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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.

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).

The Senegalese coastal and shelf systems comprises a southern part of the Canary Islands upwelling system. The present study focuses on the study of phytoplankton from meso- to submesoscale during the transition period from the warm West African monsoon season to the cold upwelling season. This period coincides with the return of sardinella from their northward migration to its second most important spawning area resulting in a high retention on the southern coast, as well as possible events of the Senegalese fishermen's skin disease (as it was the case in November 2020). This is a very poorly documented period. The last studies allowing the study of the phytoplankton compartment date from the 1980s. Several data on phytoplankton were collected during the period from 29 November to 02 December 2017 for addressing phytoplankton distribution and dynamics: pigmentary data, microscopic counts, metabarcoding analysis of plankton diversity, single-cell analysis and characterization of optical groups by automated (in vivo) flow cytometry (CytoSen) as well as in vivo characterization of spectral/pigmentary groups by multispectral fluorometry (Fluoroprobe). Environmental data was supplied by CTD RBR concerto and the analysis of several physical and chemical parameters. In particular, FluoroProbe continuous subsurface measurements and profiles made it possible to considerably improve the spatial and temporal resolution of measurements and the dynamics of phytoplankton groups at submesoscale. Moreover, it was possible to follow spatial and temporal changes in the phytoplankton community, particularly at stations sampled twice at few days interval. Many unknown species characterized this period, especially in the nanophytoplankton size range. Distinct communities were found in the upwelling on the coastal fringe and in the old waters offshore, as shown by multispectral analysis. Phytoplankton blooms were observed, some of which being caused by the upwelling of cold water, but intermittently and weakly. In some stations, toxic species were found, such as species belonging to the genus Pseudo-Nitzschia. Keywords: Upwelling, multi-spectral fluorometry, CTD, automated flow cytometry, metabarcoding, microscopy, phytoplankton diversity and dynamics.

International audience; 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 characterised 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 (physical and biological processes) in shaping the communities. Hydrological structures (frontal structures, eddies and tidal streams) were responsible for patches of phytoplankton and defined the structure at the sub-mesoscale (1–10 km) in this area.

The ability to quantify vital aquatic organisms in the 2–50 µm size range was compared between five different flow cytometers and several different microscopes. Counts of calibration beads, algal monocultures of different sizes as well as organisms in a Wadden Sea sample were compared. Flow cytometers and microscopes delivered different bead concentrations. These differences between the instruments became larger for algal monocultures and were even higher for the Wadden Sea sample. It was observed that the concentration differences were significant between flow cytometer and microscope counts, and that this difference increased with the size of the objects counted. Microscope counts were more accurate for larger (50 µm) objects because cytometers struggled with bigger particles that clogged the instruments. Contrary to microscopy, the flow cytometers were capable of accurately enumerating cultured cells in the 2–10 µm size range and cells in the lower size range of the 10–50 µm size class. Flow cytometers were also well-suited to assess low abundance samples due to their ability to process larger volumes than microscopes. The results were used to indicate which tools are suitable for ballast water monitoring: flow cytometry is a suitable technology for an indicative and real time analysis of ballast water samples whilst only microscopy would be robust enough for detailed taxonomical analyses.

16 pages; International audience; Estuaries are considered one of the most dynamic ecosystems in the world, ensuring high production and transfer of large quantities of organic matter (OM) from continents to the ocean. Despite the large influence of estuaries in the functioning of coastal ecosystems, our understanding of OM dynamics in these buffering coastal environments remains fragmented. In this frame, our study was carried out to describe and understand the main drivers of OM distribution in two estuaries (Canche, Authie) of the eastern English Channel, based on descriptive and quantitative approaches. For this purpose, in February and March 2018, surface sediments were sampled at low tide along cross-shore transects in the intertidal zone of each estuary. Analysis of sediment grain size, porosity, proportion of aggregated particles, total carbonate content and organic geochemical characteristics (total OM content, atomic TOC/TN ratio, δ13C value) of surface sediments allowed identifying four biosedimentary facies: sand flat, mud flat, low and high salt marshes. In parallel, the elemental and isotopic characterization of the suspended particulate OM inputs by the rivers, the surface biofilms and the halophytic vegetation was performed to trace the three major sources contributing to sedimentary OM in both estuaries. Spatial distribution of OM in surface sediments (ranging between 0.6 and 26.9% dry weight) evidenced higher contents along marsh platforms than in sand and mud flats. and the OM pool was mainly constituted of a mixing of C3 terrestrial vascular plants, marine and riverine phytoplankton. The comparison between both estuaries highlighted that the geomorphology impacted by natural and anthropic factors plays a preponderant role in the distribution and the sources of sedimentary OM by influencing vegetation communities and hydrodynamic processes. In the context of sea level rise, an improved understanding of the OM dynamics within each biosedimentary facies is crucial to better constrain and assess the role of macrotidal estuaries in carbon cycle.

International audience; The parasitic dinoflagellate Syltodinium listii was investigated from the open waters of the English Channel, southern North Sea 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 infect copepod eggs of different species, and even nauplii, and after each infection formed 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.

International audience; The Marine Strategy Framework Directive requires EU Member States to assess the Good Environmental Status (GES) of their marine waters in a coherent and strategic manner. For the regional assessment of biodiversity, the OSPAR Intersessional Coordination Group of Biodiversity Assessment and Monitoring (ICG-COBAM) provides substantial advice. Through expert working groups, phytoplankton indicators are currently being developed to measure the state and the change in pelagic diversity, to quantify food web dynamics and to measure the extent of eutrophication impacts. We developed a multi-metric indicator that is compliant with the common OSPAR indicator “Changes in plankton diversity” (PH3). The aim was to describe the structure of the phytoplankton community (alpha diversity) and to detect significant temporal changes (beta diversity) to evaluate the health of pelagic habitats. In this pilot study, we used three coastal time-series in the Western Channel and the north of the Bay of Biscay (North Atlantic, France) to test the efficiency and the performance of several existing diversity indices. We validated two alpha diversity indices, namely the Menhinick Index (D) and the Hulburt Index (δ), based on their complementary ecological information, their strong relationship with habitat characteristics, and their relative ease of interpretation for stakeholders. Temporal shifts or rate of change in community structure were detected by the Local Contributions to Beta Diversity index (LCBD; a beta diversity measure). For the years where significantly high LCBD values were found, the Importance Value Index (IVI) was calculated to potentially identify the taxa (genus) responsible for the “unusual” community structure. For example, at the Ouest Loscolo site in 2008, an elevated LCBD (0.45) coincided with a high dominance value (Hulburt’s Index) caused by the occurrence of a monospecific bloom of Leptocylindrus spp. (IVI = 73%) in July (2.22 × 106 cells L−1) and October (8 × 106 cells L−1). In this way, PH3 informs on different aspects of phytoplankton diversity from a community to a genus level. At the current stage of development, however, PH3 acts as a “surveillance” rather than an operational indicator since the relationship to GES is not directly tracked. In the future, by additional testing of PH3 and extending the geographical scope, the robustness of the assessment could be further determined across the OSPAR Maritime Area.

International audience; A pulse-shape recording flow cytometer (CytoSense©) was applied to the monitoring of changes in phytoplankton distribution along an inshore–offshore transect across the eastern English Channel (EEC), on 13 occasions during the main productive period of the year. Amongst the eight phytoplankton groups discriminated, picophytoplankton (picoeukaryotes and Synechococcus spp.) and Phaeocystis globosa nanoflagellates were the main contributors to total phytoplankton abundance, while Diatoms-like, Coccolithophores, and Cryptophytes represented each one less than 5%. High spatial resolution revealed important changes on relatively short distances. Moreover, a general decrease of Diatoms-like, P. globosa haploid cells, Coccolithophores, and picoeukaryote abundance was evidenced from inshore to offshore waters, associated with an increase of Synechococcus spp. abundance. Seasonal variability accounted for 71% of phytoplankton abundance changes. Compared to previous studies in the area the CytoSense allowed highlighting new players during the winter–spring–summer phytoplankton succession: (i) high abundance of Synechococcus spp. and picoeukaryotes I in winter and of Synechococcus spp. also in the summer, (ii) a transient abundance peak of picoeukaryotes II, and (iii) high abundance of Coccolithophores and Cryptophytes during the wax of P. globosa bloom and in the summer. The relationships between environmental variables and phytoplankton assemblages indicated that nutrients and the daily light intensity were the most important parameters in structuring the winter–spring–summer transitions.

Recent advances in technology and manufacturing have made it possible to create small, powerful, energy-efficient, cost-effective sensor nodes for specialized telecommunication applicationsnodes "smart" enough to be capable of adaptation, self-awareness, and self-organization. Sensor Networks for Sustainable Development examines sensor network technologies that increase the quality of human life and encourage societal progress with minimal effect on the earths natural resources and environment. Organized as a collection of articles authored by leading experts in the field, this valuable reference captures the current state of the art and explores applications where sensor networks are used for sustainable development in: Agriculture Environment Energy Healthcare Transportation Disaster management Beneficial to designers and planners of emerging telecommunication networks, researchers in related industries, and students and academia seeking to learn about the impact of sensor networks on sustainable development, Sensor Networks for Sustainable Development provides scientific tutorials and technical information about smart sensor networks and their use in everything from remote patient monitoring to improving safety on the roadways and beyond.

Rationale In various marine environments, the combination of elemental ratios and stable isotopic compositions is usually used to trace the sources of organic matter (OM) in sediments. However, in intertidal areas, the sediments might be temporarily exposed to air during a more or less prolonged duration and the impact of this exposure on the latter parameter is unknown. Methods The spatial variations of atomic Total Organic Carbon (TOC) and Total Nitrogen (TN) ratios, and δ13C and δ15N values, were measured on surface sediments of French Guiana, at the beginning and the end of five consecutive days of emersion during equinoctial tides, as well as at the beginning of a new emersion phase after returning to a normal tidal cycle. The concentrations of chlorophyll a and phaeopigments in sediments were also measured, in order to estimate the influence of microphytobenthos (MPB), growing at surface sediments, on these geochemical parameters. Results The results showed that the emersion/immersion cycles influenced the development of MPB at the surface sediments, which, in turn, significantly controlled the spatio-temporal changes in the atomic elemental ratios and the δ13C values. This variability seemed not to be significantly altered by OM degradation. On the contrary, sediments were always 15N-enriched compared with OM sources, indicating that OM diagenetic processes mainly controlled their spatio-temporal fluctuations. Conclusions The [TOC/TN]atomic ratios and the δ13C values, indicating the primary signal of OM sources, represented the most reliable geochemical proxies for calculating the relative contribution of OM sources to sediments in environments characterized by variable air exposure duration. The use of δ15N values in such environments is limited by OM degradation processes but their variation might enable the nature and the degree of these processes to be identified. Copyright © 2015 John Wiley & Sons, Ltd.

The species Amphidinium eludens, as described by Herdman (1922; Proc. Trans. Liverpool Biol. Soc. 36: 18) based on her drawing in fig. 1, has been investigated for the first time by scanning electron microscopy and phylogenetic analysis. The morphological and molecular data reveal that this species is distantly related to other known dinoflagellates. Balech [1956, Rev. Algol., n. ser. 2(1–2): 30] cited Amphidinium eludens Herdman (1922, fig. 1) as the basionym of the type of Adenoides, while he described and illustrated Amphidinium kofoidii Herdman (1922, fig. 2) as Adenoides eludens. As the nomenclatural rules do not allow the change of basionym, we have re-defined the genus Adenoides based on the characteristics of Amphidinium eludens Herdman (1922, fig. 1). The thecal plate formula of Adenoides eludens is Po, 5′, 6″, 0c, 3+s, 5′″, 3p, 1″″. This species lacks a cingulum. The apical pore complex resembles that of peridinioid dinoflagellates, while the absence of a cingular groove is reminiscent o...

International audience; This study explored the relevance of the use of a trait-based approach to explain seasonal phytoplankton succession and the underlying mechanisms that structure phytoplankton assemblages and promote nitrogen use efficiency (NUE) in the temperate coastal waters of the eastern English Channel (EEC). A 3 yr time series of phytoplankton abundance assessed by flow cytometry was combined with a selection of traits related to resource utilization (light and inorganic nutrients), grazing resistance, and maximum growth, mainly sourced from the literature. Our results showed that the identified functional groups (FGs) ranged deterministically along a temporal gradient of light and nutrient availability, according to several fundamental trade-offs. These trade-offs, which reflected different ecological strategies, were distributed along 1 axis of niche differentiation. This favoured different FGs through time, and consequently allowed them to partition those available resources. The observed functional divergence of the phytoplankton community deviated from that of the expected, random one. It showed that as light increased, the phytoplankton community assembly was mainly driven by competition and grazing pressure, which eventually favoured those FGs that were fastest growing and less vulnerable to predation. Structural equation modeling evidenced that a phytoplankton community, functionally dominated by FGs that were relatively large, fast-growing, and well-adapted to higher light, promoted NUE. Together, these results confirmed the potential use of laboratory-measured functional traits to explore environment-trait linkages in phytoplankton. They also showed the possibility of further extending this approach to identify the mechanisms driving phytoplankton community assembly, structure, and related ecosystem processes.

Benthic dinoflagellates collected in spring–summer 2010 and 2011 from intertidal sandy sediments of the shore of Wimereux (north-east English Channel, France) were examined by light microscopy, and some of them by scanning electron microscopy. High dinoflagellate species richness, 70 species, was evidenced when compared to the plankton observed in the coastal waters of the north-east English Channel. The greatest difficulty in performing accurate species identification mainly concerned the heterotrophic species of Amphidinium sensu lato, the laterally flattened species of Amphidiniopsis, as well as some heterotrophic species of Thecadinium. Several undescribed species are here illustrated, mainly within these genera. The differences in size between species of Herdmania and Sabulodinium suggest the occurrence of at least a second species for these monotypic genera. The species Amphidiniopsis hexagona, A. rotundata, A. uroensis and Sinophysis minima are reported for the first time in the Atlantic Ocean and on European coasts. Although these species were only previously known from the Pacific Ocean, they should not necessarily be considered as newcomers or invasive species due to the scarce coverage of the previous studies on sand-dwelling dinoflagellates.

Photosynthetic parameters, phytoplankton assemblages and physicochemical parameters were analysed in the Strait of Dover along an inshore–offshore transect between September 2008 and December 2009. The samples were collected weekly at 9 stations only at the surface or at both surface and depth. The photosynthetic activity was obtained by measuring Rapid Light Curves (RLC) using Pulse Amplitude Modulated (PAM) fluorometry. Temporal variability of the maximal light utilization efficiency ( α ), maximum electron transport rate (ETR m ) and light saturation coefficient ( E k ) were greater than spatial variability (in horizontal and vertical dimensions) whereas temporal variability of the maximum quantum yield ( F v / F m ) was of the same order of magnitude as its spatial variability within the water column (in the vertical dimension). ETR m and α were positively correlated and the slope of the relation varied significantly between the different depths and seasons. The highest values of ETR m and α were obtained in summer (June) and late autumn – early winter (September–October & December) and the lowest in spring (March–April). The spatial variability of these parameters was greater vertically than horizontally. Differences between depths were particularly pronounced at the station nearest to the coast where photosynthetic response seems to be controlled by the light history of the cells. Seasonal variability in photosynthetic activity was mostly related to phytoplankton assemblages, light and temperature whereas the light history of the cells within the water column could be the most important factor in depth variability.

The central Amazon floodplains are particularly productive ecosystems, where a large diversity of organic carbon sources are available for aquatic organisms. Despite the fact that C-4 macrophytes generally produce larger biomasses than C-3 macrophytes, food webs in the central Amazon floodplains appear dominantly based on a C-3 carbon source. In order to investigate the respective fate and degradation patterns of C-4 and C-3 aquatic plant-derived material in central Amazon floodplains, we developed a 23-days batch experiment. Fatty acid and carbon concentrations as well as stable isotope compositions were monitored over time in 60 L tanks. These tanks contained Amazon water, with different biomasses of C-3 and C-4 macrophyte, representative of in situ densities occurring in central Amazon floodplains. In the C-4 Paspalum repens treatments, organic (POC, DOC) and inorganic carbon (DIC) got rapidly enriched in C-13, whereas in the C-3 Salvinia auriculata treatments, POC and DOC showed little change in concentration and isotopic composition, and DIC got depleted in C-13. The contribution of P. repens to POC and DOC was estimated to reach up to 94.2 and 70.7%, respectively. In contrast, no differences were reported between the C-3 S. auriculata and control treatments, an observation attributed to the lower C-3 biomass encountered in the field, to a slower degradation rate of C-3 compared to C-4 compounds, and to similar isotopic compositions for river POC and DOC, and C-3 compounds. The C-13 enrichments of POC, DOC, and DIC from P. repens treatments were attributed to an enhanced bacterially-mediated hydrolysis and mineralization of C-4 material. Evolutions of bacterial abundance and branched fatty acid concentrations confirmed the role of heterotrophic microbial communities in the high P. repens decomposition rate. Our experiment highlights the predominant role of C-4 aquatic plants, as a large source of almost entirely biodegradable organic matter available for heterotrophic activity and CO2 outgassing to the atmosphere.

The temporal changes in major bacterial groups and bulk heterotrophic activity were determined during the growth, senescence and post-bloom phases of a Phaeocystis globosa bloom, at a coastal site in the eastern English Channel. Cell-specific exoenzymatic activities were highest dur- ing the growth period of P. globosa, while bacterial abundance and bacterial heterotrophic produc- tion peaked during the senescence of the P. globosa bloom. Bacteroidetes and Gammaproteobacteria were the most important bacterial groups during the growth period of P. globosa, contributing between 13 and 47% of bulk bacterial abundance and leucine incorporation. At the end of the phyto- plankton growth period, Gammaproteobacteria were the most important contributors to bacterial heterotrophic production, accounting for 68% of bulk leucine incorporation. During the senescent phase, 36 and 29% of bulk leucine incorporation were attributable to Bacteroidetes and Alphapro- teobacteria, respectively. Finally, after the disappearance of the bloom, Gamma- and Alphapro- teobacteria dominated by the Roseobacter clade were responsible for 33 and 43% of bulk leucine incorporation, respectively. The relative abundance of the bacterial groups showed little variability between consecutive dates during most of the study period. The contributions of different bacterial groups to bulk abundance and leucine incorporation were correlated with exo-proteolytic and -glu- cosidic activities and with particulate organic carbon, suggesting at least some specificity of these bacterial groups with respect to their metabolic properties in the environment.

International audience; The temporal variability in phytoplankton photosynthetic activity was studied in the coastal waters of the Strait of Dover and related to environmental conditions. Phytoplankton photosynthetic activity data collected from October 2008 and August 2010 at different time scales (hourly to interannual) using a nested sampling design are presented. Photosynthetic parameters including the maximum quantum yield (Fv/Fm), maximal light utilization efficiency (α), maximum electron transport rate (ETRm) and light saturation coefficient (Ek) were measured using Pulse Amplitude Modulation (PAM) fluorometry. Information on the taxonomic composition of phytoplankton assemblages and physicochemical parameters were also collected. Marked changes in photosynthetic parameters were observed at the different time scales investigated. The variability of photosynthetic parameters at sub-seasonal scale (hourly to monthly) could be of the same order of magnitude as at seasonal scale. At short time scale (hour to week), there was no consistent pattern of diel periodicity in photosynthetic parameters. There was a decline of ETRm and α during the day as often as there was a peak at the maximum of irradiance. Light conditions were the main influencing factor on photosynthetic parameters at these time scales. The optimal use of incident irradiance seemed focused on between-day rather than within-day variability. At longer time scale (seasonal to interannual), close interplays between shifts in community taxonomic composition and changes in the physicochemical characteristics of the environment controlled the variability in photosynthetic parameters. Whatever the time scale and period of year considered, variability in photosynthetic parameters was ;Ek-independent;. In well-mixed macrotidal ecosystems, such as the Strait of Dover, a nested sampling design allowing to characterize the short- (intraday and daily) as well as long-term variability (within months, monthly, seasonal, annual and interannual) in photosynthetic parameters is required to get a suitable picture of phytoplankton photosynthesis and avoid potential problems of aliasing.

International audience; Phytoplankton observation in the ocean can be a challenge in oceanography. Accurate estimations of its biomass and dynamics will help to understand ocean ecosystems and refine global climate models. Relevant data sets of phytoplankton defined at a functional level and on a sub-meso-and daily scale are thus required. In order to achieve this, an automated, high-frequency, dedicated scanning flow cytometer (SFC, Cytobuoy b.v., the Netherlands) 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 PocketFerryBox during a cruise in the North Sea, 08–12 May 2011 (DYMAPHY project, INTERREG IV A " 2 Seas "), in order to identify the phytoplankton community structure of near surface waters (6 m) with a high spatial resolution 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 analysing chlorophyll a and the scanning flow cytometer, using the integrated red fluorescence emitted by each counted cell, showed significant correlations. For the first time, the community structure observed from the automated flow cytometry data set was compared with PHYSAT reflectance anomalies over a daily scale. The number of matchups observed between the SFC automated high-frequency in situ sampling and remote sensing was found to be more than 2 times better than when using traditional water sampling strategies. Significant differences in the phyto-plankton community structure within the 2 days for which matchups were available suggest that it is possible to label PHYSAT anomalies using automated flow cytometry to resolve not only dominant groups but also community structure .

Heterotrophic bacterial standing stocks (total and viable cells) and production were determined in the coastal surface waters of the eastern English Channel, during different stages of a phytoplankton succession. Two coastal zones of variable freshwater influence were surveyed within the ‘coastal flow system’ (Wimereux and Somme Bay) where massive and recurrent Phaeocystis globosa blooms take place in spring. The proportion of intact (MEM+) cells, assessed by the LIVE/DEAD® BacLight™ (L/D) method, varied from 15 to 94% at the two coastal stations studied (median of 46%). MEM+ and total (DAPI) cell counts were significantly correlated over the study period, whereas the higher proportion of MEM+ cells did not correspond to an elevated bacterial cell production (BP). Low levels of living (potentially active) cells were nevertheless responsible for the high productivity levels within the bacterial community when the P. globosa bloom declined. Our study revealed that the bacterial carbon production/primary production ratios (BCP/PP) showed broad variations (7 to 111%) within each site, going from low values (7–16%) when the bloom was the most productive, to higher values (61–111%) at the end of the bloom. This suggested (i) a temporal uncoupling between bacteria and phytoplankton throughout the bloom duration and (ii) a drastic change of the amount of PP potentially processed by the bacterial community among high and low productive periods. The BCP increase after the decline of the P. globosa bloom implies that, at this time, a large part of the phytoplankton-derived organic matter (OM) was remineralised via the bacterial heterotrophic production. With respect to the L/D results, this bacterial remineralisation was due to a small yet productive total cell fraction.

International audience; Providing a wide variety of the most up-to-date innovations in sensor technology and sensor network, our current project should achieve two major goals. The first goal covers some issues related to public safety and security, such as the coastal and port surveillance systems. While the second one will improve the capacity of public authorities to develop and implement smart environment policies by monitoring the shallow coastal water ecosystems. At this stage of our project, a surveillance platform has been already installed near the "Molène Island" which is a small but the largest island of an archipelago of many islands located off the West coast of Brittany in France. Our final objective is to add various sensors as well as to design, develop and implement new algorithms to extend the capacity of the existing platform and reach the goals of our project. This chapter describes the whole project by focusing on the variety of used sensors and it will briefly introduce the most important required theoretical approaches such as: Blind signal processing, High Order Statistics (HOS), classification algorithms and data fusion methods which will be applied to build up an original and reliable system able to perform a sustainable and long term monitoring of coastal marine ecosystems and to enhance port surveillance capability. In addition, it discusses developed techniques and concepts to deal with several problems related to our project. The new system will address the shortcomings of traditional approaches based on measuring environmental parameters, which are expensive and fail to provide adequate large-scale monitoring. More efficient monitoring will also enable improved analysis of climate change, and provide knowledge informing the civil authority's economic relationship with its coastal marine ecosystems. Some results are given and discussed.

International audience; 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 cm3. 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.

International audience; Providing a wide variety of the most up - to - date innovations in sensor technology and sensor networks, our current project should achieve two major goals. The first goal covers various issues related to the public maritime transport safety and security, such as the coastal and port surveillance systems. While the second one w ill improve the capacity of public authorities to develop and implement smart environment policies by monitoring the shallow coastal water ecosystems. At this stage of our project, a surveillance platform has been already installed near the "Molène Island" which is a small but the largest island of an archipelago of many islands located off the West coast of Brittany in North Western France. Our final objective is to add various sensors as well as to design, develop and implement new algorithms to extend th e capacity of the existing platform and reach the goals of our project. Finally, this manuscript introduces the identified approaches as well as t he second phase of the project which consists in analyzing living underwater micro - organisms (the population o f Marine Micro - Organisms, i.e. MMOs such as Phytoplankton and Zooplankton micro - zooplankton, but also heterotrophic bacterioplankton) in order to predict the health conditions of the macro - environment s . In addition, this communication discusses developed t echniques and concepts to deal with several practical problems related to our project. Some results are given and the whole system architecture is briefly described. This manuscript will also addresses the national benefit of such projects in the case of t hree different countries (Australia, France and KSA

Bacterial and phytoplankton biomasses were estimated in a four-year study along a saline gradient (the dilution plume of the Gironde estuary on the Aquitanian continental shelf), by measuring bacterial abundance and mean cell volumes (epifluorescence counts) and chlorophyll-a concentrations tin vitro fluorescence). The spatial and temporal distribution of phytoplankton enabled us to determine the seasonal succession of algal blooms, sprouting in the marine waters of the inner shelf in early spring (picoplanktonic forms), reaching their annual maximum (10 mu g L-1) in plume waters in advanced spring, and moving to estuarine waters in the summer (> 20 mu m forms). Bacterial biomasses followed mainly a decreasing dilution gradient, especially in winter and early spring, with maximum estuarine values reaching 10(7) cell mL(-1) (more than 30 % of small attached cells and more than 60 % of free small cocci), in accordance with estuarine discharges into the inner shelf zone. Moreover, plume waters showed an additionnal peak of bacterial numbers and mean cell volumes in early summer, with increasing proportions of larger rod- and vibrio-shaped bacteria. A clear morphometrical succession was followed in marine waters, from a majority of attached and coccal cells in winter, to maximal proportions of larger vibrio-shaped bacteria, inducing a maximal spring level of total abundance (2 x 10(6) cell mL(-1)) and high mean cell volumes (0.044 mu m(3)), coinciding with the marine vernal bloom. Bacterial estimated biomass represented, consequently, a wide range of proportions compared to phytoplankton: only when a good correlation was found between them, bacterial-C/phytoplankton-C ratio was close to 1/4, a correlation that improved in warmer periods, throughout different water types. Due to the relavitely narrow range of chlorophyll-a values, we could not find a high predictive correlation when pooling all the 4-year data, a relationship that has been outlined in important reviews by pooling together different aquatic systems. We noticed, however, that in the particular environment of our study (high inputs of particulate detritic matter) bacterial-C usually dominated the microbial pool (specially in estuarine and plume waters and in light-limited conditions). This dominance, added to the frequent dominance of small-sized phytoplankton, leads to an enhanced "microbial loop" activity, defining a "maintenance system" (oligotrophic conditions), which alternates with some eutrophic periods., Les biomasses bactériennes et phytoplanctoniques ont été estimées au cours d'une étude menée sur quatre ans, le long d'un gradient halin (panache de dilution girondin, sur le plateau continental Aquitain), par des mesures globales d'abondances et biovolumes bactériens (comptages en épifluorescence) et par des mesures de chlorophylle-a (fluorimétrie extractive). La répartition spatio-temporelle des micro-algues nous a permis de préciser la succession spatiotemporelle de leurs poussées, depuis le début du printemps (formes picoplanctoniques) en eaux marines, vers une situation de poussée de panache (maximum annuel de 10 μg chl-a.L−1), puis vers la situation de poussée phytoplanctonique estivale (formes > 20 μm). Un gradient de dilution décroissant caractérise les biomasses bactériennes, spécialement en hiver et au début du printemps, les maxima estuariens atteignant les 107 cell.mL−1, 30 % de petites bactéries attachées, et plus de 60 % de formes coccoïdes libres. Les eaux de panache ont présenté un pic de biomasses à la transition printemps-été, avec encore 15 % de bactéries attachées, mais de fortes proportions en grandes formes libres (vibrioïdes et bâtonnets). En eaux marines, on décèle une succession morphométrique, avec une majorité de bactéries attachées et coccoïdes en hiver, alors que les formes libres vibrioïdes sont fortement représentées au printemps, provoquant, au moment du bloom algal, un niveau maximal d'abondances (2 × 106 cell.mL−1) et de volumes moyens cellulaires bactériens (0,044 μm3). L'importance relative des biomasses bactériennes par rapport au phytoplancton est par conséquent extrêmement variable, et la relation établie entre les deux stocks, lorsqu'elle existe, est d'autant plus significative que l'on avance dans la saison, le rapport moyen C-bact/C-phyto étant de Full-size image (

The arsenic (As) cycle in the marine environment is known to be sensitive to biological activity. Within the scope of the National Coastal Oceanography Program, we undertook a specific study of the behaviour of this element in a water column on the continental shelf of the Bay of Biscay off the Gironde estuary during two oceanographic cruises conducted in May 1994 and May 1995. Various chemical forms were measured: arsenite (As3), at-senate (As5), monomethylarsenic (MMA), dimethylarsenic (DMA) and dissolved total As after ultraviolet mineralization. The net flux of total As from the Gironde estuary was evaluated as well as its effect on the concentration in surface marine waters. The vertical profiles in the coastal zone during a period of active primary production confirmed a certain analogy between arsenates and phosphates as well as the formation of As3 and DMA. The importance of organoarsenic species not directly accessible to the formation of volatile hydrides is demonstrated. Their presence modifies assessments, reducing the deficit of dissolved total As in the euphotic layer to just 5 %. For particles, the As content in phytoplankton was estimated at 6 mu g.g(-1) compared to 20 to 30 mu g.g(-1) in iron- and aluminium-rich terrigenous particles. These results do not invalidate the role of phytoplankton in the speciation of dissolved As but indicate that their involvement in vertical transfers was apparently not predominant in the zone under study., Le cycle de l'arsenic en milieu marin est bien connu pour sa sensibilité à l'activité biologique. Dans le cadre du Programme National d'Océanographic Côtière, nous avons étudié de manière plus précise le comportement de cet élément dans la colonne d'eau sur le plateau continental du Golfe de Gascogne, au large de la Gironde. Deux campagnes océanographiques ont été réalisées en avril 1994 et mai 1995. Nous avons mesuré les diverses formes chimiques: arsénite (As3), arséniate (As5), monométhylarsenic (MMA), diméthylarsenic (DMA) ainsi que l'As total dissous après minéralisation UV. Le flux net d'As total issu de la Gironde a été évalué ainsi que son influence sur la concentration dans les eaux marines superficielles. Les profils verticaux en zone côtière, pendant une période active de production primaire, confirment une certaine analogie entre arséniates et phosphates, ainsi que la formation d'As3 et de DMA. L'importance d'espèces organoarséniées inaccessibles directement à la formation d'hydrures volatils, est démontrée. Cette présence influe sur les bilans et réduit à 5% seulement le déficit en As total dissous dans la couche euphotique. Concernant les particules, on évalue à 6 μg·g−1 la teneur en As du phytoplancton contre 20 à 30 μg·g−1 dans les particules terrigènes riches en Fe et en A1. Sans remettre en cause l'importance du phytoplancton dans la spéciation de l'As dissous, son implication dans les transferts verticaux ne semble pas prédominante dans la zone d'étude.

International audience; The dinoflagellate Dissodinium pseudolunula is the most common and widespread ecto-parasite of copepod eggs in neritic waters. When the host is absent, the species survives with a distinctive pair of twin resting cysts described as Pyrocystis margalefii. Based on live samples, the formation of the twin resting cysts is illustrated here for the first time. The gymnodinioid infective cells did not form overwintering cysts under unfavourable conditions. These are formed inside the secondary lunate sporangium.

International audience; A major challenge in ocean and coastal management is to find simple ways to evaluate the health of such complex ecosystems. This task may prove complicated as selection criteria needs to be established for choosing appropriate indicators and evaluation tools which do not mask or leave out inherent ecosystem properties and dynamics. Here, we review some empirical analyses and modelling techniques which can be used to derive environmental health indicators. With a series of case studies ranging from the combined use of structural and functional attributes of the system, to modelling outputs that integrate the biological and physical environments, we illustrate the usefulness and complementarities of these methods to assess ecosystem health. The choice of relevant indicators will depend on the ecological questions raised as well as the biological and habitat components considered which can range from a single level (individual or population) to multiple levels (community or ecosystem-based indicators) in the ecosystem. Each method has its own capabilities and limitations that may render it useful or insufficient in some cases. We suggest, however, that, whenever possible, the combination of ecological attributes and tools should be used to improve our knowledge and assessment of marine ecosystems for better management and conservation in the future.

L'évocation de l'environnement en Guyane renvoie intuitivement à la forêt amazonienne, poumon de la Terre, avec ses faunes et flores exubérantes. Il existe pourtant une autre Guyane, moins emblématique, celle des espaces côtiers et littoraux, paradoxalement moins accessible et de ce fait mieux préservée. Entre milieu marin, pointes rocheuses, plages de sable, étendues de vase, mangroves, marais, forêts et savanes, la Guyane côtière recèle en effet des écosystèmes très divers, dont on commence seulement à découvrir la richesse, l'organisation et le fonctionnement. Rédigé par un collectif de chercheurs impliqués dans l'observation, la description et l'analyse de ces environnements et de leurs biodiversités, Guyane océane présente ainsi pour la première fois ces milieux méconnus à un large public.

International audience; The bacterioplankton diversity of coastal waters along a latitudinal gradient between Puerto Rico and Argentina was analyzed using a total of 134,197 high-quality sequences from the V6 hypervariable region of the small-subunit ribosomal RNA gene (16S rRNA) (mean length of 60 nt). Most of the OTUs were identified into Proteobacteria, Bacteriodetes, Cyanobacteria, and Actinobacteria, corresponding to approx. 80% of the total number of sequences. The number of OTUs corresponding to species varied between 937 and 1946 in the seven locations. Proteobacteria appeared at high frequency in the seven locations. An enrichment of Cyanobacteria was observed in Puerto Rico, whereas an enrichment of Bacteroidetes was detected in the Argentinian shelf and Uruguayan coastal lagoons. The highest number of sequences of Actinobacteria and Acidobacteria were obtained in the Amazon estuary mouth. The rarefaction curves and Good coverage estimator for species diversity suggested a significant coverage, with values ranging between 92 and 97% for Good coverage. Conserved taxa corresponded to aprox. 52% of all sequences. This study suggests that human-contaminated environments may influence bacterioplankton diversity

Amaral-Zettler, Linda ...et al.-- 22 pages, 11 figures, 1 table, ICoMM is a project of the Census of Marine Life program funded by the Sloan Foundation. A grant from the W. M. Keck Foundation supported the 454 pyrotag sequencing conducted at the Marine Biological Laboratory, Woods Hole. Local and international funding facilitated project participation in this global initiative. GenBank sequence read archive data include SRP000903, SRP000912, SRP001108, SRP001172, SRP001206-31, SRP001242-45, SRP001259, SRP001265-66, SRP001268-70, SRP001273, SRP001309, and SRP001542-47

From 1999 to 2005, studies carried out in the frame of regional and national French programs aimed to determine whether the Phaeocystis globosa bloom affected the intertidal benthic communities of the French coast of the eastern English Channel in terms of composition and/or functioning. Study sites were chosen to cover most of the typical shore types encountered on this coast (a rocky shore, an exposed sandy beach and a small estuary). Both the presence of active Phaeocystis cells and their degradation product (foam) did have a significant impact on the studied shores. The primary production and growth rates of the kelp Saccharina latissima decreased during the bloom because of a shortage of fight and nutrient for the macroalgae. On sandy sediments, the benthic metabolism (community respiration and community primary production), as well as the nitrification rate, were enhanced during foam deposits, in relation with the presence of bacteria and active pelagic cells within the decaying colonies. In estuarine sediments, the most impressive impact was the formation of a crust at the sediment surface due to drying foam. This led to anoxic conditions in the surface sediment and resulted in a high mortality among the benthic community. Some organisms also tended to migrate upward and were then directly accessible to the higher trophic level represented by birds. Phaeocystis then created a shortcut in the estuarine trophic network. Most of these modifications lasted shortly and all the systems considered came back to their regular properties and activities a few weeks after the end of the bloom, except for the most impacted estuarine area. (C) 2008 Elsevier Ltd. All rights reserved.

International audience

A preparation protocol for scanning electron microscopy (SEM) was adapted and tested to the observation of Phaeocystis globosa morphotypes. For extra colonial cells, critical point drying (CPD) gave satisfactory results while for intra colonial cells, preservation with Lugol's iodine and/or glutaraldehyde followed by air-drying appeared as the most suitable method.

The role of the bacterial community in the annual benthic metabolism of Roscoff Aber Bay, France, was estimated during low tide at 2 sampling sites of different trophic status, located at either end of a strong environmental gradient. The benthic gross primary production (GPP) and com- munity respiration (BCR) were assessed in situ over 1 yr with a benthic chamber; simultaneously, bac- terial production (BP) was estimated by radiotracer incorporation in slurries. BP appeared to be sig- nificantly controlled by temperature during low tide. On an annual scale, microphytobenthos gross primary production (GPPa), bacterial production (BPa), meiofauna production (MePa), macrofauna production (MaPa) and benthic community respiration (BCRa) were estimated. While the estimated annual processes were generally higher at the muddy station, our results indicated that (1) the con- tribution of BPa to the annual benthic community production (CPa = BPa + MePa + MaPa) increased with increasing grain size, and (2) the bacterial community can modulate its growth efficiency (BGEa) when exposed to an environmental gradient: in intertidal sediments, the production of new cells is enhanced when the organic matter concentration is lower, sustaining the development of the commu- nity on the annual scale. This behaviour was inferred to be the predominant factor affecting the trophic state of the system.

International audience

Benthic gross primary production (GPP) and community respiration (BCR) were regularly measured on sandy beach sediment during low tide in a megatidal ecosystem. These measurements were assessed during 2 years in situ within a benthic chamber simultaneously with bacterial production (BP). Results suggested that community respiration in Wimereux sandy beach sediments was probably dominated by bacterial respiration and that the estimated benthic bacterial growth efficiency (BGE) was highly variable. Although temperature significantly controlled both BP and BCR during low tide at the annual scale, the temperature effect on BGE was not significant. The instability and sediment erosion caused by the wave action and the tidal cycle were thus thought to influence the BGE. Since the sampling site is regularly affected by Phaeocystis foam deposit (enhancing the BCR and decreasing the BGE), and since GPP rates were highly variable and supported by high assimilation numbers (i.e., >1 mgC mgChla−1 h−1), phytoplankton organic matter deposit following the immersion of the study site was thought to explain the BGE variability.

In this study, benthic metabolism was measured during low tide, in a small intertidal bay. Gross primary production (GPP) and benthic community respiration (BCR) were calculated via in situ CO2 flux measurements at the air-sediment interface within a benthic chamber. These rates (GPP and BCR) were determined simultaneously with microphytobenthos (MPB), bacterial (BB), macrofaunal (MaB) and meiofaunal (MeB) biomasses, grain size analysis and nutrient standing stocks in sediment porewater (NO2 - , NO3 - , NH4 + , SiO3 2- and PO4 3- ). The aims of this study were to deter- mine (1) the relative influence of environmental regulating factors on benthic metabolism under in situ conditions and (2) the relative contribution of benthic compartments to BCR. Among all the potential regulating factors measured (i.e. sediment temperature, dissolved inorganic nutrient con- centrations in porewater), and the entire size range of benthic organisms sampled (i.e. from macro- fauna to bacteria), results showed that (1) granulometry strongly controlled the distribution of benthic compartments at the bay scale and (2) GPP and BCR were mostly influenced by temperature at the sampling site scale. Moreover, out of bacteria, macrofauna and meiofauna, bacterial activity contributed the most to BCR (bacterial > macrofaunal > meiofaunal respiration). Mean bacterial res- piration was estimated to be 1.5 ± 0.5 mgC m -2 h -1 and represented up to 88% of BCR in fine-sand sediments.

Benthic community metabolism during emersion was measured in a three-year survey by monitoring CO2 fluxes in benthic chambers on an exposed sandy beach of the eastern English Channel (Wimereux, France). The three-year chronology of variations in benthic metabolism was characterised by a high variability around a low value for gross community primary production (GCP: 17.47 ± 40.85 mgC m−2 h−1, mean ± SD) and community respiration (CR: 1.66 ± 1.97 mgC m−2 h−1, mean ± SD). Although benthic metabolism remained low most of the time, some high values of primary production and respiration were occasionally detected. High primary production rates (up to 213.94 mgC m−2 h−1 measured at the end of summer) matched with the development of Euglena sp., together with the occurrence of phytoplanktonic species on the sediment, whereas high community respiration rates were detected at the end of spring on Phaeocystis sp. foam deposits. Community respiration was positively correlated with bacterial abundance, suggesting that CR was mainly supported by microfauna.

La biodiversidad marina en la Guyana Francesa esta fuertemente influenciada por los aportes amazonicos, los cuales constituyen un factor estructurante de los ecosistemas estuarianos, costeros y de plataforma continental. Ademas, debido a las cambiantes condiciones meteorologicas y oceanograficas, la variabilidad estacional e inter-anual puede jugar un rol importante en la estabilidad o la modificacion de los parametros medio-ambientales que afectarian la biodiversidad ecologica, poblacional y genetica de los ecosistemas locales. Los estudios llevados a cabo sobre la biologia de las especies marinas y litorales se refieren principalmente a especies de interes comercial, especies protegidas en peligro de extincion, y sobre todo a las caracteristicas del funcionamiento de ciertos ecosistemas costeros y litorales caracteristicos como los estuarios, bancos de fango, playas de arena, y sobre todo los manglares. La idea de estudios o series de estudios mejor coordinados entre si a nivel regional e internacional, emerge como una necesidad para una mejor estimacion y comprension de la biodiversidad marina. Estos estudios beneficiarian de una importante cooperacion internacional que pemitiese comparar e integrar el conjunto de datos obtenidos en el pasado, llevar a cabo misiones oceanograficas conjuntas, mutualizar y homogeneizar los protocolos analiticos, y favorecer el intercambio de tecnicas y estrategias por intermedio de intercambios de cientificos y estudiantes en formacion de postgrado. Finalmente, estudios comparativos sobre la biodiversidad de sistemas costeros analogos sudamericanos permitirian de alcanzar una mejor estimacion de la biodiversidad marina de este continente.