transect from north to south and was mostly sustained by Synechococcus in all zones. These findings are likely to have implications in terms of the trophic transfer of contaminants in planktonic food webs, as they highlight the potential role of nanoplankton in contaminants bioaccumulation processes and the potential role of Synechococcus in a likely transfer via grazing activities., (Copyright © 2022. Published by Elsevier Ltd.)

Human exposure to toxic mercury (Hg) is dominated by the consumption of seafood 1,2 . Earth system models suggest that Hg in marine ecosystems is supplied by atmospheric wet and dry Hg(II) deposition, with a three times smaller contribution from gaseous Hg(0) uptake 3,4 . Observations of marine Hg(II) deposition and Hg(0) gas exchange are sparse, however 5 , leaving the suggested importance of Hg(II) deposition 6 ill-constrained. Here we present the first Hg stable isotope measurements of total Hg (tHg) in surface and deep Atlantic and Mediterranean seawater and use them to quantify atmospheric Hg deposition pathways. We observe overall similar tHg isotope compositions, with median Δ 200 Hg signatures of 0.02‰, lying in between atmospheric Hg(0) and Hg(II) deposition end-members. We use a Δ 200 Hg isotope mass balance to estimate that seawater tHg can be explained by the mixing of 42% (median; interquartile range, 24-50%) atmospheric Hg(II) gross deposition and 58% (50-76%) Hg(0) gross uptake. We measure and compile additional, global marine Hg isotope data including particulate Hg, sediments and biota and observe a latitudinal Δ 200 Hg gradient that indicates larger ocean Hg(0) uptake at high latitudes. Our findings suggest that global atmospheric Hg(0) uptake by the oceans is equal to Hg(II) deposition, which has implications for our understanding of atmospheric Hg dispersal and marine ecosystem recovery., (© 2021. The Author(s), under exclusive licence to Springer Nature Limited.)

One pathway by which the oceans influence climate is via the emission of sea spray that may subsequently influence cloud properties. Sea spray emissions are known to be dependent on atmospheric and oceanic physicochemical parameters, but the potential role of ocean biology on sea spray fluxes remains poorly characterized. Here we show a consistent significant relationship between seawater nanophytoplankton cell abundances and sea-spray derived Cloud Condensation Nuclei (CCN) number fluxes, generated using water from three different oceanic regions. This sensitivity of CCN number fluxes to ocean biology is currently unaccounted for in climate models yet our measurements indicate that it influences fluxes by more than one order of magnitude over the range of phytoplankton investigated.

Diatoms are one of the major primary producers in the ocean, responsible annually for ~20% of photosynthetically fixed CO 2 on Earth. In oceanic models, they are typically represented as large (>20 µm) microphytoplankton. However, many diatoms belong to the nanophytoplankton (2-20 µm) and a few species even overlap with the picoplanktonic size-class (<2 µm). Due to their minute size and difficulty of detection they are poorly characterized. Here we describe a massive spring bloom of the smallest known diatom (Minidiscus) in the northwestern Mediterranean Sea. Analysis of Tara Oceans data, together with literature review, reveal a general oversight of the significance of these small diatoms at the global scale. We further evidence that they can reach the seafloor at high sinking rates, implying the need to revise our classical binary vision of pico- and nanoplanktonic cells fueling the microbial loop, while only microphytoplankton sustain secondary trophic levels and carbon export.

After the exponential growth phase, variability in the scattering efficiency of phytoplankton cells over their complete life cycle is not well characterised. Bulk measurements are impacted by senescent cells and detritrus. Thus the analysis of the evolution of the optical properties thanks to their morphological and/or intra-cellular variations remains poorly studied. Using the Cytosense flow cytometer (CytoBuoy b.v., NL), the temporal course of the forward and sideward efficiencies of two phytoplankton species (Thalassiosira pseudonana and Chlamydomonas concordia) were analyzed during a complete life-cycle. These two species differ considerably from a morphological point of view. Over the whole experiment, the forward and sideward efficiencies of Thalassiosira pseudonana were, on average, respectively 2.2 and 1.6 times higher than the efficiencies of Chlamydomonas concordia. Large intra-species variability of the efficiencies were observed over the life cycle of the considered species. It highlights the importance of considering the optical properties of phytoplankton cells as a function of the population growth stage of the considered species. Furthermore, flow cytometry measurements were combined with radiative transfer simulations and biogeochemical and optical measurements. Results showed that the real refractive index of the chloroplast is a key parameter driving the sideward signal and that a simplistic two-layered model (cytoplasm-chloroplast) seems particularly appropriate to represent the phytoplankton cells.

A methodology is developed to derive the backscattering cross section of individual particles as measured with the CytoSense (CytoBuoy b.v., NL). This in situ flow cytometer detects light scatter in forward and sideward directions and fluorescence in various spectral bands for a wide range of particles. First, the weighting functions are determined for the forward and sideward detectors to take into account their instrumental response as a function of the scattering angle. The CytoSense values are converted into forward and sideward scattering cross sections. The CytoSense estimates of uniform polystyrene microspheres from 1 to 90 μm are compared with Mie computations. The mean absolute relative differences ΔE are around 33.7% and 23.9% for forward and sideward scattering, respectively. Then, a theoretical relationship is developed to convert sideward scattering into backscattering cross section, from a synthetic database of 495,900 simulations including homogeneous and multi-layered spheres. The relationship follows a power law with a coefficient of determination of 0.95. To test the methodology, a laboratory experiment is carried out on a suspension of silica beads to compare backscattering cross section as measured by the WET Labs ECO-BB9 and derived from CytoSense. Relative differences are between 35% and 60%. They are of the same order of magnitude as the instrumental variability. Differences can be partly explained by the fact that the two instruments do not measure exactly the same parameter: the cross section of individual particles for the CytoSense and the bulk cross section for the ECO-BB9.

Phytoplankton is a key component in marine ecosystems. It is responsible for most of the marine primary production, particularly in eutrophic lagoons, where it frequently blooms. Because they are very sensitive to their environment, the dynamics of these microbial communities has to be observed over different time scales, however, assessment of short term variability is often out of reach of traditional monitoring methods. To overcome these limitations, we set up a Cytosense automated flow cytometer (Cytobuoy b.v.), designed for high frequency monitoring of phytoplankton composition, abundance, cell size, and pigment content, in one of the largest Mediterranean lagoons, the Berre lagoon (South-Eastern France). During October 2011, it recorded the cell optical properties of 12 groups of pico-, nano-, and microphytoplankton. Daily variations in the cluster optical properties were consistent with individual changes observed using microscopic imaging, during the cell cycle. We therefore used an adaptation of the size-structured matrix population model, developed by Sosik et al. (2003) to process the single cell analysis of the clusters and estimate the division rates of 2 dinoflagellate populations before, during, and after a strong wind event. The increase in the estimated in situ daily cluster growth rates suggest that physiological changes in the cells can prevail over the response of abundance.

Most of phytoplankton influence is barely understood at the sub meso scale and daily scale because of the lack of means to simultaneously assess phytoplankton functionality, dynamics and community structure. For a few years now, it has been possible to address this objective with an automated in situ high frequency sampling strategy. In order to study the influence of environmental short-term events (nutrients, wind speed, precipitation, solar radiation, temperature, and salinity) on the onset of the phytoplankton bloom in the oligotrophic Bay of Villefranche-sur-Mer (NW Mediterranean Sea), a fully remotely controlled automated flow cytometer (CytoSense) was deployed on a solar-powered platform (EOL buoy, CNRS-Mobilis). The CytoSense carried out single-cell analyses on particles (1-800 μm in width, up to several mm in length), recording optical pulse shapes when analyzing several cm(3). Samples were taken every 2 h in the surface waters during 2 months. Up to 6 phytoplankton clusters were resolved based on their optical properties (PicoFLO, Picoeukaryotes, Nanophytoplankton, Microphytoplankton, HighSWS, HighFLO). Three main abundance pulses involving the 6 phytoplankton groups monitored indicated that the spring bloom not only depends on light and water column stability, but also on short-term events such as wind events and precipitation followed by nutrient pulses. Wind and precipitation were also determinant in the collapse of the clusters' abundances. These events occurred within a couple of days, and phytoplankton abundance reacted within days. The third abundance pulse could be considered as the spring bloom commonly observed in the area. The high frequency data-set made it possible to study the phytoplankton cell cycle based on daily cycles of forward scatter and abundance. The combination of daily cell cycle, abundance trends and environmental pulses will open the way to the study of phytoplankton short-term reactivity to environmental conditions.