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Anthropogenic activities have transformed the pelagic habitat in the last decades with profound implications for its essential functions. While the EU-Marine Strategy Framework Directive 2008/56/EC and the Commission Decision (EU) 2017/848 have set criteria and methodological standards for the assessment and determination of Good Environmental Status (GES) for pelagic habitats in EU waters, there is strong evidence that Member States have not yet harmonized the pelagic GES assessment across EU marine waters. Today, pelagic habitats are assessed by evaluating whether good status is achieved by each of the pelagic indicators, but this approach fails to observe the high variability of the pelagic environment. To this end, GES is not estimated at pelagic habitats scale but only for each individual indicator. This paper synthesises the latest developments on pelagic habitats assessment and identifies the main factors limiting the consistency of the assessment across Member States: i) coarse spatial and temporal scales of sampling effort as regards to the pelagic habitat dynamics, ii) little consideration of the whole range of plankton (and, to some extent, of zooplankton) size and trophic spectra, iii) lack of integrated hydro-biogeochemical and biological studies and collaboration among experts from different scientific fields, iv) limited availability of pressure-based indicators, and v) lack of integration methods of the pelagic indicators’ status for the GES determination. This analysis demonstrates the importance of maintaining a consistent sampling frequency and a spatially extensive network of stations across the gradient of anthropogenic pressures, where spatial environmental data can help objectively extrapolating field data.

The recent development of biological sensors has extended marine plankton studies from conducting laboratory bench work to in vivo and real-time observations. Flow cytometry (FCM) has shed new light on marine microorganisms since the 1980s through its single-cell approach and robust detection of the smallest cells. FCM records valuable optical properties of light scattering and fluorescence from cells passing in a single file in front of a narrow-collimated light source, recording tens of thousands of cells within a few minutes. Depending on the instrument settings, the sampling strategy, and the automation level, it resolves the spatial and temporal distribution of microbial marine prokaryotes and eukaryotes. Cells are usually classified and grouped on cytograms by experts and are still lacking standards, reducing data sharing capacities. Therefore, the need to make FCM data sets FAIR (Findability, Accessibility, Interoperability, and Reusability of digital assets) is becoming critical. In this paper, we present a consensus vocabulary for the 13 most common marine microbial groups observed with FCM using blue and red-light excitation. The authors designed a common layout on two-dimensional log-transformed cytograms reinforced by a decision tree that facilitates the characterization of groups. The proposed vocabulary aims at standardising data analysis and definitions, to promote harmonisation and comparison of data between users and instruments. This represents a much-needed step towards FAIRification of flow cytometric data collected in various marine environments.

Submesoscale processes have a determinant role in the dynamics of oceans by transporting momentum, heat, mass, and particles. Furthermore, they can define niches where different phytoplankton species flourish and accumulate not only by nutrient provisioning but also by modifying the water column structure or active gathering through advection. In coastal areas, however, submesoscale oceanic processes act together with coastal ones, and their effect on phytoplankton distribution is not straightforward. The present study brings the relevance of hydrodynamic variables, such as vorticity, into consideration in the study of phytoplankton distribution, via the analysis of in situ and remote multidisciplinary data. In situ data were obtained during the ETOILE oceanographic cruise, which surveyed the Capbreton Canyon area in the southeastern part of the Bay of Biscay in early August 2017. The main objective of this cruise was to describe the link between the occurrence and distribution of phytoplankton spectral groups and mesoscale to submesoscale ocean processes. In situ discrete hydrographic measurements and multi-spectral chlorophyll a (chl a) fluorescence profiles were obtained in selected stations, while temperature, conductivity, and in vivo chl a fluorescence were also continuously recorded at the surface. On top of these data, remote sensing data available for this area, such as high-frequency radar and satellite data, were also processed and analysed. From the joint analysis of these observations, we discuss the relative importance and effects of several environmental factors on phytoplankton spectral group distribution above and below the pycnocline and at the deep chlorophyll maximum (DCM) by performing a set of generalized additive models (GAMs). Overall, salinity is the most important parameter modulating not only total chl a but also the contribution of the two dominant spectral groups of phytoplankton, brown and green algae groups. However, at the DCM, among

Plankton form the base of the marine food web and are sensitive indicators of environmental change. Plankton time series are therefore an essential part of monitoring progress towards global biodiversity goals, such as the Convention on Biological Diversity Aichi Targets, and for informing ecosystem-based policy, such as the EU Marine Strategy Framework Directive. Multiple plankton monitoring programmes exist in Europe, but differences in sampling and analysis methods prevent the integration of their data, constraining their utility over large spatio-temporal scales. The Plankton Lifeform Extraction Tool brings together disparate European plankton datasets into a central database from which it extracts abundance time series of plankton functional groups, called “lifeforms”, according to shared biological traits. This tool has been designed to make complex plankton datasets accessible and meaningful for policy, public interest, and scientific discovery. It allows examination of large-scale shifts in lifeform abundance or distribution (for example, holoplankton being partially replaced by meroplankton), providing clues to how the marine environment is changing. The lifeform method enables datasets with different plankton sampling and taxonomic analysis methodologies to be used together to provide insights into the response to multiple stressors and robust policy evidence for decision making. Lifeform time series generated with the Plankton Lifeform Extraction Tool currently inform plankton and food web indicators for the UK's Marine Strategy, the EU's Marine Strategy Framework Directive, and for the Convention for the Protection of the Marine Environment of the North-East Atlantic (OSPAR) biodiversity assessments. The Plankton Lifeform Extraction Tool currently integrates 155 000 samples, containing over 44 million plankton records, from nine different plankton datasets within UK and European seas, collected between 1924 and 2017. Additional datasets can be added, and

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Gómez, F., Artigas, L.F., Gast, R.J. Phylogeny and synonymy of Gyrodinium heterostriatum comb. nov. (Dinophyceae), a common unarmored dinoflagellate in the world oceans. Acta Protozoologica, 59 (2), (2020): 77-87, doi: 10.4467/16890027AP.20.007.12675., The North Sea and the English Channel are regions with a long tradition of plankton studies, where the colony-forming haptophyte Phaeocystis globosa dominates the spring phytoplankton blooms. Among its predators, we investigated an abundant unarmored dinoflagellate (~3000 cells per liter) in the North Sea in May 2019. It has been reported in the literature as Gymnodinium heterostriatum or G. striatissimum, and often identified as Gyrodinium spirale. Phylogenetic analyses using the small-, large subunit- and Internal Transcriber Spacers of the ribosomal RNA (SSU-, LSU-, ITS rRNA) gene sequences indicate that our isolates clustered within the Gyrodinium clade. The new sequences formed a sister group with sequences of the freshwater taxon Gyrodinium helveticum, being one of the infrequent marine-freshwater transitions in the microbial world. This isolate is the first characterized member of a clade of numerous environmental sequences widely distributed from cold to tropical seas. This common and abundant taxon has received several names due to its morphological plasticity (changes of size and shape, often deformed after engulfing prey) and the difficulty in discerning surface striation. We conclude that the priority is for the species name Gymnodinium heterostriatum Kofoid & Swezy 1921, a new name that was proposed for Gymnodinium spirale var. obtusum sensu Dogiel 1906. The species Gyrodinium striatissimum (Hulburt 1957) Gert Hansen & Moestrup 2000 and Gymnodinium lucidum D. Ballantine in Parke & Dixon 1964 (=G. hyalinum M. Lebour 1925) are posterior synonyms. We propose Gyrodinium heterostriatum comb. nov. for Gymnodinium heterostriatum., F.G. was partly supported by the convention #2101893310 between CNRS INSU and the French Ministry of Ecology (MTES) for the implementation of the Monitoring Program of the European Marine Strategy Framework directive (MSFD) for pelagic habitats and the descriptor ‘biodiversity’. Samples were collected within the framework of JERICO-NEXT (www.jerico-ri.eu), a European (H2020) project to establish a joint international network of coastal observatories, during a 4-day collaborative monitoring campaign of the Southern North Sea. Part of the infrastructure and data were provided by VLIZ (Flanders Marine Institute) and funded by Research Foundation-Flanders (FWO) as part of the Belgian contribution to the LifeWatch project.

Author Posting. © The Author(s), 2021. This is the author's version of the work. It is posted here by permission of John Wiley & Sons for personal use, not for redistribution. The definitive version was published in Journal of Phycology, doi:10.1111/jpy.13135., Gymnodinium gracile, described from the coasts of Denmark in 1881, is one of the first described unarmored dinoflagellates. Individuals which morphologically fit with the original description were isolated from the English Channel (North‐East Atlantic). The SSU rRNA gene sequences were identical to the sequences identified as Balechina pachydermata and Gymnodinium amphora from the Mediterranean Sea and Brazil. We propose the transfer of Gymnodinium gracile into the genus Balechina as B. gracilis comb. nov. These sequences constitute an independent lineage, clustering with numerous environmental sequences from polar to tropical waters. The widespread distribution, the high plasticity in size, shape and coloration and the difficulties in discerning the fine longitudinal striae have contributed to the description of numerous synonyms: Amphidinium vasculum, Balechina pachydermata (=Gymnodinium pachydermatum), Gymnodinium achromaticum, G. abbreviatum, G. amphora, G. dogielii, G. lohmannii (=G. roseum sensu Lohmann 1908), G. situla and Gyrodinium cuneatum (=G. gracile sensu Pouchet 1885)., F.G. was supported by the convention #2101893310 between CNRS INSU and the French Ministry of Ecology (MTES) for the implementation of the Monitoring Program of the European Marine Strategy Framework directive (MSFD) for pelagic habitats and the descriptor ‘biodiversity’. Samples were collected during the ECOPEL Manche 2018 spring and summer cruises (CNRS-LOG) onboard R/V "Antea" (IRD, Institut de Recherche pour le Développement) in the frame of the cited convention and the CPER ‘Hauts de France’ project MARCO supported by the French state, the ‘Hauts de France’ French Region and the European Regional Development Founds (ERDF).

Gymnodinium gracile, described from the coasts of Denmark in 1881, is one of the first described unarmored dinoflagellates. Individuals which morphologically fit with the original description were isolated from the English Channel (North‐East Atlantic). The SSU rRNA gene sequences were identical to the sequences identified as Balechina pachydermata and Gymnodinium amphora from the Mediterranean Sea and Brazil. We propose the transfer of Gymnodinium gracile into the genus Balechina as B. gracilis comb. nov. These sequences constitute an independent lineage, clustering with numerous environmental sequences from polar to tropical waters. The widespread distribution, the high plasticity in size, shape and coloration and the difficulties in discerning the fine longitudinal striae have contributed to the description of numerous synonyms: Amphidinium vasculum, Balechina pachydermata (=Gymnodinium pachydermatum), Gymnodinium achromaticum, G. abbreviatum, G. amphora, G. dogielii, G. lohmannii (=G. roseum sensu Lohmann 1908), G. situla and Gyrodinium cuneatum (=G. gracile sensu Pouchet 1885).

Automated pulse shape-recording flow cytometry was applied to address phytoplankton spatial distribution, at high frequency, in stratified and well mixed water masses in the Western and Central English Channel during the summer-fall transition. Cytometric pulse shapes derived from optical features of single cells allowed the characterization of eight phytoplankton groups. Abundance and total red fluorescence (chlorophyll a autofluorescence) per group were used to define six phytoplankton communities. Their distribution revealed high spatial heterogeneity. Abundance presented a longitudinal gradient for six over the eight groups and succession of brutal shifts along the cruise. Maximum values were often located near the Ushant front in the Western English Channel. A latitudinal gradient characterized the Central English Channel waters under the influence of the Seine estuary. Picophytoplankton (Synechococcus-like cells and picoeukaryotes) represented up to 96% of total abundance and half of the total red fluorescence of the communities near the main front and the Bay of Seine, whereas nanoeukaryotes and microphytoplankton, represented only 4% and less than 1% respectively of total abundance. Both nanoeukaryotes and microphytoplankton dominated the total red fluorescence of the communities of the Central English Channel. The study of traits within each group showed a high variability of traits between communities. The comparison between traits showed that they were independent from each other for some groups (size and red fluorescence per cell for PicoHighFLR and Coccolithophore-like cells; orange and red fluorescence for all the groups), whereas they were dependent for other groups (red fluorescence per cell was dependent of size for picophytoplankton, NanoLowFLR, NanoHighFLR, Cryptophyte-like cells and Microphytoplankton). Variance partitioning revealed that the environmental parameters (temperature, salinity and turbidity) accounted less than spatial descriptors (p

The genus Centrodinium contains oceanic and predominantly tropical species that have received little attention. Three species of Centrodinium were examined using thecal plate dissociation, scanning electron microscopy, and molecular sequences. The apical horn of Centrodinium intermedium and C. eminens is formed by the elongation of the fourth apical plate, and a second apical split into two plates. In C. punctatum two apical plates (2′ and 4′) almost completely encircle the apical pore plate (Po), while the contact with the plate 1′ in the ventral side is much reduced, and the plate 3′ does not reach the Po. Moreover, its left posterior lateral sulcal plate is longer than its right pair, while reversed in the typical Centrodinium spp. The sulcal posterior plate of C. punctatum is located in the left-ventral side below the plates 1′′′ and 2′′′, while the sulcal posterior plate located in the right face below the plates 4′′′ and 5′′′ in the typical Centrodinium spp. Phylogenetic analyses based on the small and large subunit of the rRNA gene showed that Centrodinium spp. and Alexandrium affine/A. gaarderae clustered as a sister clade of the Alexandrium tamarense/catenella/fraterculus groups. The clade of the subgenus Gessnerium, and the clade of the type species of Alexandrium, A. minutum, with four divergent species, clustered in more basal positions. The polyphyly of Alexandrium is solved with the split into four genera: (1) Alexandrium sensu stricto for the species of the clade of A. minutum and four divergent species; (2) the reinstatement of the genus Gessnerium for the species of the clade of A. monilatum; (3) the reinstatement of genus Protogonyaulax for the species of the tamarense/catenella/fraterculus groups, and (4) the new genus Episemicolon gen. nov. for A. affine and A. gaarderae. New combinations in the genera Gessnerium, Protogonyaulax, and Episemicolon are proposed.

In this paper we review the technologies available to make globally quantitative observations of particles in general—and plankton in particular—in the world oceans, and for sizes varying from sub-microns to centimeters. Some of these technologies have been available for years while others have only recently emerged. Use of these technologies is critical to improve understanding of the processes that control abundances, distributions and composition of plankton, provide data necessary to constrain and improve ecosystem and biogeochemical models, and forecast changes in marine ecosystems in light of climate change. In this paper we begin by providing the motivation for plankton observations, quantification and diversity qualification on a global scale. We then expand on the state-of-the-art, detailing a variety of relevant and (mostly) mature technologies and measurements, including bulk measurements of plankton, pigment composition, uses of genomic, optical and acoustical methods as well as analysis using particle counters, flow cytometers and quantitative imaging devices. We follow by highlighting the requirements necessary for a plankton observing system, the approach to achieve it and associated challenges. We conclude with ranked action-item recommendations for the next 10 years to move toward our vision of a holistic ocean-wide plankton observing system. Particularly, we suggest to begin with a demonstration project on a GO-SHIP line and/or a long-term observation site and expand from there, ensuring that issues associated with methods, observation tools, data analysis, quality assessment and curation are addressed early in the implementation. Global coordination is key for the success of this vision and will bring new insights on processes associated with nutrient regeneration, ocean production, fisheries and carbon sequestration.

© The Author(s), 2019. This is the author's version of the work and is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Gómez Fernando, Felipe Artigas Luis, J. Gast Rebecca. Molecular phylogeny of the parasitic dinoflagellate Syltodinium listii (Gymnodiniales, Dinophyceae) and generic transfer of Syltodinium undulans comb. nov. (=Gyrodinium undulans). European Journal of Protistology, (2019): 125636, doi:10.1016/j.ejop.2019.125636., The parasitic dinoflagellate Syltodinium listii was investigated from the open waters of the English Channel and the NW Mediterranean Sea. Syltodinium listii has been unreported since its original description in the North Sea. Cells of S. listii were able to immediately infect copepod eggs of different species, and even nauplii, and after each infection to form up to 32 cells embedded in a mucous envelope. Infection of the same host by more than one dinoflagellate was frequent; although overall, the progeny were reduced in number. Molecular phylogeny based on the small subunit ribosomal RNA (SSU rRNA) gene revealed that S. listii clusters with a group of environmental sequences from the cold North Atlantic region as a sister group of Gymnodinium aureolum. The large subunit ribosomal RNA (LSU rRNA) gene sequences of S. listii from the English Channel and cf. Gyrodinium undulans from the Mediterranean Sea were identical. Thus, we propose Syltodinium undulans comb. nov. for Gyrodinium undulans. The first internal transcribed spacer (ITS) and complete SSU rRNA gene sequences of Dissodinium pseudolunula are provided. The parasitic species of Chytriodinium, Dissodinium and Syltodinium cluster together within the family Chytriodiniaceae, including the free-living species Gymnodinium aureolum, G. corollarium and G. plasticum., F.G. was supported by the Ministerio Español de Ciencia y Tecnología [contract JCI-2010-08492], and by the convention #2101893310 between CNRS-INSU and the French Ministry for the Ecological and Solidary Transition (MTES) for the implementation of the Monitoring Program of the European Marine Strategy Framework Directive (MSFD), which also supported the ECOPEL-Manche cruises., 2020-09-17