Synthetic normalized biomass size spectra (NBSS) comprising non-synoptically sampled phytoplankton, meso- and macrozooplankton, and micronekton including mesopelagic fishes were explored to analyze pelagic community structure in seven regions of the tropical and the subtropical Atlantic representative of different water bodies (NE Brazil shelf, NE Brazil oceanic islands, northern and southern offshore Benguela Upwelling System, northern offshore Canary Current Upwelling System, equatorial region, southern Canary Current Upwelling System oxygen minimum zone). For mesopelagic fishes and micronekton, conversions were applied accounting for sampling biases in relation to other ecosystem components. Three main results were obtained. Firstly, NBSS slopes based on biovolume were significantly shallower than slopes based on carbon contents, as revealed in part through pairwise comparisons of linear models and by ANOVA. The ensemble mean slope for six regions combined (one region omitted due to missing zooplankton data) measured in terms of biovolume was −0.866, and the respective value in terms of carbon biomass was −0.894. Secondly, log ratios of spectral densities, that is, contrasts, between consumers and phytoplankton increased with decreasing primary production. Contrasts for total micronekton and mesopelagic fishes relative to phyto- and zooplankton varied with primary production, indicating that below a primary production of 650 mg C m−2 day−1, their spectral densities were higher than predicted by phytoplankton. Above this level, however, the spectral densities were lower. Thirdly, regional population marginal means were positively correlated with primary production in terms of carbon biomass (p = 0.01) but not biovolume (p = 0.48). Biovolume NBSS slopes were negatively correlated with primary production (p = 0.02), if the northern Benguela Upwelling System was not included (else p = 0.11). The increase in biovolume relative to the carbon biomass of gelatinous organisms is discussed as allometric advantage to enhance trophic transfer efficiency. Trophic transfer efficiencies ranged from 28.9% to 36.8% for open-ocean systems and from 36.8% to 49.7% for coastal and oceanic island habitats. The results suggest that synthetic pelagic size spectra provide a powerful framework to detect regional and functional shifts in Atlantic pelagic communities, offering predictive value for future ocean changes under climate scenarios.

Abstract The equatorial Atlantic Ocean is characterized by seasonal upwelling and complex nutrient dynamics. These processes shape the temporal and spatial distribution of primary productivity causing a pronounced east-west chlorophyll-a gradient. But whether this surface biomass pattern is reflected in particle production and export remains uncertain. We analyze vertical high-resolution particle size distribution data from Underwater Vision Profilers and physical oceanographic observations collected during two trans-Atlantic cruises conducted in contrasting seasons. During the higher productivity fall season, upwelling and tropical instability waves enhanced local primary production and supported deep export of large particles. In contrast, during the lower productivity boreal spring, unexpectedly high concentrations of small particles (0.1-0.5 mm) were observed in the central basin, concentrated within the Equatorial Undercurrent (EUC), which is supplied by the energetic North Brazil Current retroflection. Backward trajectory analysis and biological and hydrographic evidence suggest that these particles originate from the South American continental margin and are laterally transported eastward along a short advective pathway into the EUC. Estimating Particulate Organic Carbon (POC) flux from the particle size distributions, we find that during the low-productivity period, between 15-35°W, over 70% of the POC flux in the upper 200 m might be attributed to small particles (0.05-0.1mm) carried within the EUC. These findings highlight the importance of lateral subsurface transport for equatorial carbon cycling, thereby influencing deep-sea and benthic ecosystem structure.

Abstract. The biological carbon pump (BCP) comprises a wide variety of processes involved in transferring organic carbon from the surface to the deep ocean. This results in long-term carbon sequestration. Without the BCP, atmospheric CO2 concentrations would be around 200 ppm higher. This study reveals that ocean dynamics at the mesoscale and submesoscale could have a major impact on particulate organic matter (POM) vertical distribution. Our results indicate that intense submesoscale frontal regions, such as those between mesoscale eddies, could lead to an important accumulation and transport of POM from the mixed-layer depth (MLD) down to the mesopelagic zone. To reach these conclusions, a multifaceted approach was applied. It included in situ measurements and marine snow images from a BGC-Argo float equipped with an Underwater Vision Profiler (UVP6), satellite altimetry data, and Lagrangian diagnostics. We focused our study on three intense features in marine snow distribution, observed during the 17-month-long float mission in the Cape Basin in the southwest of Africa. These features were located in the frontal region between mesoscale eddies. Our study suggests that a particle injection pump induced by a frontogenesis-driven mechanism has the potential to enhance the effectiveness of the biological pump by increasing the depth at which carbon is injected into the water column. This work also emphasizes the importance of establishing repeated sampling campaigns targeting the interface zones between eddies. This could improve our understanding of the mechanisms involved in the deep accumulation of marine snow observed at eddy interfaces.

Abstract. The marine biological carbon pump (BCP) plays a central role in the global carbon cycle, transporting carbon from the surface to the deep ocean and sequestering it for long periods. Sinking of surface-produced particles, known as the Biological Gravity Pump (BGP) constitutes the main component of the BCP. To study the BGP in the equatorial Atlantic upwelling region, a biogeochemical (BGC) Argo float equipped with an Underwater Vision Profiler 6 (UVP6) camera was deployed from July 2021 to March 2022. The float was recovered after its eastward drift from 23 to 7° W along the equator, during which it conducted profiles to 2000 m depth every 3 d. For the first time in this oceanic region, in situ images and physical and biogeochemical data from a BGC-Argo float were acquired and analyzed in combination with satellite data. During the float trajectory, two blooms were recorded followed by two main export events of sinking aggregates that lasted for over a month, consistently reaching 2000 m depth. A Lagrangian approach was applied to investigate the production, transformation, and deep export of marine particles. Based on the characterization of the morphology of detritus within and outside of the plumes, five particle morphotypes with different sinking properties were detected. Small and dense aggregates were present throughout the water column while porous morphotypes, despite being larger, were predominantly concentrated in the surface layer. Export was driven by small and compact particles with higher particle abundance and flux during upwelling and export events. Our investigation reveals the stability of the equatorial Atlantic BCP system during this period, yielding an export efficiency of 6 %–7 % during and outside of export events. This study highlights the importance of using new technologies on autonomous platforms to characterize the temporal variability in the magnitude and functioning of the BCP.

Simultaneous measurements of marine snow (particles larger than 600 µm) morphologies, estimates of their in situ sinking speeds, and midwater attenuation in export plumes were performed for the first time using a biogeochemical (BGC)-Argo float equipped with optical and imaging sensors. The float was deployed and recovered after drifting for 1 year in the sluggish-flow regime of the Angola Basin. Six consecutive chlorophyll a and particulate matter accumulation events were recorded at the surface, each followed by an export plume of sinking aggregates. Objects larger than 600 µm were classified using machine learning recognition and clustered into four morphological categories of marine aggregates. Plankton images were validated by an expert in a few broad categories. Results show that different types of aggregates were produced and exported from the different blooms. The different morphological categories of marine snow had different sinking speeds and attenuation for a similar size, indicating the effect of morphology on sinking speed. However, a typical size-to-sinking relationship for two of the categories and over the larger observed size range (100 µm to a few millimeters) was also observed, indicating the importance of size for sinking. Surprisingly, in situ-calculated sinking speeds were constantly in the lower range of known values usually assessed ex situ, suggesting a methodological effect, which is discussed. Moving away from purely size-based velocity relationships and incorporating these additional morphological aggregate properties will help to improve the mechanistic understanding of particle sinking and provide more accurate flux estimates. When used from autonomous platforms at high frequency, they will also provide increased spatio-temporal resolution for the observation of intermittent export events naturally occurring or induced by human activities.

Diatoms constitute one of the most diverse and ecologically important phytoplankton groups, yet their large-scale diversity patterns and drivers of abundance are unclear due to limited observations. Here, we utilize Tara Oceans molecular and morphological data, spanning pole to pole, to describe marine diatom diversity, abundance, and environmental adaptation and acclimation strategies. The dominance of diatoms among phytoplankton in terms of relative abundance and diversity is confirmed, and the most prevalent genera are Chaetoceros , Thalassiosira , Actinocyclus and Pseudo-nitzschia . We define 25 distinct diatom communities with varying environmental preferences illustrative of different life strategies. The Arctic Ocean stands out as a diatom hotspot with 6 of the diatom communities being exclusive to it. Light harvesting and photoprotection are among the cellular functions in which natural diatom populations invest the bulk of their transcriptional efforts. This comprehensive study sheds light on marine diatom distributions, offering insights to assess impacts of global change and oceanic anthropogenic impacts.

Abstract The use of trait-based approaches and trait data in zooplankton ecology is rapidly growing to better understand and predict the patterns of zooplankton distributions and their role in aquatic ecosystems and biogeochemical cycles. Although the number of zooplankton trait-based studies and available trait datasets is increasing, several challenges remain for the findability, accessibility, interoperability, and reusability (FAIR) in trait-based approaches that, if unaddressed, may stifle progress in this research area. Here, we review recent applications of trait-based approaches in zooplankton research and summarize the currently available trait data resources. To realize the potential of trait-based approaches to resolve ecological roles of zooplankton, datasets and approaches must adhere to FAIR principles. We provide recommendations and pathways forward to ensure FAIRness while highlighting the importance of collaborative efforts. These practical and easily implementable strategies will enhance the FAIRness of trait data, ultimately advancing zooplankton ecological research and connecting these findings to aquatic ecosystem functioning.

Abstract. In marine ecosystems, most physiological, ecological, or physical processes are size dependent. These include metabolic rates, the uptake of carbon and other nutrients, swimming and sinking velocities, and trophic interactions, which eventually determine the stocks of commercial species, as well as biogeochemical cycles and carbon sequestration. As such, broad-scale observations of plankton size distribution are important indicators of the general functioning and state of pelagic ecosystems under anthropogenic pressures. Here, we present the first global datasets of the Pelagic Size Structure database (PSSdb), generated from plankton imaging devices. This release includes the bulk particle normalized biovolume size spectrum (NBSS) and the bulk particle size distribution (PSD), along with their related parameters (slope, intercept, and R2) measured within the epipelagic layer (0–200 m) by three imaging sensors: the Imaging FlowCytobot (IFCB), the Underwater Vision Profiler (UVP), and benchtop scanners. Collectively, these instruments effectively image organisms and detrital material in the 7–10 000 µm size range. A total of 92 472 IFCB samples, 3068 UVP profiles, and 2411 scans passed our quality control and were standardized to produce consistent instrument-specific size spectra averaged to 1° × 1° latitude and longitude and by year and month. Our instrument-specific datasets span most major ocean basins, except for the IFCB datasets we have ingested, which were exclusively collected in northern latitudes, and cover decadal time periods (2013–2022 for IFCB, 2008–2021 for UVP, and 1996–2022 for scanners), allowing for a further assessment of the pelagic size spectrum in space and time. The datasets that constitute PSSdb's first release are available at https://doi.org/10.5281/zenodo.11050013 (Dugenne et al., 2024b). In addition, future updates to these data products can be accessed at https://doi.org/10.5281/zenodo.7998799.

Since most physiological, ecological, or physical processes in marine ecosystems are size-dependent, plankton size spectra are important indicators of the efficiency of the biological carbon pump and other plankton-mediated fluxes. Global predictions of plankton size spectra have recently started to integrate direct size measurements provided by imaging sensors, albeit they currently do not resolve plankton diversity within their size distributions. Using imaging datasets recently compiled as part of the Pelagic Size Structure database initiative (https://pssdb.net/), we investigate the size distribution of numerically important taxa at the global scale. More specifically, we assessed the size spectra of Rhizarians, Crustaceans and colonial N2 fixers and explored their relationships with environmental factors. We found strong linkages between temperature and the size structure of all the groups, but individual responses to iron acquisition or mesoscale circulation helped distinguish specific niches within the plankton community. We used these responses to predict the biogeography of different plankton groups, each showing good agreement with independent observations. Such analysis should help constrain the stocks (i.e. integral of the size spectrum) and the roles of these significant actors of marine biogeochemical cycles with respect to various ecological and biogeochemical processes.

Abstract The South Atlantic Ocean (SAO) is an under‐sampled ocean where the influence of environmental drivers on copepod body size is poorly understood. This study investigated the body size distribution of copepods from 13°S to 64°S to test Bergmann's rule, which predicts the occurrence of smaller organisms in warmer areas. We hypothesized that additional influence of oceanographic features strengthens this pattern. Zooplankton were sampled during the austral summer from the chlorophyll maximum depth up to the surface, at approximately 100 m depth, using a 200‐ μ m net. The samples were analyzed using the ZooScan imaging system and were classified using the Ecotaxa tool. We estimated copepod family abundance, biomass, and size structure, and their relationships with environmental variables were assessed through generalized linear mixed models (GLMM). Although most copepods increased in size at higher latitudes, not all families followed Bergmann's rule. Small adults of Clausocalanidae, Paracalanidae, Corycaeidae, and Oncaeidae contributed mostly in the Brazil Current (BC), while Calanidae copepodites disproportionately contributed to overall biomass, and Oithonidae adults were the most abundant in high latitudes. Copepod abundance or biomass hotspots were present in the southern limit of the warm BC, at the Subtropical Confluence Zone, and in the subantarctic waters at the Drake passage. Our results suggest that oceanographic features strengthen latitudinal body size relationships due to food availability, and the importance of different life history strategies.

Thriving in both epipelagic and mesopelagic layers, Rhizaria are biomineralizing protists, mixotrophs or flux-feeders, often reaching gigantic sizes. In situ imaging showed their contribution to oceanic carbon stock, but left their contribution to element cycling unquantified. Here, we compile a global dataset of 167,551 Underwater Vision Profiler 5 Rhizaria images, and apply machine learning models to predict their organic carbon and biogenic silica biomasses in the uppermost 1000 m. We estimate that Rhizaria represent up to 1.7% of mesozooplankton carbon biomass in the top 500 m. Rhizaria biomass, dominated by Phaeodaria, is more than twice as high in the mesopelagic than in the epipelagic layer. Globally, the carbon demand of mesopelagic, flux-feeding Phaeodaria reaches 0.46 Pg C y −1 , representing 3.8 to 9.2% of gravitational carbon export. Furthermore, we show that Rhizaria are a unique source of biogenic silica production in the mesopelagic layer, where no other silicifiers are present. Our global census further highlights the importance of Rhizaria for ocean biogeochemistry.

Summary paragraph Plankton are essential in marine ecosystems. However, our knowledge of overall community structure is sparse due to inconsistent sampling across their very large organismal size range. Here we use diverse imaging methods to establish complete plankton inventories of organisms spanning five orders of magnitude in size. Plankton community size and trophic structure variation validate a long-held theoretical link between organism size-spectra and ecosystem trophic structures. We found that predator/grazer biomass and biovolume unexpectedly exceed that of primary producers at most (55%) locations, likely due to our better quantification of gelatinous organisms. Bottom- heavy ecosystems (the norm on land) appear to be rare in the ocean. Collectively, gelatinous organisms represent 30% of the total biovolume (8-9% of carbon) of marine plankton communities from tropical to polar ecosystems. Communities can be split into three extreme typologies: diatom/copepod-dominated in eutrophic blooms, rhizarian/chaetognath-dominated in oligotrophic tropical oceans, and gelatinous-dominated elsewhere. While plankton taxonomic composition changes with latitude, functional and trophic structures mostly depend on the amount of prey available for each trophic level. Given future projections of oligotrophication of marine ecosystems, our findings suggest that rhizarian and gelatinous organisms will increasingly dominate the apex position of planktonic ecosystems, leading to significant changes in the ocean’s carbon cycle.

Plankton size spectra are important indicators of the ecosystem state, yet such measurements are typically biased by the available sampling methods. Here, we combined individual size measurement from two zooplankton imaging approaches—in situ observation by the Underwater Vision Profiler5 and Multinet-collection supplemented by ex situ imaging via Zooscan—obtained in the global ocean, to calculate zooplankton normalized biovolume size spectra (NBSS) for all organisms larger than 1 mm. The reconstructed NBSS combining both datasets resulted in increased biomass estimates by adding organisms poorly sampled by either of the methods. The optimal values measured by both methods are used to reconstruct the zooplankton biovolume and biomass distributions. The reconstructed slopes appeared steeper and closer to those measured only by the UVP5 (+7.6%) and flatter than those obtained only from the Multinet (−20%), particularly in tropical and temperate latitudes. The main difference in tropical and temperate NBSS from the two devices is due to the fragile rhizarians that were not accounted for when using net data. When possible, we suggest using in situ and ex situ technologies together, and we provide potential indications on how to correct for missing components of the community when only one method is available.

The Underwater Vision Profiler (UVP) has been developed to study the number, size and shape of particles (size \textgreater 80µm) and plankton (size \textgreater 700µm) in situ. Over the last decade, thousands of profiles have been collected in the world's oceans by the UVP5 to better understand and quantify processes affecting community compositions of large plankton and the biological carbon pump. These data, used together with modeling approaches helped estimate plankton global carbon biomass and particle vertical flux. The most recent UVP (UVP6) sensors have been developed to be mounted on autonomous platforms, mooring and CTD rosettes down to 6000 m depth. Fully inter-calibrated, they record particles and identify plankton and marine snow after recovery or during deployment using an embedded recognition algorithm. A complete software ecosystem is used to pilot the instrument, record the data, and make them available to fulfill the global need of easy data access expressed by scientists, policy makers and the public. Because of the cost reduction of the UVP6, its capability to be mounted on many platforms including autonomous ones, the Ocean is being quickly populated by this sensor (125 sensors have been in operation in the last 2 years). Recent plankton community composition, particle mass, and flux data from three different basins in the Atlantic will be presented. In the next decade, the massive global monitoring of these key biological Essential Oceanographic Variables will significantly advance our understanding of key aquatic processes including the biological carbon pump.

Biodiversity is studied notably because of its reciprocal relationship with ecosystem functions such as production. Diversity is traditionally described from a taxonomic, genetic or functional point of view but the diversity in organism morphology is seldom explicitly considered, except for body size. We describe morphological diversity of marine zooplankton seasonally and over 12 years using quantitative imaging of weekly plankton samples, in the northwestern Mediterranean Sea. We extract 45 morphological features on greater than 800 000 individuals, which we summarize into four main morphological traits (size, transparency, circularity and shape complexity). In this morphological space, we define objective morphological groups and, from those, compute morphological diversity indices (richness, evenness and divergence) using metrics originally defined for functional diversity. On both time scales, morphological diversity increased when nutritive resources and plankton concentrations were low, thus matching the theoretical reciprocal relationship. Over the long term at least, this diversity increase was not fully attributable to taxonomic diversity changes. The decline in the most common plankton forms and the increase in morphological variance and in extreme morphologies suggest a mechanism akin to specialization under low production, with likely consequences for trophic structure and carbon flux.

Abstract Export of sinking particles from the surface ocean is critical for carbon sequestration and to provide energy to the deep biosphere. The magnitude and spatial patterns of this export have been estimated in the past by in situ particle flux observations, satellite‐based algorithms, and ocean biogeochemical models; however, these estimates remain uncertain. Here, we use a recent machine learning reconstruction of global ocean particle size distributions (PSDs) from Underwater Vision Profiler 5 measurements to estimate carbon fluxes by sinking particles (35 μm–5 mm equivalent spherical diameter) from the surface ocean. We combine global maps of PSD properties with empirical relationships constrained against in situ flux observations to calculate particulate carbon export from the euphotic zone (5.8 ± 0.1 Pg C y −1 ) and annual maximum mixed layer depths (6.1 ± 0.1 Pg C y −1 ). The new flux reconstructions suggest a less variable seasonal cycle in the tropical ocean and a more persistent export in the Southern Ocean than previously recognized. Smaller particles (less than 418 μm) contribute most of the flux globally, while larger particles become more important at high latitudes and in tropical upwelling regions. Export from the annual maximum mixed layer exceeds that from the euphotic zone over most of the low‐latitude ocean, suggesting shallow particle recycling and net heterotrophy in the deep euphotic zone. These estimates open the way to fully three‐dimensional global reconstructions of particle fluxes in the ocean, supported by the growing database of in situ optical observations.

How plankton and particles are arranged spatially and the configurations of their co-occurrence shape the rates of organic matter production, utilization, and export within marine systems. The aim of this study was to examine whether the composition of marine snow (particles and aggregates >500 µm) and its coexistence with zooplankton change with depth layer, level of zooplankton dominance, chlorophyll fluorescence, and turbidity across the coastal–offshore gradients of hydrographically different Arctic fjords. The distribution and concentrations of zooplankton and marine snow were assessed in situ using an underwater vision profiler (UVP) in Svalbard waters during summer 2019. UVP counts of marine snow drastically outnumbered zooplankton at glacial stations, whereas zooplankton dominated offshore and in upper water layers, even in coastal waters. The most common compositional structure was dominance by an elongated morphotype of marine snow, often co-occurring with small dark (opaque) particles below 40 m depth, implying that these were the typical forms exported directly from surface layers. The other widespread type of structuring was dominance of UVP counts by copepods. They often coexisted with a flake morphotype of marine snow associated with high chlorophyll fluorescence. Structuring dominated by dark morphotypes was observed mainly near glaciers and in deep fjord basins. The highest amount of marine snow, represented by a high degree of dark morphotype, was observed in Hornsund, the most Arctic-type fjord. A Phaeocystis-associated agglomerated morphotype of marine snow occurred scarcely and only in more Atlantic-influenced fjords. A bimodal distribution pattern, with one abundance peak at the surface and another in deeper layers (>80 m) was observed offshore and in Kongsfjorden. This study emphasizes the high potential of UVPs for tracking links between plankton and detritus directly in their natural environment, and that variation in their co-occurrence may provide a proxy for the state of a pelagic ecosystem.

Aim The distribution of mesoplankton communities have been poorly studied at global scale, especially from in situ instruments. This study aims to (1) describe the global distribution of mesoplankton communities in relation with their environment and (2) assess the ability of various environmental-based ocean regionalisations to explain the distribution of these communities. Location Global ocean, 0-500 m depth. Time period 2008 - 2019 Major taxa studied 28 groups of large mesoplanktonic and macroplanktonic organ- isms, covering Metazoa, Rhizaria and Cyanobacteria. Methods From a global data set of 2500 vertical profiles making use of the Underwater Vision Profiler 5 (UVP5), an in situ imaging instrument, we studied the global distribu- tion of large (> 600 μm) mesoplanktonic organisms. Among the 6.8 million imaged ob- jects, 330,000 were large zooplanktonic organisms and phytoplankton colonies, the rest consisting of marine snow particles. Multivariate ordination (PCA) and clustering were used to describe patterns in community composition, while comparison with existing regionalisations was performed with regression methods (RDA). Results Within the observed size range, epipelagic plankton communities were Trichodesmium-enriched in the intertropical Atlantic, Copepoda-enriched at high latitudes and in upwelling areas, and Rhizaria-enriched in oligotrophic areas. In the mesopelagic layer, Copepoda-enriched communities were also found at high latitudes and in the At- lantic Ocean, while Rhizaria-enriched communities prevailed in the Peruvian upwelling system and a few mixed communities were found elsewhere. The comparison between the distribution of these communities and a set of existing regionalisations of the ocean suggested that the structure of plankton communities described above is mostly driven by basin-level environmental conditions. Main conclusions n both layers, three types of plankton communities emerged and seemed to be mostly driven by regional environmental conditions. This work sheds light on the role not only of metazoans, but also of unexpected large protists and cyanobacteria in structuring large mesoplankton communities.

Plankton size spectra are important indicators of the ecosystem state, as they illustrate the quantity of organisms available for higher marine food web and reflect multiple size-dependent processes. Yet, such measurements are typically biased by the available sampling methods, either disrupting fragile organisms or lacking good resolution (in size and/or time and space). In this study, we combined two of the most common approaches to measure zooplankton Normalized Biomass/Biovolume Size Spectra (NBSS) to calculate a complete zooplankton distribution for organisms larger than 1 mm. The reconstructed NBSS slopes appeared steeper and closer to those measured by the UVP5 (+7.6%) and flatter than those of the Multinet (- 20%) particularly in tropics and temperate latitudes. The overall gain in polar biomass was relatively small for reconstructed biomass compared to bulk estimates from Multinet (+0.24 mgC/m3 or +4.25%) and high from the UVP5 (+2.0 mgC/m3 or +53%). In contrast, in the tropical and temperate ecosystems, the gain in biomass was small for UVP5 (+0.67 mgC/m3 or +30.44% and +0.74 mgC/m3 or +19.59% respectively) and high for Multinet (+1.66 mgC/m3 or +136% and +3.4 mgC/m3 or +309% respectively). Given these differences, we suggest here to combine in situ imaging sensors and net data in any comprehensive study exploring key living players in the ocean ecosystem and their contributions to the biological pump.

Zooplankton are major consumers of phytoplankton primary production in marine ecosystems. As such, they represent a critical link for energy and matter transfer between phytoplankton and bacterioplankton to higher trophic levels and play an important role in global biogeochemical cycles. In this Review, we discuss key responses of zooplankton to ocean warming, including shifts in phenology, range, and body size, and assess the implications to the biological carbon pump and interactions with higher trophic levels. Our synthesis highlights key knowledge gaps and geographic gaps in monitoring coverage that need to be urgently addressed. We also discuss an integrated sampling approach that combines traditional and novel techniques to improve zooplankton observation for the benefit of monitoring zooplankton populations and modelling future scenarios under global changes.

Biodiversity is a measure of interest in many studies of global change. Depending on the question addressed, it takes a taxonomic, genetic, phylogenetic or functional perspective. Although aspects of morphology might be part of functional metrics, organism morphology is rarely considered explicitly in this context. We describe the changes in morphological diversity of marine zooplankton on the seasonal and long-term timescale. We digitalized weekly plankton samples collected from 2009-2020 in the NW Mediterranean Sea and automatically extracted 45 morphological features on > 800,000 individuals. Applying dimensional reduction (PCA) followed by clustering, we synthesized these features into four main morphological traits (describing size, transparency, circularity and shape complexity) and defined morphological groups (or ”morphs”). Based on these morphs, we computed time-series of morphological diversity indices (richness, divergence and evenness) relaying to metrics originally developed for functional diversity. Over the 12-year period, morphological – but not taxonomic – diversity increased while zooplankton concentration decreased. The environmental changes during this period consisted mainly in an increase in temperature and salinity and an overall impoverishment of surface waters, suggesting that niche specialization under low productivity increased the morphological divergence. Notably, an increased variability in the four morphological traits and higher proportions of extreme individuals caused this trend, with likely consequences for the ecosystem.

Abstract Satellite remote sensing is a powerful tool to monitor the global dynamics of marine plankton. Previous research has focused on developing models to predict the size or taxonomic groups of phytoplankton. Here, we present an approach to identify community types from a global plankton network that includes phytoplankton and heterotrophic protists and to predict their biogeography using global satellite observations. Six plankton community types were identified from a co-occurrence network inferred using a novel rDNA 18 S V4 planetary-scale eukaryotic metabarcoding dataset. Machine learning techniques were then applied to construct a model that predicted these community types from satellite data. The model showed an overall 67% accuracy in the prediction of the community types. The prediction using 17 satellite-derived parameters showed better performance than that using only temperature and/or the concentration of chlorophyll a . The constructed model predicted the global spatiotemporal distribution of community types over 19 years. The predicted distributions exhibited strong seasonal changes in community types in the subarctic–subtropical boundary regions, which were consistent with previous field observations. The model also identified the long-term trends in the distribution of community types, which suggested responses to ocean warming.

For decades, marine plankton have been investigated for their capacity to modulate biogeochemical cycles and provide fishery resources. Between the sunlit (epipelagic) layer and the deep dark waters, lies a vast and heterogeneous part of the ocean: the mesopelagic zone. How plankton composition is shaped by environment has been well-explored in the epipelagic but much less in the mesopelagic ocean. Here, we conducted comparative analyses of trans-kingdom community assemblages thriving in the mesopelagic oxygen minimum zone (OMZ), mesopelagic oxic, and their epipelagic counterparts. We identified nine distinct types of intermediate water masses that correlate with variation in mesopelagic community composition. Furthermore, oxygen, NO 3 − and particle flux together appeared as the main drivers governing these communities. Novel taxonomic signatures emerged from OMZ while a global co-occurrence network analysis showed that about 70% of the abundance of mesopelagic plankton groups is organized into three community modules. One module gathers prokaryotes, pico-eukaryotes and Nucleo-Cytoplasmic Large DNA Viruses (NCLDV) from oxic regions, and the two other modules are enriched in OMZ prokaryotes and OMZ pico-eukaryotes, respectively. We hypothesize that OMZ conditions led to a diversification of ecological niches, and thus communities, due to selective pressure from limited resources. Our study further clarifies the interplay between environmental factors in the mesopelagic oxic and OMZ, and the compositional features of communities.

Plankton ecologists have long used the Normalized Biomass Size Spectrum (NBSS) as a common framework to study the size distribution of aquatic bacteria, phytoplankton, and zooplankton across various temporal and spatial scales. Systematic NBSS measurements have shown that its shape varies across ecosystems and could be used as an indicator of the state of the ecosystem. Indeed, NBSS slopes typically indicate how efficiently biomass is transferred across sizes, impacting the throughput of the biological carbon pump. Zooplankton, in particular, influences the carbon pump by feeding on and repackaging phytoplankton production, as well as respiring O2 at rates that may exceed its replenishment, contributing to the existence of Oxygen Minimum Zones (OMZ) located in the Pacific, Indian, and Atlantic Oceans. Using a range of non-intrusive imaging devices, which produce community composition datasets along with complementary size measurements of individual organisms, we investigate the size distribution of zooplankton in the Atlantic Ocean. As part of our ongoing efforts to create a Pelagic Size Structure database (PSSdb, https://www.st.nmfs.noaa.gov/copepod/pssdb/), we will present a regional assessment of zooplankton NBSSs computed at different scales and compare them to estimates generated at the global scale. We will also investigate the response of zooplankton to environmental factors, including low concentrations of dissolved O2, to foresee how the gatekeepers of the marine biological carbon pump may be impacted by future anthropogenic pressures.

Aquatic ecologists face challenges in identifying the general rules of the functioning of ecosystems. A common framework, including freshwater, marine, benthic, and pelagic ecologists, is needed to bridge communication gaps and foster knowledge sharing. This framework should transcend local specificities and taxonomy in order to provide a common ground and shareable tools to address common scientific challenges. In a recent review paper published in Limnology and Oceanography (Martini et al., 2021), we advocated the use of functional trait-based approaches (FTBAs) for aquatic ecologists and proposed concrete paths to go forward. In this presentation, we will first present an overview of this synthesis work. Then, using a few examples of recent results, including from quantitative imaging, genomics, and machine learning, we will then concretely illustrate how FTBAs can allow aquatic ecologists to tackle some of the scientific challenges identified in the paper.

Quantitative imaging instruments produce a large number of images of plankton and marine snow, acquired in a controlled manner, from which the visual characteristics of individual objects and their in situ concentrations can be computed. To exploit this wealth of information, machine learning is necessary to automate tasks such as taxonomic classification. Through a review of the literature, we highlight the progress of those machine classifiers and what they can and still cannot be trusted for. Several examples showcase how the combination of quantitative imaging with machine learning has brought insights on pelagic ecology. They also highlight what is still missing and how images could be exploited further through trait-based approaches. In the future, we suggest deeper interactions with the computer sciences community, the adoption of data standards, and the more systematic sharing of databases to build a global community of pelagic image providers and users. Expected final online publication date for the Annual Review of Marine Science, Volume 14 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Zooplankton plays a major role in ocean food webs and biogeochemical cycles, and provides major ecosystem services as a main driver of the biological carbon pump and in sustaining fish communities. Zooplankton is also sensitive to its environment and reacts to its changes. To better understand the importance of zooplankton, and to inform prognostic models that try to represent them, spatially-resolved biomass estimates of key plankton taxa are desirable. In this study we predict, for the first time, the global biomass distribution of 19 zooplankton taxa (1-50 mm Equivalent Spherical Diameter) using observations with the Underwater Vision Profiler 5, a quantitative in situ imaging instrument. After classification of 466,872 organisms from more than 3,549 profiles (0-500 m) obtained between 2008 and 2019 throughout the globe, we estimated their individual biovolumes and converted them to biomass using taxa-specific conversion factors. We then associated these biomass estimates with climatologies of environmental variables (temperature, salinity, oxygen, etc.), to build habitat models using boosted regression trees. The results reveal maximal zooplankton biomass values around 60°N and 55°S as well as minimal values around the oceanic gyres. An increased zooplankton biomass is also predicted for the equator. Global integrated biomass (0-500 m) was estimated at 0.403 PgC. It was largely dominated by Copepoda (35.7%, mostly in polar regions), followed by Eumalacostraca (26.6%) Rhizaria (16.4%, mostly in the intertropical convergence zone). The machine learning approach used here is sensitive to the size of the training set and generates reliable predictions for abundant groups such as Copepoda (R2 ≈ 20-66%) but not for rare ones (Ctenophora, Cnidaria, R2 < 5%). Still, this study offers a first protocol to estimate global, spatially resolved zooplankton biomass and community composition from in situ imaging observations of individual organisms. The underlying dataset covers a period of 10 years while approaches that rely on net samples utilized datasets gathered since the 1960s. Increased use of digital imaging approaches should enable us to obtain zooplankton biomass distribution estimates at basin to global scales in shorter time frames in the future.

Over the last decade, plankton research has experienced extensive developments in automatic image acquisition for identifying and quantifying plankton species. This information is useful for the reporting of plankton occurrences and ecological data. Imagery instruments can vary in the way they sample (benchtop or in situ imagers) and the particle’s size range they target (see Lombard et al. (2019) for an extensive comparison of instruments and specifications). However, due to the wide variety of instruments and their (automatic) output data and formats, it is challenging to integrate datasets that originate from different sources. For this reason, we developed recommendations for plankton imagery data management, which can promote the ability to make these datasets as FAIR (Findable, Accessible, Interoperable and Reusable principles), as possible. The workflow presented here could inspire other Biodiversity Information Standards TDWG communities working with (automated) imagery data (e.g., camera traps) such as the Audubon Core and Machine Observations Interest Group. The recommended data format follows the OBIS-ENV-DATA format (De Pooter et al. 2017), a Darwin Core-based approach to standardise biodiversity data (Wieczorek et al. 2012) used in EurOBIS, the European node of the Ocean Biodiversity Information System (OBIS) and EMODnet Biology, the European Marine Biodiversity Data Network. However, this format does not include sufficient information for imagery data, therefore we propose the use of additional Darwin Core terms. For example, by including the terms identifiedBy, identificationVerificationStatus and identificationReferences in the Occurrence table, more clarity is reported regarding the uncertainty of the classification made by an algorithm. Thus, data providers can publish manually validated datasets or datasets produced by fully automated plankton identification workflows; and users can choose to use validated or not validated data. See in Suppl. material 1 a practical example on how to report an imagery dataset following the best practices. Moreover, the OBIS-ENV-DATA format allows the ingestion of additional information thanks to the use of the Darwin Core (DwC) Extended Measurement Or Facts or eMoF extension in the DwC Event core. The eMoF stores biotic, abiotic and sampling measurements and facts that are related to the Event and Occurrence table. An important aspect of this extension is that it includes standardised terms and controlled vocabularies, such as the British Oceanographic Data Centre (BODC) vocabularies, to standardise parameters that are not covered by DwC. The advantages of these is to unambiguously report information and to include those measurements that cannot be reported in the Event and Occurrence table (e.g., reporting abundance or biomass of plankton), and that are crucial to investigate ecosystem functioning questions. As a consequence, biodiversity data aggregators can extend their scope beyond species occurrence data. Fig. 1 summarises a typical dataflow that goes from imagery data acquisition to publication in several steps: Images are cropped and classified with software. This can be done in EcoTaxa, a web application that allows users to taxonomically classify images of individual organisms. Data is formatted in OBIS-ENV-DATA format. This format can be exported from EcoTaxa through its API. Data is submitted to EurOBIS via the IPT (Integrated Publishing Toolkit). Data is quality controlled by the BioCheck tool. Data in EurOBIS can flow to EMODnet Biology, OBIS and GBIF (Global Biodiversity Information Facility). Images are cropped and classified with software. This can be done in EcoTaxa, a web application that allows users to taxonomically classify images of individual organisms. Data is formatted in OBIS-ENV-DATA format. This format can be exported from EcoTaxa through its API. Data is submitted to EurOBIS via the IPT (Integrated Publishing Toolkit). Data is quality controlled by the BioCheck tool. Data in EurOBIS can flow to EMODnet Biology, OBIS and GBIF (Global Biodiversity Information Facility). Plankton imagery instrument operators now have the possibility to format their data following the best practices and recommendations for plankton imagery data management (Martin-Cabrera et al. 2022). After a dataset is formatted following these guidelines, it can be submitted to the international biodiversity data aggregators, EurOBIS, EMODnet Biology and GBIF. Additionally a (semi) automated dataflow is presented where data providers can classify images in EcoTaxa and export the data in the required formats using an API before submission to EurOBIS. The next steps are to disseminate these best practices, encouraging plankton imagery data generators to implement these workflows to share their data easily, enriching these data portals and encouraging cross collaborations to create data products covering broader geographic scales and plankton species.

Vertical variations in physical and chemical conditions drive changes in marine zooplankton community composition. In turn, zooplankton communities play a critical role in regulating the transfer of organic matter produced in the surface ocean to deeper layers. Yet, the links between zooplankton community composition and the strength of vertical fluxes of particles remain elusive, especially on a global scale. Here, we provide a comprehensive analysis of variations in zooplankton community composition and vertical particle flux in the upper kilometer of the global ocean. Zooplankton samples were collected across five depth layers and vertical particle fluxes were assessed using continuous profiles of the Underwater Vision Profiler (UVP5) at 57 stations covering seven ocean basins. Zooplankton samples were analysed using a Zooscan and individual organisms were classified into 19 groups for the quantitative analyses. Zooplankton abundance, biomass and vertical particle flux decreased from the surface to 1000 m depth at all latitudes. The zooplankton abundance decrease rate was stronger at sites characterised by oxygen minima (<5µmol O₂.kg⁻¹) where most zooplankton groups showed a marked decline in abundance, except the jellyfishes, molluscs, annelids, large protists and a few copepod families. The attenuation rate of vertical particle fluxes was weaker at such oxygen-depleted sites. Canonical redundancy analyses showed that the epipelagic zooplankton community composition depended on the temperature, on the phytoplankton size distribution and the surface large particulate organic matter while oxygen was an additional important factor for structuring zooplankton in the mesopelagic. Our results further suggest that future changes in surface phytoplankton size and taxa composition and mesopelagic oxygen loss might lead to profound shift in zooplankton abundance and community structure in both the euphotic and mesopelagic ocean. These changes may affect the vertical export and hereby the strength of the biological carbon pump.

Abstract In the Gulf of Lions, small pelagic fish have shown reduced body size and body condition after 2007 that would result from changes in zooplankton community. We therefore examined zooplankton density, body size, and taxonomic composition at the closest long-term monitoring station (1995–2019): the coastal Point-B. To cover a broader spectrum of zooplankton community, samples obtained from two nets, the WP2 (200 µm mesh size) and the Regent (690 µm), were analysed with the imaging Zooscan method. One important result was the high stability through time of the zooplankton community. No long-term monotonous trends in density, size, and taxonomic composition were detected. Interannual variations in zooplankton size and density were not significantly correlated to any environmental variable, suggesting the possible importance of biotic interactions. Still, an increase in temperature was followed by a sharp decrease of zooplankton density in 2015, after which only gelatinous groups recovered. No change in the zooplankton community was detected around 2007 to support bottom-up control on small pelagic fish. Whether this derives from different local processes between the Gulf of Lions and the Ligurian Sea cannot be excluded, highlighting the need for simultaneous monitoring of different ecosystem compartments to fully understand the impact of climate change.

Marine particles of different nature are found throughout the global ocean. The term “marine particles” describes detritus aggregates and fecal pellets as well as bacterioplankton, phytoplankton, zooplankton and nekton. Here, we present a global particle size distribution dataset obtained with several Underwater Vision Profiler 5 (UVP5) camera systems. Overall, within the 64 µm to about 50 mm size range covered by the UVP5, detrital particles are the most abundant component of all marine particles; thus, measurements of the particle size distribution with the UVP5 can yield important information on detrital particle dynamics. During deployment, which is possible down to 6000 m depth, the UVP5 images a volume of about 1 L at a frequency of 6 to 20 Hz. Each image is segmented in real time, and size measurements of particles are automatically stored. All UVP5 units used to generate the dataset presented here were inter-calibrated using a UVP5 high-definition unit as reference. Our consistent particle size distribution dataset contains 8805 vertical profiles collected between 19 June 2008 and 23 November 2020. All major ocean basins, as well as the Mediterranean Sea and the Baltic Sea, were sampled. A total of 19 % of all profiles had a maximum sampling depth shallower than 200 dbar, 38 % sampled at least the upper 1000 dbar depth range and 11 % went down to at least 3000 dbar depth. First analysis of the particle size distribution dataset shows that particle abundance is found to be high at high latitudes and in coastal areas where surface productivity or continental inputs are elevated. The lowest values are found in the deep ocean and in the oceanic gyres. Our dataset should be valuable for more in-depth studies that focus on the analysis of regional, temporal and global patterns of particle size distribution and flux as well as for the development and adjustment of regional and global biogeochemical models. The marine particle size distribution dataset (Kiko et al., 2021) is available at https://doi.org/10.1594/PANGAEA.924375.

Marine plankton mitigate anthropogenic greenhouse gases, modulate biogeochemical cycles, and provide fishery resources. Plankton is distributed across a stratified ecosystem of sunlit surface waters and a vast, though understudied, mesopelagic ‘dark ocean’. In this study, we mapped viruses, prokaryotes, and pico-eukaryotes across 32 globally-distributed cross-depth samples collected during the Tara Oceans Expedition, and assessed their ecologies. Based on depth and O 2 measurements, we divided the marine habitat into epipelagic, oxic mesopelagic, and oxygen minimum zone (OMZ) eco-regions. We identified specific communities associated with each marine habitat, and pinpoint environmental drivers of dark ocean communities. Our results indicate that water masses primarily control mesopelagic community composition. Through co-occurrence network inference and analysis, we identified signature communities strongly associated with OMZ eco-regions. Mesopelagic communities appear to be constrained by a combination of factors compared to epipelagic communities. Thus, variations in a given abiotic factor may cause different responses in sunlit and dark ocean communities. This study expands our knowledge about the ecology of planktonic organisms inhabiting the mesopelagic zone.

Abstract Testing hypothesis about the biogeography of genes using large data resources such as Tara Oceans marine metagenomes and metatranscriptomes requires significant hardware resources and programming skills. The new release of the ‘Ocean Gene Atlas’ (OGA2) is a freely available intuitive online service to mine large and complex marine environmental genomic databases. OGA2 datasets available have been extended and now include, from the Tara Oceans portfolio: (i) eukaryotic Metagenome-Assembled-Genomes (MAGs) and Single-cell Assembled Genomes (SAGs) (10.2E+6 coding genes), (ii) version 2 of Ocean Microbial Reference Gene Catalogue (46.8E+6 non-redundant genes), (iii) 924 MetaGenomic Transcriptomes (7E+6 unigenes), (iv) 530 MAGs from an Arctic MAG catalogue (1E+6 genes) and (v) 1888 Bacterial and Archaeal Genomes (4.5E+6 genes), and an additional dataset from the Malaspina 2010 global circumnavigation: (vi) 317 Malaspina Deep Metagenome Assembled Genomes (0.9E+6 genes). Novel analyses enabled by OGA2 include phylogenetic tree inference to visualize user queries within their context of sequence homologues from both the marine environmental dataset and the RefSeq database. An Application Programming Interface (API) now allows users to query OGA2 using command-line tools, hence providing local workflow integration. Finally, gene abundance can be interactively filtered directly on map displays using any of the available environmental variables. Ocean Gene Atlas v2.0 is freely-available at: https://tara-oceans.mio.osupytheas.fr/ocean-gene-atlas/.

The abundance and size distribution of marine particles control a range of biogeochemical and ecological processes in the ocean, including carbon sequestration. These quantities are the result of complex physical-biological interactions that are difficult to observe, and their spatial and temporal patterns remain uncertain. Here, we present a novel analysis of particle size distributions (PSDs) from a global compilation of in situ Underwater Vision Profiler 5 (UVP5) optical measurements. Using a machine learning algorithm, we extrapolate sparse UVP5 observations to the global ocean from well-sampled oceanographic variables. We reconstruct global maps of PSD parameters (biovolume [BV] and slope) for particles at the base of the euphotic zone. These reconstructions reveal consistent global patterns, with high chlorophyll regions generally characterized by high particle BV and flatter PSD slope, that is, a high relative abundance of large versus small particles. The resulting negative correlations between particle BV and slope further suggests synergistic effects on size-dependent processes such as sinking particle fluxes. Our approach and estimates provide a baseline for an improved understanding of particle cycles in the ocean, and pave the way to global, three-dimensional reconstructions of PSD and sinking particle fluxes from the growing body of UVP5 observations.

Autonomous and cabled platforms are revolutionizing our understanding of ocean systems by providing 4D monitoring of the water column, thus going beyond the reach of ship-based surveys and increasing the depth of remotely sensed observations. However, very few commercially available sensors for such platforms are capable of monitoring large particulate matter (100-2000 μm) and plankton despite their important roles in the biological carbon pump and as trophic links from phytoplankton to fish. Here, we provide details of a new, commercially available scientific camera-based particle counter, specifically designed to be deployed on autonomous and cabled platforms: the Underwater Vision Profiler 6 (UVP6). Indeed, the UVP6 camera-and-lighting and processing system, while small in size and requiring low power, provides data of quality comparable to that of previous much larger UVPs deployed from ships. We detail the UVP6 camera settings, its performance when acquiring data on aquatic particles and plankton, their quality control, analysis of its recordings, and streaming from in situ acquisition to users. In addition, we explain how the UVP6 has already been integrated into platforms such as BGC-Argo floats, gliders and long-term mooring systems (autonomous platforms). Finally, we use results from actual deployments to illustrate how UVP6 data can contribute to addressing longstanding questions in marine science, and also suggest new avenues that can be explored using UVP6-equipped autonomous platforms.

Plankton imaging systems supported by automated classification and analysis have improved ecologists' ability to observe aquatic ecosystems. Today, we are on the cusp of reliably tracking plankton populations with a suite of lab-based and in situ tools, collecting imaging data at unprecedentedly fine spatial and temporal scales. But these data streams have potential well beyond examining the abundances of different taxa; the individual images themselves contain a wealth of information on functional traits. Here we outline traits that could be measured from image data, suggest computer vision approaches to extract functional trait information from the images, and discuss promising avenues for novel studies. The approaches we discuss are data agnostic and are broadly applicable to other aquatic or terrestrial organisms.

The organic carbon produced in the ocean's surface by phytoplankton is either passed through the food web or exported to the ocean interior as marine snow. The rate and efficiency of such vertical export strongly depend on the size, structure and shape of individual particles, but apart from size, other morphological properties are still not quantitatively monitored. With the growing number of in situ imaging technologies, there is now a great possibility to analyze the morphology of individual marine snow. Thus, automated methods for their classification are urgently needed. Consequently, here we present a simple, objective categorization method of marine snow into a few ecologically meaningful functional morphotypes using field data from successive phases of the Arctic phytoplankton bloom. The proposed approach is a promising tool for future studies aiming to integrate the diversity, composition and morphology of marine snow into our understanding of the biological carbon pump.

Abstract Ocean plankton comprise organisms from viruses to fish larvae that are fundamental to ecosystem functioning and the provision of marine services such as fisheries and CO 2 sequestration. The latter services are partly governed by variations in plankton community composition and the expression of traits such as body size at community-level. While community assembly has been thoroughly studied for the smaller end of the plankton size spectrum, the larger end comprises ectotherms that are often studied at the species, or group-level, rather than as communities. The body size of marine ectotherms decreases with temperature, but controls on community-level traits remain elusive, hindering the predictability of marine services provision. Here, we leverage Tara Oceans datasets to determine how zooplankton community composition and size structure varies with latitude, temperature and productivity-related covariates in the global surface ocean. Zooplankton abundance and median size decreased towards warmer and less productive environments, as a result of changes in copepod composition. However, some clades displayed the opposite relationships, which may be ascribed to alternative feeding strategies. Given that climate models predict increasingly warmed and stratified oceans, our findings suggest that zooplankton communities will shift towards smaller organisms which might weaken their contribution to the biological carbon pump.

As phytoplankton is essential in supporting food webs and mediating biogeochemical cycles, it became crucial to complement discrete sampling and laboratory methods to address this compartment at its finest temporal and spatial scale. Within the “Joint European Research Infrastructure for Coastal Observatories – Novel EXperTise” (JERICO-NEXT), scientists proceeded to the exploration of novel phytoplankton automated in vivo/in situ techniques, based on single cell/particle or bulk optical characteristics. These techniques were implemented in a variety of monitoring platforms (fixed stations, moorings, research vessels, ships of opportunity), from oligotrophic (West Mediterranean) to mesotrophic and eutrophic marine coastal waters (English Channel, North Sea and Baltic Sea). These approaches could represent warning systems in water quality through phytoplankton total abundance and biomass, composition changes and the occurrence of blooms, including harmful algal blooms HAB, of special interest in areas of fishing, aquaculture and tourism. At the dawn of the UN Decade of the Ocean, the JERICO-S3 (Science, Services, Sustainability) project tends to generalise these approaches and seeks to standardise as much as possible their operability and capacity in addressing phytoplankton diversity and productivity, moving towards a new approach of Essential Ocean Variables (EOVs). Moreover, the development of automated tools for data analysis, using machine-learning and deep learning and will allow integrating these data into European marine data infrastructures available for research and marine management.

Aquatic ecologists face challenges in identifying the general rules of the functioning of ecosystems. A common framework, including freshwater, marine, benthic, and pelagic ecologists is needed to bridge communication gaps and foster knowledge sharing. This framework should transcend local specificities and taxonomy in order to provide a common ground and shareable tools to address common scientific challenges. Here, we advocate the use of functional trait-based approaches (FTBAs) for aquatic ecologists, and propose concrete paths to go forward. Firstly, we propose to unify existing definitions in FTBAs to adopt a common language. Secondly, we list the numerous databases referencing functional traits for aquatic organisms. Thirdly, we present a synthesis on traditional as well as recent promising methods for the study of aquatic functional traits, including imaging and genomics. Finally, we conclude with a highlight on scientific challenges and promising venues for which FTBAs should foster opportunities for future research. By offering practical tools, our framework provides a clear path forward to the adoption of trait-based approaches in aquatic ecology.

Plankton imaging instruments generate an ever increasing volume of data which is mostly processed through machine learning algorithms. However, classifying plankton images is a challenging computer science task in its own right: datasets are strongly unbalanced; the dominant classes are often not biologically interesting (artefacts, bubbles) and/or very heterogeneous looking (marine snow); and images span a large size range. Despite a wealth of reports on the performance of automatic plankton images classifiers, we still do not have a definitive idea regarding how methods compare with each other and where they can systematically be trusted. This is mostly because those reports rely on rather small unpublished datasets, not necessarily representative of real-life biological samples in terms of size, number of categories and proportions. Here we report the performance of a classic classification method (Random Forest on handcrafted image features) and a more recent one (a Convoluted Neural Network) on large publicly released datasets, from five widely used plankton imaging instruments. We show that CNN improve classification performance but only noticeably on poorly represented (a few hundred images) classes. Finally, we showcase the difference between the predictions of the two classifiers and a human-checked truth on several real-world datasets, to give insights regarding which ecological questions can or cannot be studied from computer-generated classifications only.

Biological diversity encompasses all the variations of life, from genes to ecosystems, and is typically described from a taxonomic, genetic, phylogenetic, or functional point of view. Here we describe the changes in morphological diversity of zooplankton along a coastal time series. Morphology is of course characteristic of taxa but also has functional consequences; size, for example, is often considered as a dominant functional trait for zooplankton. Using high-throughput imaging of weekly plankton samples, collected from 2009 to 2017 in the Mediterranean Sea, we automatically measured ~40 morphological traits on ~542,000 individuals. A reduced morphological space was defined through Principal Component Analysis and individuals were regrouped in 200 "morphs" through clustering in that space. In this morphological space, time series of indices of morphological richness, divergence, and evenness were computed using the same metrics as the ones usually defined for functional diversity. Size, circularity, and opacity were the characteristics of the organisms that varied the most along the series. The morphs were homogeneous in appearance and recognisable, but often comprised more than one taxon. All morphological diversity indices were lower in the spring. This seemed related to the dominance of copepods during this season, which are quite homogeneous in appearance. But this could also be caused by selective disadvantages of extreme (and specialised) morphological types in this relatively eutrophic time of the year. Over the nine years, morphological divergence increased significantly while overall plankton concentrations decreased; since 2001, surface waters became significantly warmer and more oligotrophic. Overall, this fits the theory that oligotrophy leads to niche specialisation which, here, translates into morphological divergence.

An important decrease in small pelagic fish condition and size has been observed in the most productive ecosystem of the Mediterranean Sea, the Gulf of Lions, since 2008, leading to an important fishery crisis. Previous studies suggested bottom-up control to be the most probable cause for these changes. Here, we investigate whether an environmental change might have caused such a situation. In the absence of zooplankton time series, this study aims at describing temporal changes in key abiotic factors for the planktonic and fish production of the Gulf of Lions, such as SST, meso-scale fronts, wind-induced coastal upwelling, river discharge, water stratification and deep convection and then at understanding potential link on Chl-a concentration as well as small pelagic fish populations. Our results indicate that the environmental conditions have broadly changed in the Gulf of Lion, with a major change in the mid-2000s, affecting the Chla concentration (which showed a regime shift in 2007), but also the SST, the upwelling and frontal activities, the Rhone river discharge (and particularly the N and P nutrients inputs) as well as the deep winter convection. Those changes could have affected the plankton production and consequently the small pelagic fish community that displayed similar patterns of variations as the environmental conditions.

In recent years, autonomous platforms have been improved with the objective of observing the deep ocean. Many prototypes have reached 6,000 m, but only a few are commercially available. Imaging sensors have been developed to study the numbers, sizes and shapes of particles and plankton. These have been deployed independently or mounted on CTD rosettes (e.g. the UVP5 Underwater Vision Profiler). In some areas, they observed high concentrations of large particles down to the bottom of the ocean, showing intense carbon export. They also documented the presence of fragile organisms, such as rhizarians, whose key ecological roles in the ocean was unknown until then. The new miniaturized UVP6-LP (Low Power) sensor, developed to be mounted on autonomous platforms, is complementary to the larger sensors deployed on CTD rosettes. It also records and identifies particles and plankton, using imagery. It counts and sizes particles \textgreater80 µM ESD and identifies large aggregates and plankton \textgreater700µM ESD. This, at low cost and with very low power. Six prototypes of the sensor have been inter-calibrated with the reference UVP5. The instrument can be deployed down to 6,000 m, which corresponds to 97% of the ocean surface. A UVP6-LP was used to quantify particles released from a deep-sea mining experiment at 4,300 m. Others performed transects on gliders and vertical profiles on a float. A UVP6-LP was moored for one year at 50 m at 82°N. Other UVP6-LP will be deployed on the a cabled observatory in the Mediterranean Sea at 2,200 m, and on the SeaCycler mooring in the Labrador Sea. The very low power required for the operation of the UVP6-LP allows to optimize its use on profiling floats and gliders. Autonomous platforms cannot transmit images due to the limitation of satellite bandwidth or acoustic telemetry. To overcome this limitation, the UVP6-LP includes an embedded algorithm for the automatic classification of large aggregates and plankton images, which provides data that are accurate enough for monitoring programs and scientific studies. Because scientists, policy makers and the public require easy access to data, a complete software ecosystem is used to pilot the instrument, record the data, and make them freely available to the scientists and the public. When the instruments are recovered after deployment, their data include classified images.

“Imagery data” can be referred as qualitative and quantitative information from a collection of images. Imaging systems are used more and more frequently in the marine domain to generate huge amounts of imagery data. For example, automatic image classification is used to determine the abundance, size and biomass of plankton communities. In addition, the recent advances of imaging sensors and the growing datasets, highlight the importance of the management and storage capacity of these data. Thus, establishing data standards, optimized data flows and quality control procedures will promote the ability to make these datasets findable, accessible, interoperable and reusable (FAIR principles).At the moment, there are a number of online open-access databases that collect marine biodiversity data, such as the Ocean Biodiversity Information System (OBIS), and more specialized in plankton observations such as the COPEPOD for plankton biomass and ECOTAXA for taxonomic annotation of plankton images. However, they currently lack relevant standards to link metadata of the images.International biodiversity data standards, such as Darwin Core (DwC), are already widely used in OBIS and the Global Biodiversity Information Facility (GBIF). OBIS, has recently adopted the OBIS-ENV-DATA, a format that follows the DwC-Archive (DwC-A) standard, consisting of a DwC Event table in combination with an Occurrence an extended Measurement or Fact table. This structure enables the linkage of quantitative and qualitative properties to both sampling events and species occurrences. It also includes additional fields for property standardization, such as the BODC (British Oceanographic Data Centre) controlled vocabularies, the World Register of Marine Species (WoRMS), which provides crucial quality control support for taxonomic data, and Marine Regions, a database that provides standardized marine georeferenced place names and areas. However, there are no clear guidelines on how to include imagery metadata and derived data in OBIS-ENV-DATA.During this TDWG 2020 symposium, we would like to present and discuss our ongoing work to establish best practices and standardized protocols for imaging data and metadata acquired by a large spectrum of bio-optic sensors. Furthermore, we highlight how the integration of the metadata will flow to existing biodiversity data portals, the European EMODnet Biology portal, (EurOBIS) and OBIS.

The pulse of organic matter and the subsequent transfer of carbon out of the photic zone to the deep ocean is limited to a very short time period in the Arctic, especially in areas temporarily covered by sea ice. The quantity and quality of matter produced in the form of marine snow results from many processes related to the dynamics and relationships among ice, phytoplankton and zooplankton. Those are extremely difficult to assess due to technical limitations of their collection and in situ observations. Using the Underwater Vision Profiler (UVP), we were able to observe the spatio-temporal dynamics (190 stations) of marine snow formation, transformation and downward transport in two crucial deep water Arctic basins (Baffin Bay and Fram Strait). Each marine snow particle in the water column was photographed and described by 24 morphological traits, referring to its size, shape, transparency and structure. Those descriptors were used to cluster marine snow into a few morphological groups, such as filaments, faecal pellets, Phaeocystis flocs, and various forms of aggregates. The spatio-temporal mapping of those morphological groups enabled to clearly follow the succession of different forms of marine snow particles and their probable export to the deep sea. Under sea ice marine snow was dominated by dark and elongated forms, while with progressing bloom and the switch from diatoms to Phaeocystis, the importance of lighter and more heterogeneous forms increased, which in turn were mostly avoided by zooplankton. The size range of marine snow was wider in the upper 250 m than in deeper layers, where the increase in its circularity was observed. We believe that the approach of analysing the morphological traits of marine snow will broaden our understanding of not only particle vertical fluxes, but also of the role of phytoplankton and zooplankton activity for marine snow formation and transformation.

Current climate change is significantly modifying Arctic ecosystems and their components, but the reference and direction of these changes are still undefined. The aim of this study was to provide well-grounded data on the present composition and structure of zooplankton from boreal to Arctic latitudes. This comparative study was performed with a unified methodology in six fjords located along the west coasts of Norway and Svalbard. Comparisons between the fjords' environmental characteristics (temperature, salinity, chlorophyll, and particles) and the zooplankton community, described with several metrics (abundance and biovolume) and traits (taxonomy and size), were performed to recognise the potential of various ecological indicators for future monitoring. While hydrography and the taxonomic composition of zooplankton were specific to each fjord and changed along the latitudinal environmental gradient, the clustering of particle characteristics (size, concentration, and transparency) and zooplankton size structures alludes to their susceptibility to additional, local processes. The differences in the biotic and abiotic characteristics distinguished the semi-closed fjords from the fjords prone to Atlantic water advection. The fjords with a limited water mass exchange incorporated local or Arctic-type waters and were host to specific zooplankton communities and particles, with the marked presence of species adapted to high particle concentrations (Microsetella norvegica) or species of Arctic affiliation (Calanus glacialis). In the open fjords, zooplankton communities were characterised by the predomination of Oithona similis and Calanus finmarchicus, confirming influence of Atlantic water. The zooplankton community size structure, expressed as abundance, was mainly shaped by changes in the contributions of small copepods, whereas the size structure expressed as biovolume reflected the differences in the co-occurring sibling species of Calanus spp. and/or differences in their dominating life stages. The results of this integrative across-system study constitute a necessary baseline for the future monitoring of changes in the zooplankton communities, which are likely to occur in response to climate change at high latitudes.

In spite of the paramount ecological and socioeconomic relevance of tropical reef ecosystems, the dynamics of their meroplankton abundance remain poorly characterized. The small-scale distribution and detailed analysis of individual biomass of mesozooplankton were studied in the coastal reefs of Tamandaré (Brazil). Mesozooplankton (> 300 μm) was collected during nocturnal ebb tides at new moon, using three different devices to sample at three different environments: a standard ring net that was towed at subsurface, the Channel Midwater Neuston Net that collected at midwater in channels between patch reefs and the Reef Edge Net that captured organisms that are washed by ebb currents from reef tops toward the reef edge. Samples were analyzed using a ZooScan to obtain abundances and biovolume of each taxonomic group. Specific biomass measurements were taken to obtain allometric equations used to calculate zooplankton biomass from biovolume. The mesozooplankton were significantly more abundant at subsurface and at the reef edge compared to channel environments. The high abundance of organisms at reef edges suggests a low predation pressure on zooplankton at near-bottom areas, since the reefs of Tamandaré present a low coverage of planktivorous corals, being dominated by macroalgae. These results show that rather than sinks these ecosystems may be considered important sources of zooplankton available for planktivorous species. Regarding zooplankton composition, we found large amounts of initial stages of meroplanktonic larvae and newly hatched fish eggs, which presented consistently greater abundances compared to holoplankton and emergent benthic taxa. Decapod larvae were the most abundant group of the meroplankton, but cirripedian nauplii, stomatopod larvae, fish larvae and fish eggs were also abundant. More than 50% of the total biomass was due to meroplankton taxa, mainly composed of decapod larvae. This study indicates that the contribution of meroplankton to mesozooplankton composition and biomass off tropical reefs may have been underestimated.

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 ocean is home to myriad small planktonic organisms that underpin the functioning of marine ecosystems. However, their spatial patterns of diversity and the underlying drivers remain poorly known, precluding projections of their responses to global changes. Here we investigate the latitudinal gradients and global predictors of plankton diversity across archaea, bacteria, eukaryotes, and major virus clades using both molecular and imaging data from Tara Oceans. We show a decline of diversity for most planktonic groups toward the poles, mainly driven by decreasing ocean temperatures. Projections into the future suggest that severe warming of the surface ocean by the end of the 21st century could lead to tropicalization of the diversity of most planktonic groups in temperate and polar regions. These changes may have multiple consequences for marine ecosystem functioning and services and are expected to be particularly significant in key areas for carbon sequestration, fisheries, and marine conservation. VIDEO ABSTRACT.

Marine Protected Areas have become a major tool for the conservation of marine biodiversity and resources. Yet our understanding of their efficacy is often limited because it is measured for a few biological components, typically top predators or species of commercial interest. To achieve conservation targets, marine protected areas can benefit from ecosystem-based approaches. Within such an approach, documenting the variation of plankton indicators and their covariation with climate is crucial as plankton represent the base of the food webs. With this perspective, we sought to document the variations in the emerging properties of the plankton to better understand the dynamics of the pelagic fishes, mammals and seabirds that inhabit the region. For the first time, we analyze the temporal variations of the entire plankton community of one of the widest European protected areas, the Parc Naturel Marin de la Mer d’Iroise. We used data from several sampling transects carried out in the Iroise Sea from 2011 to 2015 to explore the seasonal and inter-annual variations of phytoplankton and mesozooplankton abundance, composition and size, as well as their covariation with abiotic variables, through multiple multivariate analyses. Overall, our observations are coherent with the plankton dynamics that have been observed in other regions of the North-East Atlantic. We found that both phytoplankton and zooplankton show consistent seasonal patterns in taxonomic composition and size structure but also display inter-annual variations. The spring bloom was associated with a higher contribution of large chain-forming diatoms compared to nanoflagellates, the latter dominating in fall and summer. Dinoflagellates show marked inter-annual variations in their relative contribution. The community composition of phytoplankton has a large impact on the mesozooplankton together with the distance to the coast. The size structure of the mesozooplankton community, examined through the ratio of small to large copepods, also displays marked seasonal patterns. We found that larger copepods (members of the Calanidae) are more abundant in spring than in summer and fall. We propose several hypotheses to explain the observed temporal patterns and we underline their importance for understanding the dynamics of other components of the food-web (such as sardines). Our study is a first step toward the inclusion of the planktonic compartment into the planning of the resources and diversity conservation within the Marine Protected Area.

Plankton plays a key role in the biological pump and has a big impact on marine living resources. However, plankton is difficult to observe in a consistent manner across its extended size range and by the multiple observers that uses protocols that are not inter calibrated. Imaging sensors have the potential to provide key ``ecosystem essential ocean variables'' eEOVs (plankton biodiversity, morphological traits) that complement other sensors such as optical ones. Lab and in-situ imaging sensors have been deployed the 10 last years to provide insights into local dynamics in the frame of time series programs (from daily to decadal scales) and during oceanographic surveys across ocean basins. Combining observations from the different programmes has sometimes allowed to detect concomitant changes in different areas or provide a better spatial distribution of plankton communities. For example, such efforts were supported by the European FP7 JERICO, H2020 JERICO-NEXT, BRIDGES, EURO-BASIN programs. Most of the observation efforts were performed independently and hundreds of millions of images have been collected (and billions to come as sensors are getting more available). All those sparsely distributed images are usually not available for the users because of limited development in software solutions for identification, archiving and distribution, which are in a current improving process. Several attempts for developing web based services for image recognition, distribution and archiving have been performed (ecotaxa.obs-vlfr.fr) but only a fraction of the existing and future data can be treated by them. Based on the past ten years of effort, we will present a synthesis of successful developments in using imaging systems to provide information on plankton community at local, regional and ultimately global scales. These examples will show how relevant they are for ecosystem monitoring (e.g. detection of ecosystem changes and regime-shifts) and services (e.g. aquaculture, fisheries, biological carbon pump). We will then build on these examples to discuss future developments with the aim of, better observing, harmonizing practices and developing state of the art marine data and information management in order to increase the connection with the relevant stakeholders and community of users among researchers, conservation managers and private companies.

Impermanence is an ecological principle1 but there are times when changes occur nonlinearly as abrupt community shifts (ACSs) that transform the ecosystem state and the goods and services it provides2. Here, we present a model based on niche theory3 to explain and predict ACSs at the global scale. We test our model using 14 multi-decadal time series of marine metazoans from zooplankton to fish, spanning all latitudes and the shelf to the open ocean. Predicted and observed fluctuations correspond, with both identifying ACSs at the end of the 1980s4,5,6,7 and 1990s5,8. We show that these ACSs coincide with changes in climate that alter local thermal regimes, which in turn interact with the thermal niche of species to trigger long-term and sometimes abrupt shifts at the community level. A large-scale ACS is predicted after 2014—unprecedented in magnitude and extent—coinciding with a strong El Niño event and major shifts in Northern Hemisphere climate. Our results underline the sensitivity of the Arctic Ocean, where unprecedented melting may reorganize biological communities5,9, and suggest an increase in the size and consequences of ACS events in a warming world.

Gelatinous zooplankton hold key functions in the ocean and have been shown to significantly influence the transport of organic carbon to the deep sea. We discovered a gelatinous, flux-feeding polychaete of the genus Poeobius in very high abundances in a mesoscale eddy in the tropical Atlantic Ocean, where it co-occurred with extremely low particle concentrations. Subsequent analysis of an extensive in situ imaging dataset revealed that Poeobius sp. occurred sporadically between 58S-208N and 168W-468W in the upper 1000 m. Abundances were significantly elevated and the depth distribution compressed in anticyclonic modewater eddies (ACMEs). In two ACMEs, high Poeobius sp. abundances were associated with strongly reduced particle concentrations and fluxes in the layers directly below the polychaete. We discuss possible reasons for the elevated abundances of Poeobius sp. in ACMEs and provide estimations showing that a single zooplankton species can completely intercept the downward particle flux by feeding with their mucous nets, thereby substantially altering the biogeochemical setting within the eddy.

Plankton was sampled with various nets, from bottom or 500m depth to the surface, in many oceans of the world. Samples were imaged with a ZooScan. The full images were processed with ZooProcess which generated regions of interest (ROIs) around each individual object and a set of associated features measured on the object (see Gorsky et al 2010 for more information). The same objects were re-processed to compute features with the scikit-image toolbox (http://scikit-image.org). The 1,433,278 resulting objects were sorted by a limited number of operators, following a common taxonomic guide, into 93 taxa, using the web application EcoTaxa (http://ecotaxa.obs-vlfr.fr). The archive contains: taxa.csv.gz Table of the classification of each object in the dataset, with columns - objid: unique object identifier in EcoTaxa (integer number). - taxon: taxonomic name. Ambiguous names are made unique by including the name of the parent taxon in parentheses, after the name of the taxon. - lineage: full taxonomic lineage corresponding to this taxon. features_native.csv.gz Table of morphological features computed by ZooProcess. All features are computed on the object only, not the background. All area/length measures are in pixels. All grey levels are in encoded in 8 bits (0=black, 255=white). With columns - objid: same as above - area: area - mean: mean grey - stddev: standard deviation of greys - mode: modal grey - min: minimum grey - max: maximum grey - perim.: perimeter - width,height dimensions - major,minor: length of major,minor axis of the best fitting ellipse - circ.: circularity: 4pi(area/perim.^2) - feret: maximal feret diameter - intden: integrated density: mean*area - median: median grey - skew,kurt: skewness,kurtosis of the histogram of greys - %area: proportion of the image corresponding to the object - area_exc: area excluding holes - fractal: fractal dimension of the perimeter - skelarea: area of the one-pixel wide skeleton of the image - slope: slope of the cumulated histogram of greys - histcum1,2,3: grey level at quantiles 0.25, 0.5, 0.75 of the histogram of greys - nb1,2,3: number of objects after thresholding at the grey levels above - symetrieh,symetriev: index of horizontal,vertical symmetry - symetriehc,symetrievc: same but after thresholding at level histcum1 - convperim,convarea: perimeter,area of the convex hull of the object - fcons: contrast - thickr: thickness ratio: maximum thickness/mean thickness - elongation: elongation index: major/minor - range: range of greys: max-min - meanpos: relative position of the mean grey: (max-mean)/range - cv: coefficient of variation of greys: 100*(stddev/mean) - sr: index of variation of greys: 100*(stddev/range) - perimferet: index of the relative complexity of the perimeter: perim/feret - perimmajor: index of the relative complexity of the perimeter: perim/major features_skimage.csv.gz Table of morphological features recomputed with skimage.measure.regionprops on the ROIs produced by ZooProcess. See http://scikit-image.org/docs/dev/api/skimage.measure.html#skimage.measure.regionprops for documentation. inventory.txt Tree view of the taxonomy and number of images in each taxon, displayed as text. map.png Map of the sampling locations, to give an idea of the diversity sampled in this dataset. imgs Directory containing images of each object, named according to the object id objid and sorted in subdirectories according to their taxon.

Single-celled eukaryotes (protists) are critical players in global biogeochemical cycling of nutrients and energy in the oceans. While their roles as primary producers and grazers are well appreciated, other aspects of their life histories remain obscure due to challenges in culturing and sequencing their natural diversity. Here, we exploit single-cell genomics and metagenomics data from the circumglobal $Tara$ Oceans expedition to analyze the genome content and apparent oceanic distribution of seven prevalent lineages of uncultured heterotrophic stramenopiles. Based on the available data, each sequenced genome or genotype appears to have a specific oceanic distribution, principally correlated with water temperature and depth. The genome content provides hypotheses for specialization in terms of cell motility, food spectra, and trophic stages, including the potential impact on their lifestyles of horizontal gene transfer from prokaryotes. Our results support the idea that prominent heterotrophic marine protists perform diverse functions in ocean ecology.

A unique collection of oceanic samples was gathered by the Tara Oceans expeditions (2009–2013), targeting plankton organisms ranging from viruses to metazoans, and providing rich environmental context measurements. Thanks to recent advances in the field of genomics, extensive sequencing has been performed for a deep genomic analysis of this huge collection of samples. A strategy based on different approaches, such as metabarcoding, metagenomics, single-cell genomics and metatranscriptomics, has been chosen for analysis of size-fractionated plankton communities. Here, we provide detailed procedures applied for genomic data generation, from nucleic acids extraction to sequence production, and we describe registries of genomics datasets available at the European Nucleotide Archive (ENA, www.ebi.ac.uk/ena). The association of these metadata to the experimental procedures applied for their generation will help the scientific community to access these data and facilitate their analysis. This paper complements other efforts to provide a full description of experiments and open science resources generated from the Tara Oceans project, further extending their value for the study of the world’s planktonic ecosystems.

In the epipelagic ocean, the genus Oithona is considered as one of the most abundant and widespread copepods and plays an important role in the trophic food web. Despite its ecological importance, little is known about Oithona and cyclopoid copepods genomics. Therefore, we sequenced, assembled and annotated the genome of Oithona nana. The comparative genomic analysis integrating available copepod genomes highlighted the expansions of genes related to stress response, cell differentiation and development, including genes coding Lin12‐Notch‐repeat (LNR) domain proteins. The Oithona biogeography based on 28S sequences and metagenomic reads from the Tara Oceans expedition showed the presence of O. nana mostly in the Mediterranean Sea (MS) and confirmed the amphitropical distribution of Oithona similis. The population genomics analyses of O. nana in the Northern MS, integrating the Tara Oceans metagenomic data and the O. nana genome, led to the identification of genetic structure between populations from the MS basins. Furthermore, 20 loci were found to be under positive selection including four missense and eight synonymous variants, harbouring soft or hard selective sweep patterns. One of the missense variants was localized in the LNR domain of the coding region of a male‐specific gene. The variation in the B‐allele frequency with respect to the MS circulation pattern showed the presence of genomic clines between O. nana and another undefined Oithona species possibly imported through Atlantic waters. This study provides new approaches and results in zooplankton population genomics through the integration of metagenomic and oceanographic data.

Marine Bacteroidetes constitute a very abundant bacterioplankton group in the oceans that plays a key role in recycling particulate organic matter and includes several photoheterotrophic members containing proteorhodopsin. Relatively few marine Bacteroidetes species have been described and, moreover, they correspond to cultured isolates, which in most cases do not represent the actual abundant or ecologically relevant microorganisms in the natural environment. In this study, we explored the microdiversity of 98 Single Amplified Genomes (SAGs) retrieved from the surface waters of the underexplored North Indian Ocean, whose most closely related isolate is Kordia algicida OT-1. Using Multi Locus Sequencing Analysis (MLSA) we found no microdiversity in the tested conserved phylogenetic markers (16S rRNA and 23S rRNA genes), the fast-evolving Internal Transcribed Spacer and the functional markers proteorhodopsin and the beta-subunit of RNA polymerase. Furthermore, we carried out a Fragment Recruitment Analysis (FRA) with marine metagenomes to learn about the distribution and dynamics of this microorganism in different locations, depths and size fractions. This analysis indicated that this taxon belongs to the rare biosphere, showing its highest abundance after upwelling-induced phytoplankton blooms and sinking to the deep ocean with large organic matter particles. This uncultured Kordia lineage likely represents a novel Kordia species (Kordia sp. CFSAG39SUR) that contains the proteorhodopsin gene and has a widespread spatial and vertical distribution. The combination of SAGs and MLSA makes a valuable approach to infer putative ecological roles of uncultured abundant microorganisms.

High primary productivity in the equatorial Atlantic and Pacific oceans is one of the key features of tropical ocean biogeochemistry and fuels a substantial flux of particulate matter towards the abyssal ocean. How biological processes and equatorial current dynamics shape the particle size distribution and flux, however, is poorly understood. Here we use high-resolution size-resolved particle imaging and Acoustic Doppler Current Profiler data to assess these influences in equatorial oceans. We find an increase in particle abundance and flux at depths of 300 to 600 m at the Atlantic and Pacific equator, a depth range to which zooplankton and nekton migrate vertically in a daily cycle. We attribute this particle maximum to faecal pellet production by these organisms. At depths of 1,000 to 4,000 m, we find that the particulate organic carbon flux is up to three times greater in the equatorial belt (1 degrees S-1 degrees N) than in off-equatorial regions. At 3,000 m, the flux is dominated by small particles less than 0.53 mm in diameter. The dominance of small particles seems to be caused by enhanced active and passive particle export in this region, as well as by the focusing of particles by deep eastward jets found at 2 degrees N and 2 degrees S. We thus suggest that zooplankton movements and ocean currents modulate the transfer of particulate carbon from the surface to the deep ocean.

Collodaria are heterotrophic marine protists that exist either as large colonies composed of hundreds of cells or as large solitary cells. All described species so far harbour intracellular microalgae as photosymbionts. Although recent environmental diversity surveys based on molecular methods demonstrated their consistently high contribution to planktonic communities and their worldwide occurrence, our understanding of their diversity and biogeography is still very limited. Here we estimated the 18S ribosomal DNA (rDNA) gene copies per collodarian cell for solitary (5770 +/- 1960 small subunit (SSU) rDNA copies) and colonial specimens (37 474 +/- 17 799 SSU rDNA copies, for each individual cell within a colony) using single-specimen quantitative PCR. We then investigated the environmental diversity of Collodaria within the photic zone through the metabarcoding survey from the Tara Oceans expedition and found that the two collodarian families Collosphaeridae and Sphaerozoidae contributed the most to the collodarian diversity and encompassed mostly cosmopolitan taxa. Although the biogeographical patterns were homogeneous within each biogeochemical biome considered, we observed that coastal biomes were consistently less diverse than oceanic biomes and were dominated by the Sphaerozoidae while the Collosphaeridae were dominant in the open oceans. The significant relationships with six environmental variables suggest that collodarian diversity is influenced by the trophic status of oceanic provinces and increased towards more oligotrophic regions.

The biological carbon pump is the process by which CO2 is transformed to organic carbon via photosynthesis, exported through sinking particles, and finally sequestered in the deep ocean. While the intensity of the pump correlates with plankton community composition, the underlying ecosystem structure driving the process remains largely uncharacterized. Here we use environmental and metagenomic data gathered during the Tara Oceans expedition to improve our understanding of carbon export in the oligotrophic ocean. We show that specific plankton communities, from the surface and deep chlorophyll maximum, correlate with carbon export at 150 m and highlight unexpected taxa such as Radiolaria and alveolate parasites, as well as Synechococcus and their phages, as lineages most strongly associated with carbon export in the subtropical, nutrient-depleted, oligotrophic ocean. Additionally, we show that the relative abundance of a few bacterial and viral genes can predict a significant fraction of the variability in carbon export in these regions.

Mesoscale eddies in the ocean strongly impact the distribution of planktonic particles, mediating carbon fluxes over similar to 1/3 of the world ocean. However, mechanisms controlling particle transport through eddies are complex and challenging to measure in situ. Here we show the subsurface distribution of eddy particles funneled into a wineglass shape down to 1000 m, leading to a sevenfold increase of vertical carbon flux in the eddy center versus the eddy flanks, the ``wineglass effect''. We show that the slope of the wineglass (R) is the ratio of particle sinking velocity to the radially inward velocity, such that R represents a tool to predict radial particle movement (here 0.05 m s(-1)). A simple model of eddy spindown predicts such an ageostrophic flow concentrating particles in the eddy center. We explore how size-specific particle flux toward the eddy center impacts eddies' biogeochemistry and export fluxes.

The present work aims to show that high throughput imaging systems can be useful to estimate mesozooplankton community size and taxonomic descriptors that can be the base for consistent large scale monitoring of plankton communities. Such monitoring is required by the European Marine Strategy Framework Directive (MSFD) in order to ensure the Good Environmental Status (GES) of European coastal and offshore marine ecosystems. Time and cost-effective, automatic, techniques are of high interest in this context. An imaging-based protocol has been applied to a high frequency time series (every second day between April 2003 to April 2004 on average) of zooplankton obtained in a coastal site of the NW Mediterranean Sea, Villefranche Bay. One hundred eighty four mesozooplankton net collected samples were analysed with a Zooscan and an associated semi-automatic classification technique. The constitution of a learning set designed to maximize copepod identification with more than 10,000 objects enabled the automatic sorting of copepods with an accuracy of 91% (true positives) and a contamination of 14% (false positives). Twenty seven samples were then chosen from the total copepod time series for detailed visual sorting of copepods after automatic identification. This method enabled the description of the dynamics of two well-known copepod species, Centropages typicus and Temora stylifera, and 7 other taxonomically broader copepod groups, in terms of size, biovolume and abundance–size distributions (size spectra). Also, total copepod size spectra underwent significant changes during the sampling period. These changes could be partially related to changes in the copepod assemblage taxonomic composition and size distributions. This study shows that the use of high throughput imaging systems is of great interest to extract relevant coarse (i.e. total abundance, size structure) and detailed (i.e. selected species dynamics) descriptors of zooplankton dynamics. Innovative zooplankton analyses are therefore proposed and open the way for further development of zooplankton community indicators of changes

In this study, we investigated, for the first time, the potential impact of environmental changes on zooplankton abundance over a fourteen year period (2000–2013) at an offshore station in the Eastern Mediterranean Sea (the Levantine basin, offshore Lebanon). Samples were collected monthly and analyzed using the semi-automated system ZooScan. Salinity, temperature and phytoplankton abundance (nano and microphytoplankton) were also measured. Results show no significant temporal trend in sea surface temperature over the years. Between 2005–2010, salinity in the upper layer (0–80 m) of the Levantine basin increased (~0.3°C). During this 5 year period, total zooplankton abundance significantly increased. These modifications were concomitant to the activation of Aegean Sea as a source of dense water formation as part of the " Eastern Mediterranean Transient-like " event. The results of the present study suggested that zooplankton benefited from enhanced phytoplankton production during the mixing years of the event. Changes in the phenology of some taxa were observed accordingly with a predominantly advanced peak of zooplankton abundance. In conclusion, long-term changes in zooplankton abundance were related to the Levantine thermohaline circulation rather than sea surface warming. Sampling must be maintained to assess the impact of long-term climate change on zooplankton communities.

Zooplankton present characteristics of high interest in the frame of investigation for organisms sensitive to environmental changes and/or anthropogenic pressures. Such indicators are particularly needed in the present context of European legislation (Marine Strategy Framework Directive). However, zooplankton have not been given the interest they should have in regards to these issues. The aim of the present study is to provide an attempt of proposition of indicators of good environmental status and associated thresholds based on zooplankton data. Zooplankton time-series (2002–2013) from the Toulon Bay in the Mediterranean was used. This time-series presents the great characteristics that the sampling has be done jointly in two areas of the Bay of Toulon known to differ in term of anthropogenic pressures. The study focus on the copepod assemblage and different potential indicators are tested: ratio of copepod families on total copepod and diversity index (Piélou's evenness). The indicators relevance was evaluated per season by looking at the importance of the overlapping region between density's distributions for each indicator in both bays. This methodology well-recognized is commonly used, particularly in the medical sector, for a long time. The results show that the Oithonidae relative abundance and the Piélou's evenness index are the best indicators of anthropogenic pollution for this case study. Thresholds related to the selected indicators are also proposed in order to characterize the degree of anthropogenic pressure for the Toulon Bay and to provide a first evaluation for potential environmental management. Applicability of the selected indicators and future development needed are also discussed. This study is a first step in the investigation for operational zooplankton indicators and should open the way for additional studies in coastal anthropized area such as the Mediterranean coast where it is more urgently needed. &

Planktonic organisms play crucial roles in oceanic food webs and global biogeochemical cycles1, 2. Most of our knowledge about the ecological impact of large zooplankton stems from research on abundant and robust crustaceans, and in particular copepods3, 4. A number of the other organisms that comprise planktonic communities are fragile, and therefore hard to sample and quantify, meaning that their abundances and effects on oceanic ecosystems are poorly understood. Here, using data from a worldwide in situ imaging survey of plankton larger than 600 μm, we show that a substantial part of the biomass of this size fraction consists of giant protists belonging to the Rhizaria, a super-group of mostly fragile unicellular marine organisms that includes the taxa Phaeodaria and Radiolaria (for example, orders Collodaria and Acantharia). Globally, we estimate that rhizarians in the top 200 m of world oceans represent a standing stock of 0.089 Pg carbon, equivalent to 5.2% of the total oceanic biota carbon reservoir5. In the vast oligotrophic intertropical open oceans, rhizarian biomass is estimated to be equivalent to that of all other mesozooplankton (plankton in the size range 0.2–20 mm). The photosymbiotic association of many rhizarians with microalgae may be an important factor in explaining their distribution. The previously overlooked importance of these giant protists across the widest ecosystem on the planet6 changes our understanding of marine planktonic ecosystems.

Ecological succession provides a widely accepted description of seasonal changes in phy-toplankton and mesozooplankton assemblages in the natural environment, but concurrent changes in smaller (i.e. microbes) and larger (i.e. macroplankton) organisms are not included in the model because plankton ranging from bacteria to jellies are seldom sampled and analyzed simultaneously. Here we studied, for the first time in the aquatic literature, the succession of marine plankton in the whole-plankton assemblage that spanned 5 orders of magnitude in size from microbes to macroplankton predators (not including fish or fish lar-vae, for which no consistent data were available). Samples were collected in the northwestern Mediterranean Sea (Bay of Villefranche) weekly during 10 months. Simultaneously collected samples were analyzed by flow cytometry, inverse microscopy, FlowCam, and ZooScan. The whole-plankton assemblage underwent sharp reorganizations that corresponded to bottom-up events of vertical mixing in the water-column, and its development was top-down controlled by large gelatinous filter feeders and predators. Based on the results provided by our novel whole-plankton assemblage approach, we propose a new comprehensive conceptual model of the annual plankton succession (i.e. whole plankton model) characterized by both stepwise stacking of four broad trophic communities from early spring through summer, which is a new concept, and progressive replacement of ecological plankton categories within the different trophic communities, as recognised traditionally.

The biological carbon pump causes carbon sequestration in deep waters by downward transfer of organic matter, mostly as particles. This mechanism depends to a great extent on the uptake of CO2 by marine plankton in surface waters and subsequent sinking of particulate organic carbon (POC) through the water column. Most of the sinking POC is remineralized during its downward transit, and modest changes in remineralization have substantial feedback on atmospheric CO2 concentrations, but little is known about global variability in remineralization. Here we assess this variability based on modern underwater particle imaging combined with field POC flux data and discuss the potential sources of variations. We show a significant relationship between remineralization and the size structure of the phytoplankton assemblage. We obtain the first regionalized estimates of remineralization in biogeochemical provinces, where these estimates range between -50 and +100% of the commonly used globally uniform remineralization value. We apply the regionalized values to satellite-derived estimates of upper ocean POC export to calculate regionalized and ocean-wide deep carbon fluxes and sequestration. The resulting value of global organic carbon sequestration at 2000m is 0.33PgCyr(-1), and 0.72PgCyr(-1) at the depth of the top of the permanent pycnocline, which is up to 3 times higher than the value resulting from the commonly used approach based on uniform remineralization and constant sequestration depth. These results stress that variable remineralization and sequestration depth should be used to model ocean carbon sequestration and feedback on the atmosphere.

Marine plankton support global biological and geochemical processes. Surveys of their biodiversity have hitherto been geographically restricted and have not accounted for the full range of plankton size. We assessed eukaryotic diversity from 334 size-fractionated photic-zone plankton communities collected across tropical and temperate oceans during the circumglobal Tara Oceans expedition. We analyzed 18S ribosomal DNA sequences across the intermediate plankton-size spectrum from the smallest unicellular eukaryotes (protists, > 0.8 micrometers) to small animals of a few millimeters. Eukaryotic ribosomal diversity saturated at similar to 150,000 operational taxonomic units, about one-third of which could not be assigned to known eukaryotic groups. Diversity emerged at all taxonomic levels, both within the groups comprising the similar to 11,200 cataloged morphospecies of eukaryotic plankton and among twice as many other deep-branching lineages of unappreciated importance in plankton ecology studies. Most eukaryotic plankton biodiversity belonged to heterotrophic protistan groups, particularly those known to be parasites or symbiotic hosts.

The Tara Oceans expedition (2009–2013) sampled contrasting ecosystems of the world oceans, collecting environmental data and plankton, from viruses to metazoans, for later analysis using modern sequencing and state-of-the-art imaging technologies. It surveyed 210 ecosystems in 20 biogeographic provinces, collecting over 35,000 samples of seawater and plankton. The interpretation of such an extensive collection of samples in their ecological context requires means to explore, assess and access raw and validated data sets. To address this challenge, the Tara Oceans Consortium offers open science resources, including the use of open access archives for nucleotides (ENA) and for environmental, biogeochemical, taxonomic and morphological data (PANGAEA), and the development of on line discovery tools and collaborative annotation tools for sequences and images. Here, we present an overview of Tara Oceans Data, and we provide detailed registries (data sets) of all campaigns (from port-to-port), stations and sampling events.

Regime shifts are characterized by sudden, substantial and temporally persistent changes in the state of an ecosystem. They involve major biological modifications and often have important implications for exploited living resources. In this study, we examine whether regime shifts observed in 11 marine systems from two oceans and three regional seas in the Northern Hemisphere (NH) are synchronous, applying the same methodology to all. We primarily infer marine pelagic regime shifts from abrupt shifts in zooplankton assemblages, with the exception of the East Pacific where ecosystem changes are inferred from fish. Our analyses provide evidence for quasi-synchronicity of marine pelagic regime shifts both within and between ocean basins, although these shifts lie embedded within considerable regional variability at both year-to-year and lower-frequency time scales. In particular, a regime shift was detected in the late 1980s in many studied marine regions, although the exact year of the observed shift varied somewhat from one basin to another. Another regime shift was also identified in the mid-to late 1970s but concerned less marine regions. We subsequently analyse the main biological signals in relation to changes in NH temperature and pressure anomalies. The results suggest that the main factor synchronizing regime shifts on large scales is NH temperature; however, changes in atmospheric circulation also appear important. We propose that this quasi-synchronous shift could represent the variably lagged biological response in each ecosystem to a large-scale, NH change of the climatic system, involving both an increase in NH temperature and a strongly positive phase of the Arctic Oscillation. Further investigation is needed to determine the relative roles of changes in temperature and atmospheric pressure patterns and their resultant teleconnections in synchronizing regime shifts at large scales.

Field and laboratory characterization of marine particles is laborious and expensive. Proxies of particle properties have been developed that allow researchers to obtain high frequency distributions of such properties in space or time. We focus on optical techniques used to characterize marine particles in-situ, with a focus on GEOTRACES-relevant properties, such as bulk properties including particle mass, cross-sectional area, particle size distribution, particle shape information, and also single particle optical properties, such as individual particle type and size. We also address the use of optical properties of particles to infer particulate organic or inorganic carbon. In addition to optical sensors we review advances in imaging technology and its use to study marine particles in situ. This review addresses commercially available technology and techniques that can be used as a proxy for particle properties and the associated uncertainties with particular focus to open ocean environments, the focus of GEOTRACES. (C) 2014 Elsevier Ltd. All rights reserved.

Microbes are dominant drivers of biogeochemical processes, yet drawing a global picture of functional diversity, microbial community structure, and their ecological determinants remains a grand challenge. We analyzed 7.2 terabases of metagenomic data from 243 Tara Oceans samples from 68 locations in epipelagic and mesopelagic waters across the globe to generate an ocean microbial reference gene catalog with >40 million nonredundant, mostly novel sequences from viruses, prokaryotes, and picoeukaryotes. Using 139 prokaryote-enriched samples, containing >35,000 species, we show vertical stratification with epipelagic community composition mostly driven by temperature rather than other environmental factors or geography. We identify ocean microbial core functionality and reveal that >73% of its abundance is shared with the human gut microbiome despite the physicochemical differences between these two ecosystems.

We estimated the relative contribution of atmosphere (ic Nitrogen (N) input (wet and dry deposition and N fixation) to the epipelagic food web by measuring N isotopes of different functional groups of epipelagic zooplankton along 23°W (17°N-4°S) and 18°N (20-24°W) in the Eastern Tropical Atlantic. Results were related to water column observations of nutrient distribution and vertical diffusive flux as well as colony abundance of Trichodesmium obtained with an Underwater Vision Profiler (UVP5). The thickness and depth of the nitracline and phosphocline proved to be significant predictors of zooplankton stable N isotope values. Atmospheric N input was highest (61% of total N) in the strongly stratified and oligotrophic region between 3 and 7°N, which featured very high depth-integrated Trichodesmium abundance (up to 9.4×104 colonies m-2), strong thermohaline stratification and low zooplankton δ15N (~2‰). Relative atmospheric N input was lowest south of the equatorial upwelling between 3 and 5°S (27%). Values in the Guinea Dome region and north of Cape Verde ranged between 45 and 50%, respectively. The microstructure-derived estimate of the vertical diffusive N flux in the equatorial region was about one order of magnitude higher than in any other area (approximately 8 mmol m-2 d 1). At the same time, this region received considerable atmospheric N input (35% of total). In general, zooplankton δ15N and Trichodesmium abundance were closely correlated, indicating that N fixation is the major source of atmospheric N input. Although Trichodesmium is not the only N fixing organism, its abundance can be used with high confidence to estimate the relative atmospheric N input in the tropical Atlantic (r2 = 0.95). Estimates of absolute N fixation rates are two- to tenfold higher than incubation-derived rates reported for the same regions. Our approach integrates over large spatial and temporal scales and also quantifies fixed N released as dissolved inorganic and organic N. In a global analysis, it may thus help to close the gap in oceanic N budgets.

Environmental changes resulting from anthropogenic CO2 emissions occur at global and local levels and have potentially harmful effects, particularly for calcifying taxa in the marine environment. A time series of pteropod abundance covering the period 1967-2003 was isolated from the Point B (northwestern Ligurian Sea) zooplankton time series. Inter-and intra-annual changes in the abundance of 3 families (Limacinidae, Cavoliniidae and Creseidae) were compared with the copepod time series to identify any differential effects driven by ocean acidification and temperature. pH values were hind-cast from total alkalinity estimated from local temperature and salinity measurements, and atmospheric CO2 taken from the Mauna Loa time series. Although surface waters were supersaturated with respect to aragonite throughout the study period, it is estimated that pH declined by 0.05 units. All pteropod groups displayed a trend of increasing abundance, suggesting that any deleterious effect of declining pH(T) in the range of 0.05 units has not caused sufficient reductions in fitness as to decrease local abundances between 1967-2003. Pteropod populations are influenced by inter-annual changes in summer temperatures. Spectral analysis identified a similar to 14 yr periodic oscillation in sea surface temperature. Similarly timed oscillations in abundance are present for all pteropod families but not for copepods, indicating a possible influence of the North Atlantic quasi-decadal mode on pteropod populations. While laboratory studies have shown pteropods to be sensitive to changes in pH, this analysis suggests that local and regional scale drivers have had a greater effect on pteropod populations in the northwestern Mediterranean Sea in recent decades. It should be noted that pH changes in laboratory studies exceed 0.05 pH units and that the saturation state with respect to aragonite (Oar) is usually much lower than that of the Mediterranean.

While production of aggregates and their subsequent sinking is known to be one pathway for the downward movement of organic matter from the euphotic zone, the rapid transition from non-aggregated to aggregated particles has not been reported previously. We made one vertical profile of particle size distributions (PSD; sizes ranging from 0.052 to several millimeters in equivalent spherical diameter) at pre-bloom stage and seven vertical profiles 3 weeks later over a 48 h period at early bloom stage using the Underwater Vision Profiler during the Kerguelen Ocean and Plateau Compared Study cruise 2 (KEOPS2, October– November 2011). In these naturally iron-fertilized waters southeast of Kerguelen Island (Southern Ocean), the total particle numerical abundance increased by more than four-fold within this time period. A massive total volume increase associated with particle size distribution changes was observed over the 48 h survey, showing the rapid formation of large particles and their accumulation at the base of the mixed layer. The results of a one-dimensional particle dynamics model support coagulation as the mechanism responsible for the rapid aggregate formation and the development of the V T subsurface maxima. The comparison of V T profiles between early bloom stage and pre-bloom stage indicates an increase of particulate export below 200 m when bloom has developed. These results highlight the role of coagulation in forming large particles and triggering carbon export at the early stage of a naturally iron-fertilized bloom, while zoo-plankton grazing may dominate later in the season. The rapid changes observed illustrate the critical need to measure carbon export flux with high sampling temporal resolution. Our results are the first published in situ observations of the rapid accumulation of marine aggregates and their export and the general agreement of this rapid event with a model of phyto-plankton growth and coagulation.

The holoplanktonic jellyfish Pelagia noctiluca is renowned for periods of high abundance, causing considerable problems to tourism and aquaculture. Little is understood about the drivers of its periodic presence and absence or how it survives unfavourable periods. Studying the effect of starvation, we evaluated the main metabolic expenses (reproduction, respiration and excretion) during those periods. P. noctiluca could shrink in size, losing up to 85% of their mass (6.6-7.1% loss day(-1)), while continuing to release eggs quasi-daily over a 28-day period. Egg production was proportional to size (mean 759 eggs day(-1) at 6 cm bell diameter), with up to 19 526 eggs released in a single spawn, thereby providing huge potential for population growth despite undergoing starvation. Small food rations decreased the rate of shrinking to 3.1% day(-1), prolonging life (49 days), potentially enhancing the chances of encountering more prey and regrowing. Metabolism increased with wet mass (allometric exponent: 0.93 for respiration, 0.82 for ammonium), however reproduction was the greatest carbon expenditure for individuals larger than 9 cm bell diameter. Temperature (9-29 degrees C) also significantly increased both respiration and, to a greater extent, excretion (Q(10) = 2.25 and 4.76). Consequentially a warming ocean may negatively affect survival rates unless prey abundance balances the increased metabolic demands.

A closed eddy core in the Subantarctic Atlantic Ocean was fertilized twice with two tons of iron (as FeSO4), and the 300 km2 fertilized patch was studied for 39 days to test whether fertilization enhances downward particle flux into the deep ocean. Chlorophyll a and primary productivity doubled after fertilization, and photosynthetic quantum yield (FV/FM) increased from 0.33 to ≥0.40. Silicic acid (<2 µmol L⁻¹) limited diatoms, which contributed <10% of phytoplankton biomass. Copepods exerted high grazing pressure. This is the first study of particle flux out of an artificially fertilized bloom with very low diatom biomass. Net community production (NCP) inside the patch, estimated from O2:Ar ratios, averaged 21 mmol POC m−2 d−1, probably ±20%. ²³⁴Th profiles implied constant export of ~6.3 mmol POC m⁻² d⁻¹ in the patch, similar to unfertilized waters. The difference between NCP and ²³⁴Th-derived export partly accumulated in the mixed layer and was partly remineralized between the mixed layer and 100 m. Neutrally buoyant sediment traps at 200 and 450 m inside and outside the patch caught mostly <1.1 mmol POC m⁻² d⁻¹, predominantly of fecal origin; flux did not increase upon fertilization. Our data thus indicate intense flux attenuation between 100 and 200 m, and probably between the mixed layer and 100 m. We attribute the lack of fertilization-induced export to silicon limitation of diatoms and reprocessing of sinking particles by detritus feeders. Our data are consistent with the view that nitrate-rich but silicate-deficient waters are not poised for enhanced particle export upon iron addition.

Based on a multidisciplinary survey in the Iberian upwelling during late summer 2007, this paper analysed comparatively the cross-shore variability and offshore transport across the upwelling front and within a mesoscale filament. Along the East-West (EW) sections, transient upwelling pulses bring regularly cold, fresh and nutrient-enriched waters to the surface, triggering intense biological responses. Offshore advection by wind-forced Ekman drift of the successive fronts,

A better understanding of how environmental changes affect organic matter fluxes in Arctic marine ecosystems is sorely needed. Here we combine mooring times series, ship-based measurements and remote sensing to assess the variability and forcing factors of vertical fluxes of particulate organic carbon (POC) across the Mackenzie Shelf in 2009. We developed a geospatial model of these fluxes to proceed to an integrative analysis of their determinants in summer. Flux data were obtained with sediment traps moored around 125m and via a regional empirical algorithm applied to particle size distributions (17 classes from 0.08-4.2 mm) measured by an Underwater Vision Profiler 5. The low fractal dimension (i.e., porous, fluffy particles) derived from the algorithm (1.26 +/- 0.34) and the dominance (similar to 77 %) of rapidly sinking small aggregates (< 0.5 mm) in total fluxes suggested that settling material was the product of recent aggregation processes between marine detritus, gel-like substances, and ballast minerals. Modeled settling velocity of small and large aggregates was, respectively, higher and lower than in previous studies within which a high fractal dimension (i.e., more compact particles) was consequential of deep-trap collection (similar to 400-1300 m). Redundancy analyses and forward selection of abiotic/biotic parameters, linear trends, and spatial structures (i.e., principal coordinates of neighbor matrices, PCNM) were conducted to partition the variation of the 17 POC flux size classes. Flux variability was explained at 69.5% by the addition of a temporal trend, 7 significant PCNM, and 9 biophysical variables. The first PCNM canonical axis (44.5% of spatial variance) reflected the total magnitude of POC fluxes through a shelf-basin gradient controlled by bottom depth and sea ice concentration (p < 0.01). The second most important spatial structure (5.0 %) corresponded to areas where shelf break upwelling is known to occur under easterlies and where phytoplankton was dominated by diatoms. Among biophysical parameters, bacterial production and northeasterly wind (upwelling-favorable) were the two strongest corollaries of POC fluxes (r(2) cum. = 0.37). Bacteria were correlated with small aggregates, while northeasterly wind was associated with large size classes (> 1mm ESD), but these two factors were weakly related with each other. Copepod biomass was overall negatively correlated (p < 0.05) with vertical POC fluxes, implying that metazoans acted as regulators of export fluxes, even if their role was minor given that our study spanned the onset of diapause. Our results demonstrate that on interior Arctic shelves where productivity is low in mid-summer, localized upwelling zones (nutrient enrichment) may result in the formation of large filamentous phytoaggregates that are not substantially retained by copepod and bacterial communities.

Understanding pelagic ecology and quantifying energy fluxes through the trophic web and from the surface to the deep ocean requires the ability to detect and identify all organisms and particles in situ and in a synoptic manner. An idealized sensor should observe both the very small living or dead particles such as picoplankton and detritus, respectively, and the large particles such as aggregates and meso- to macroplankton. Such an instrument would reveal an astonishing amount and diversity of living and nonliving particles present in a parcel of water. Unfortunately such sensors do not exist. However, complex interactions constrain the space, temporal, and size distributions of these objects in such ways that general rules can be inferred from the measurement of their optical properties. Recent technological developments allow for the in situ measurement of the optical properties and size distributions of particles and plankton in a way such that synoptic surveys are possible. This review deals with particle and plankton size distributions (PSDs) as well as how particles' geometry and nature affect their optical properties. Finally, we propose the integration of the PSD into size-structured mathematical models of biogeochemical fluxes.

In the North Pacific Subtropical Gyre (NPSG), the regular occurrence of summer phytoplankton blooms contributes to marine ecosystem productivity and the annual carbon export. The mechanisms underlying the formation, maintenance, and decay of these blooms remain largely unknown; nitrogen fixation, episodic vertical mixing of nutrients, and meso- (<100 km) and submesoscale (<10 km) physical processes are all hypothesized to contribute to bloom dynamics. In addition, zones of convergence in the ocean's surface layers are known to generate downwelling and/or converging currents that affect plankton distributions. It has been difficult to quantify the importance of these convergence zones in the export flux of particulate organic carbon (POC) in the open ocean. Here we use two high-resolution ocean transects across a pair of mesoscale eddies in the vicinity of Station ALOHA (22 degrees 45'N, 158 degrees 00'W) to show that horizontal turbulent stirring may have been a dominant control on the spatial distribution of the nitrogen fixing cyanobacterium Trichodesmium spp. Fast repetition rate fluorometry measurements suggested that this distribution stimulated new primary production; this conclusion was not confirmed by C-14-based measurements, possibly because of different sampling scales for the two methods. Our observations of particle size distributions along the two transects showed that stretching by the mesoscale eddy field produced submesoscale features that mediated POC export via frontogenetically generated downwelling currents. This study highlights the need to combine high-resolution biogeochemical and physical data sets to understand the links between Trichodesmium spp. surface distribution and POC export in the NPSG at the submesoscale level.

The size distribution and mean spatial trends of large particles (> 100 mu m, in equivalent spherical diameter, ESD) and mesozooplankton were investigated across the Mackenzie Shelf (southeast Beaufort Sea, Arctic Ocean) in July-August 2009. Our main objective was to combine results from an Underwater Vision Profiler 5 (UVP5) and traditional net tows (200 mu m mesh size) to characterize the structural diversity and functioning of the Arctic shelf-basin ecosystem and to assess the large-scale correspondence between the two methodological approaches. The core dataset comprised 154 UVP5 profiles and 29 net tows conducted in the shelf (< 100 m isobath), slope (100-1000 m) and basin (> 1000 m) regions of the study area. The mean abundance of total particles and zooplankton in the upper water column (< 75 m depth) declined exponentially with increasing distance from shore. Vertical and latitudinal patterns in total particle concentration followed those of chlorophyll a (chl a) concentration, with maximum values between 30 and 70 m depth. Based on the size-spectra derived from the UVP5 dataset, living organisms (0.1-10 mm ESD) accounted for an increasingly large proportion of total particle abundance (from 0.1 % to > 50 %) when progressing offshore and as the ESD of particles was increasing. Both the UVP5 and net tows determined that copepods dominated the zooplankton community (similar to 78-94 % by numbers) and that appendicularians were generally the second most abundant group (similar to 1-11 %). The vertical distribution patterns of copepods and appendicularians indicated a close association between \\mbox\primary\ production and the main grazers. Manual taxonomic counts and ZooScan image analyses shed further light on the size-structure and composition of the copepod community - which was dominated at similar to 95 % by a guild of 10 typical taxa. The size distributions of copepods, as evaluated with the 3 methods (manual counts, ZooScan and UVP5), showed consistent patterns co-varying in the same order of magnitude over the upper size range (> 1 mm ESD). Copepods < 1 mm were not well quantified by the UVP5, which estimated that only similar to 13-25 % of the assemblage was composed of copepods < 1 mm ESD compared with similar to 77-89 % from the net tow estimates. However, the biovolume of copepods was overwhelmingly dominated (similar to 93-97 %) by copepods > 1 mm ESD. Our results illustrate that the combination of traditional sampling methods and automated imaging techniques is a powerful approach that enabled us to conclude on the prevalence of a relatively high productivity regime and dominant herbivorous food web over the shelf when compared with the low-productive recycling system detected offshore.

Body size constrains prey-predator interactions and physiology, therefore plankton size spectra have been appointed as synthetic descriptors of plankton community structure and functioning. Recently developed imaging systems and supervised classification tools provide size measurements of any object in situ or in net samples and automatically classify them into previously defined categories. But because the nature of objects detected by these imaging systems is diverse, from non-living detritus to organisms of different plankton taxa, and because the steps in the analysis could introduce specific biases, a careful analysis of such plankton size spectra is needed before going deeper into ecological considerations. Using a WP2 net time series, we propose a general framework to analyze and validate zooplankton size spectra collected with nets and analyzed with the ZooScan integrated system that includes supervised classification. Size spectra were controlled, at each step of the procedure, to assess the modification of their shape due to several possible biases: (i) the effect of objects touching each other during the image acquisition, (ii) the error of the automatic classification differing among size classes and (iii) the choice of model to estimate body biovolume.

The semi-enclosed nature of the Mediterranean Sea, together with its smaller inertia due to the relative short residence time of its water masses, make it highly reactive to external forcings, in particular variations of water, energy and matter fluxes at the interfaces. This region, which has been identified as a “hotspot” for climate change, is therefore expected to experience environmental impacts that are considerably greater than those in many other places around the world. These natural pressures interact with the increasing demographic and economic developments occurring heterogeneously in the coastal zone, making the Mediterranean even more sensitive. This review paper aims to provide a review of the state of current functioning and responses of Mediterranean marine biogeochemical cycles and ecosystems with respect to key natural and anthropogenic drivers and to consider the ecosystems’ responses to likely changes in physical, chemical and socio-economical forcings induced by global change and by growing anthropogenic pressure at the regional scale. The current knowledge on and expected changes due to single forcing (hydrodynamics, solar radiation, temperature and acidification, chemical contaminants) and combined forcing (nutrient sources and stoichiometry, extreme events) affecting the biogeochemical fluxes and ecosystem functioning are explored. Expected changes in biodiversity resulting from the combined action of the different forcings are proposed. Finally, modeling capabilities and necessity for modeling are presented. A synthesis of our current knowledge of expected changes is proposed, highlighting relevant questions for the future of the Mediterranean ecosystems that are current research priorities for the scientific community. Finally, we discuss how these priorities can be approached by national and international multi-disciplinary research, which should be implemented on several levels, including observational studies and modeling at different temporal and spatial scales.

Copepod, chaetognath, decapod larva, siphonophore and jellyfish monthly abundances, from 1974 to 2003 at Point B (northwestern Mediterranean), were obtained with the ZooScan. Principal component analysis (PCA) was performed on zooplankton, and another PCA on local environment. Almost-decadal periods (1974-1982, 1983-1991, 1992-1999, and 2000-2003) were distinguished in the 1st PC of zooplankton, and that of local environment (1974-1980, 1981-1991, 1992-1998, and 1999-2003). The 1st PC of local environment was correlated with winter North Atlantic Oscillation (NAO) until early 19905. In early 1980s, all groups increased and the majority of the decade abundances were above the long-term average for most groups. In the 1990s, all decreased, and in early 2000s they increased. This synchrony suggests bottom-up control as main mechanism structuring these groups. The 1980s were characterized by low winter temperature and high salinity. We hypothesize that phytoplankton production was favored during that decade due to increased nutrient uprise to surface by strong winter vertical mixing. In the 1990s salinity decreased probably to the detriment of vertical mixing and carrying capacity of the system. These results stress the role of salinity as physical forcing on water-column stability, in the NW Mediterranean, and the importance of winter conditions to determine the state of pelagic ecosystems. (C) 2011 Elsevier B.V. All rights reserved.

An integrated analysis of the pelagic ecosystems of the Ligurian Sea is performed combining time series (1995-2005) of several zooplankton groups (one group for copepods smaller than 0.724mm(3) and nine groups for individuals larger than 0.724mm(3), i.e. large copepods, decapod larvae other crustaceans, chaetognaths, appendicularians, pteropods, thaliaceans, gelatinous predators and other zooplankton), chlorophyll-a, nutrients, salinity, temperature, density, and local weather at Point B coastal station (Northern Ligurian Sea). From 1995 to 2000 winters were wet and mild resulting in lower winter sea surface density. These years showed lower than average nutrients and zooplankton concentrations while chlorophyll-a biomass was high. After 2000, winters were colder and dryer resulting in higher sea surface density. Nutrients and zooplankton showed higher concentrations while chlorophyll-a was lower than average. The ca. 2000 change was observed for most zooplankton groups with a one-year delay for some groups. Inter-annual variability within each period was also observed. The observed patterns suggest that the pelagic ecosystem trophic state at the studied point is mostly set by the winter forcing on the vertical mixing that upwells nutrients to the surface sustaining primary production. Surprisingly, low chlorophyll-a biomass in high nitrate and zooplankton conditions during the well mixed years suggest that phytoplankton biomass is controlled by grazers. The proposed mechanisms of stronger winter vertical mixing hold for most of the time series, but specific years with contradicting patterns suggest also the possible influence of the summer climate. A review of recent literature suggests that changes in the pelagic ecosystem are not limited to the studied site but concern also the central Ligurian Sea.

We recorded vertical profiles of size distributions of particles (ranging from 0.052 to several mm in equivalent spherical diameter) in the natural iron-fertilized bloom southeast of Kerguelen Island (Southern Ocean) and in surrounding high-nutrient, low-chlorophyll (HNLC) waters with an Under Water Video Profiler during the Kerguelen Ocean and Plateau Compared Study cruise (Jan-Feb 2005). Total particle numerical abundance and total particle volume (TPV) in the 0-200-m layer were respectively 3-fold and 20-fold higher in the bloom, and integrated TPV was correlated to integrated chlorophyll concentration. The difference persisted well into the ocean interior with a 10-fold higher TPV at 400-m depth beneath the natural iron-fertilized bloom. Below 400 m, increases in TPV values at the bloom stations reflect the suspension of bottom sediments. Bloom waters had a greater proportion of large particles from the surface to 400 m and also exhibited an increase of this proportion with depth compared to HNLC waters. Multiple visits to the bloom reference Sta. A3, suggest preferential removal of large particles as the bloom declined. Comparing our particle abundance size spectra with those observed previously in polyacrylamide gel-filled sediment traps allows us to estimate mesopelagic particle sinking rates. These results suggest that particles sink faster in the HNLC waters than beneath the bloom. The fact that sinking speeds were not a simple monotonic function of particle size and varied spatially highlights the need to go beyond parameterizations of sinking rate as a function of size alone.

In the framework of the Marine Strategy Framework Directive (MSFD), and for the first time, a census and analysis of the available metadata on zooplankton along the French coasts have been conducted (for both long term time series and short term oceanographic cruises). This study provided a comprehensive examination of zooplankton within the French metropolitan coastal system, i.e., the North Sea, the English Channel, the Atlantic Ocean and the Mediterranean Sea.The investigation revealed a wide disparity in the spatial distribution of studies highlighting some well sampled areas as well as other regions quite unexplored. In addition, this approach also exposed the heterogeneity in zooplankton sampling methods and taxonomic determination levels. The wide variety of sampling methods defined the whole zooplankton community, from the smallest fauna (such as crustacean nauplii) to the largest (such as euphausiids) to the most delicate (gelatinous forms). Unfortunately, the possibilities for cross analysis of Zooplankton meta data census 12 the different data are limited. This paper presents a preliminary analysis of the data available for meta analysis (in term of sampling method and taxonomic determination). In order to understand current and future environmental fluctuations (climate change, ocean acidification, anthropogenic pollution and persistent overfishing), it is essential to identify and analyze all the biological data collected in the different French marine areas. This indispensable first step is crucial for defining the environmental status of marine waters.The nexus of our results provides recommendations for a standardization of procedures to be followed in subsequent studies of zooplankton, specifically sampling strategies, sampling methods and taxonomic determinations

ZooScan with ZooProcess and Plankton Identifier (PkID) software is an integrated analysis system for acquisition and classification of digital zooplankton images from preserved zooplankton samples. Zooplankton samples are digitized by the ZooScan and processed by ZooProcess and PkID in order to detect, enumerate, measure and classify the digitized objects. Here we present a semi-automatic approach that entails automated classification of images followed by manual validation, which allows rapid and accurate classification of zooplankton and abiotic objects. We demonstrate this approach with a biweekly zooplankton time series from the Bay of Villefranche-sur-mer, France. The classification approach proposed here provides a practical compromise between a fully automatic method with varying degrees of bias and a manual but accurate classification of zooplankton. We also evaluate the appropriate number of images to include in digital learning sets and compare the accuracy of six classification algorithms. We evaluate the accuracy of the ZooScan for automated measurements of body size and present relationships between machine measures of size and C and N content of selected zooplankton taxa. We demonstrate that the ZooScan system can produce useful measures of zooplankton abundance, biomass and size spectra, for a variety of ecological studies.

So far, appendicularians role in the biogeochemical cycling of organic matter has been overlooked. Appendicularians represent only a fraction of total mesozooplankton biomass, however these ubiquitous zooplankters have very high filtration and growth rates compared to copepod, and produce numerous fecal pellets and filtering houses contributing to the export production by aggregating small marine particles. To study their quantitative impact on biogeochemical fluxes, we have included this group in the Biogeochemical Flux Model (BFM), using a recently developed ecophysiological model. One dimensional annual simulations of the pelagic ecosystem including appendicularians were conducted with realistic surface forcing for year 2000, using data from the DyFAMed open ocean station. The appendicularian grazing impact was generally low, but appendicularians increased detritus production by 8% and export production by 55% compared to a simulation without appendicularians. Therefore present biogeochemical models lacking appendicularians probably under, or misestimate the detritus and export production by omitting the pathway from small sized plankton to fast sinking detritus. Detritus production and export rates are 60% lower than estimates from mesotrophic sites, showing that appendicularians' role is lower but still significant in oligotrophic environments. The simulated annual export at 200 m exceeds sediment trap values by 44%, suggesting an intense degradation during the sinking of appendicularian detritus, supported by observations made in other sites. Thus degradation and grazing of appendicularians detritus need a better quantification if we are to accurately assess the appendicularian role in the export flux.

The inter-annual variability of the pelagic ecosystems of the Ligurian Sea is investigated combining original datasets (from 1995 to 2006 collected weekly) of zooplankton abundances, hydrology and local weather conditions obtained in the bay of Villefranche-sur-mer. Two main patterns of zooplankton dynamics were observed with a shift between 1999 and 2000. The first period was characterized by high precipitation and mild air temperature during the winter. This induced lower salinity and higher seawater temperature and low density of surface seawater during the winter. These waters were characterize by low loads of nutrients. During these years, zooplankton total biovolume was also lower as shown by the strong negative anomalies in the time series. Starting in 2000, the climate changed toward drier and colder winters with denser surface water and more intense convections as suggested by higher nutrients concentrations. An increase of the abundances of all zooplankton categories was observed with a doubling of the total zooplankton average annual means and a change in the zooplankton phenology with a spring development happening 2.5 weeks earlier during these years. These results could be explained by a strong bottom-up control on the pelagic ecosystem of the Ligurian Sea at the inter-annual scale. Whereas the summer thermal stratification increase was often suggested to drive long-term dynamic in Ligurian Sea zooplankton, our results highlight the strong influence of the Winter convection properties as the main factor governing inter-annual changes in zooplankton abundance. The effect of global climate cycles will be discussed as being possible factors driving the pelagic ecosystem in the NW Mediterranean Sea.

The Underwater Vision Profiler (UVP) was developed to quantify the vertical distribution of macroscopic particles and zooplankton > 100 mu m in size. The smaller size limit is fixed by optical resolution, whereas the larger size limit is determined by the volume of water illuminated per image. The new fifth generation instrument (UVP5) is compact (30 kg in air) and operates either as a stand-alone instrument with an independent power supply for use on a mooring or free-drifting array, or as a component of a Conductivity, Temperature, and Depth (CTD)-rosette package. Images are recorded at a frequency up to 6 Hz. If the UVP5 is interfaced with a CTD, these images are acquired and analyzed in real time. Images are recorded every 20 cm at the 1 m s(-1) lowering speed. The current maximum deployment depth is 3000 m. The recorded volume per image is 1.02 L, and the conversion equation from pixel area to size in mm(2) is S-m = 0.003S(p)(1.3348) where S-p is the surface of the particle in pixels and S-m the surface in mm(2). Comparisons between the earlier UVP versions and UVP5 indicate that images ranging in size from 105 mu m to 2.66 mm are identical so historical and contemporary data sets can be compared.

We recorded vertical profiles of size distributions of large particles (> 100 mu m) to a 1000-m depth in the Atlantic, Indian, and Pacific Oceans and in the Mediterranean Sea with the Underwater Video Profiler. Of the 410 profiles used in our analysis, 193 also included temperature, salinity, and high-performance liquid chromatography (HPLC)-resolved pigments, which were used to characterize the size structure of the phytoplankton community. Classification analysis identified six clusters of vertical profiles of size distributions of particles. Each cluster was characterized by the size distribution of its particles in the mesopelagic layer and the change of the particle-size distribution with depth. Clusters with large particles in the mesopelagic layer corresponded to surface waters dominated by microphytoplankton, and those with small particles corresponded to surface waters dominated by picophytoplankton. We estimated the mass flux at 400 m using a relationship between particle size and mass flux. Principal-component regression analysis showed that 68% of the variance of the mass flux at 400 m was explained by the size structure of the phytoplankton community and integrated chlorophyll a in the euphotic zone. We found that coefficient k in the Martin power relationship, which describes the decrease in the vertical mass flux with depth, varies between 0.2 and 1.0 in the world ocean, and we provided an empirical relationship to derive k from the size structure of phytoplankton biomass in the euphotic zone. Biogeochemists and modelers could use that relationship to obtain a realistic description of the downward particle flux instead of using a constant k value as often done.

Fourteen dives were conducted with the ROVs Aglantha and Bathysaurus to depths of 2335 m along the Mid-Atlantic Ridge (42 degrees 52'-53 degrees 17'N). The most frequently observed gelatinous fauna in order of overall abundance included medusae, ctenophores, siphonophores, appendicularians, and tunicates. All of these animals, except the tunicates, occurred throughout the water column. Their relative abundances differed with depth and location. Identification to species was limited to easily recognized fauna because relatively few gelatinous animals were collected. Each group of gelatinous zooplankton tended to be most numerous in a region just south of the Charlie-Gibbs Fracture Zone. Medusae (mainly Aeginura grimaldii) were the most frequently encountered animals (LIP to 25 individuals per 100 m(3)). Oil a vertical scale their abundance peaked from 550 to 800 m and these maxima were consistently within the SAIW and NACWe. In the NACW their densities were notably lower (up 2 individuals per 100 m(3)) and the majority of the population was deeper, ranging from 800 to 1050 m. Ctenophores (mainly Bathocyroe fosteri) were most prominent (as many as 27 individuals per 100 m(3)) in a zone from 300 to 600 m in the NACWe. Appendicularians (primarily oikopleurids) had a broader vertical distribution in all water masses, mainly from 450 to 1000 m. Up to 12 houses per 100 m(3) were noted in the NACWe, and these estimates are considered to be very conservative. Sorties near the sea floor (as deep as 2100 m) indicated these detritivores were a prominent component (up to 5 houses per 100 m(3)) of the epibenthic macrozooplankton. Siphonophores (mostly calycophorans) reached densities of about 14 colonies per 100 m(3) in the NACWe and occurred mainly from 300 to 600 m, at most locations. Tunicates (salps and doliolids) were patchy in their distribution and infrequently observed. Salps were numerous (up to 3 solitary individuals per 100 m(3)) at only one location (sta. 50) near the surface. Deep-living doliolids (up to 1 individual per 100 m(3)) appeared from 400 to 500 m at this site and occasionally within the same depth range at most of the other stations. (c) 2007 Elsevier Ltd. All rights reserved.

The French JGOFS BIOSOPE cruise crossed the South Pacific Gyre (SPG) on a transect between the Marquesas Islands and the Chilean coast on a 7500 km transect (8° S–34° S and 8° W–72° W). The number and volume distributions of small (3.5<<i>d</i><30 µm) and large particles (<i>d</i>>100 µm) were analysed combining two instruments, the HIAC/Royco Counter (for the small particles) and the Underwater Video Profiler (UVP, for the large particles). For the HIAC analysis, samples were collected from 12 L CTD Rosette bottles and immediately analysed on board while the UVP provided an estimate of in situ particle concentrations and size in a continuous profile. Out of 76 continuous UVP and 117 discrete HIAC vertical profiles, 25 had both sets of measurements, mostly at a site close to the Marquesas Islands (site MAR) and one in the center of the gyre (site GYR). At GYR, the particle number spectra from few µm to few mm were fit with power relationships having slopes close to -4. At MAR, the high abundance of large objects, probably living organisms, created a shift in the full size spectra of particles such that a single slope was not appropriate. The small particle pool at both sites showed a diel pattern while the large did not, implying that the movement of mass toward the large particles does not take place at daily scale in the SPG area. Despite the relatively simple nature of the number spectra, the volume spectra were more variable because what were small deviations from the straight line in a log-log plot were large variations in the volume estimates. In addition, the mass estimates from the size spectra are very sensitive to crucial parameters such as the fractal dimension and the POC/Dry Weight ratio. Using consistent values for these parameters, we show that the volume of large particles can equal the volume of the smaller particles. However the proportion of material in large particles decreased from the mesotrophic conditions at the border of the SPG to the ultra-oligotrophy of the center in the upper 200 m depth. We expect large particles to play a major role in the trophic interaction in the upper waters of the South Pacific Gyre.

Large sinking particles transport organic and inorganic matter into the deeper layers of the oceans. Between 70 and 90% of the aggregates exported from the surface mixed layer are disaggregated within the upper 1000 m. This decrease with depth indicates that fragmentation and remineralization processes are intense during sedimentation. Generally, the estimates of vertical flux rely on sediment trap data but difficulties inherent in their design limit the reliability of this information. During the BIOSOPE study in the southeastern Pacific, 76 vertical casts using the Underwater Video Profiler (UVP) and deployments of drifting sediment traps provided an opportunity to fit the UVP data to sediment trap flux measurements. We applied the calculated UVP flux in the upper 1000 m to the whole 8000 km BIOSOPE transect. Comparison between the large particulate material (LPM) abundance and the estimated fluxes from both UVP and sediment traps showed different patterns in different regions. On the western end of the BIOSOPE section the standing stock of particles in the surface layer was high but the export between 150 and 250 m was low. Below this layer the flux values increased. High values of about 30% of the calculated UVP maximum surface zone flux were observed below 900 m at the HNLC station. The South Pacific Gyre exported about 2 mg m(-2) d(-1). While off Chilean coast 95% of the surface mixed layer matter was disaggregated, remineralized or advected in the upper kilometer, 20% of the surface zone flux was observed below 900 m near the Chilean coast. These results suggest that the export to deep waters is spatially heterogeneous and related to the different biotic and abiotic factors.

The vertical distribution (0-1000 m depth) of macrozooplankton along the northern portion of the Mid-Atlantic Ridge (59 degrees 58N, 25 degrees 53W to 41 degrees 29N, 28 degrees 19W) was investigated during the MAR-ECO program (June and July 2004) using the Underwater Video Profiler (UVP). Twelve relatively large (> 1 cm) groups were selected from the recorded images: sarcodines (with two sub-groups), crustaceans (excluding copepods), chaetognaths, ctenophores (with two sub-groups cyclippids and lobates), siphonophores, medusae (with three subgroups Aeginura grimaldii, Aglantha spp. and all other medusae), appendicularians, and thaliaceans. The numerically dominant groups over the whole area were crustaceans (26%), medusae (20%) and appendicularians (17%). The gelatinous fauna were consistently most numerous at 400-900 m. Appendicularians, ctenophores and Aeginura grimaldii occurred mostly below 300 m (maximum concentrations of 75, 58, and 30 individuals 100 m(-3), respectively). Sipbonophores, Aglantha spp. and the other medusae were more uniformly distributed in the water column (maxima of 42, 42 and 300 individuals 100 m(-3), respectively). The macrozooplankton community below 200 m varied with the spatial distribution of the water masses, suggesting that the Sub-Polar Front restricts the mixing of macrozooplankton communities down to 1000 m depth. (c) 2007 Published by Elsevier Ltd.

Large sinking particles transport organic and inorganic matter into the deeper layers of the oceans. From 70 to 90% of the superficial particulate material is disaggregated within the upper 1000 m. This decrease with depth indicates that remineralization processes are intense during sedimentation. Generally, the estimates of vertical flux rely on the sediment trap data but difficulties inherent in their design, limit the reliability of this information. During the BIOSOPE study in the southeastern Pacific, 76 vertical casts using the Underwater Video Profiler (UVP) and deployments of a limited number of drifting sediment traps provided an opportunity to fit the UVP data to sediment trap flux measurements. We applied than the calculated UVP flux in the upper 1000 m to the whole 8000 km BIOSOPE transect. Comparison between the large particulate material (LPM) abundance and the estimated fluxes from both UVP and sediment traps showed different patterns in different regions. On the western end of the BIOSOPE section the standing stock of particles in the superficial layer was high but the export between 150 and 250 m was low. Below this layer the flux values increased. High values of about 30% of the calculated UVP maximum superficial flux were observed below 900 m at the HNLC station. The South Pacific Gyre exported about 2 mg m^-2 d^-1. While off Chilean coast 95% of the superficial matter was remineralized or advected in the upper kilometer, 20% of the superficial flux was observed below 900 m near the Chilean coast. These results suggest that the export to deep waters is spatially heterogeneous and related to the different biotic and abiotic factors.

Large sinking particles transport organic and inorganic matter into the deeper layers of the oceans. Between 70 and 90% of the aggregates exported from the surface mixed layer are disaggregated within the upper 1000 m. This decrease with depth indicates that fragmentation and remineralization processes are intense during sedimentation. Generally, the estimates of vertical flux rely on sediment trap data but difficulties inherent in their design limit the reliability of this information. During the BIOSOPE study in the south-eastern Pacific, 76 vertical casts using the Underwater Video Profiler (UVP) and deployments of drifting sediment traps provided an opportunity to fit the UVP data to sediment trap flux measurements. We applied the calculated UVP flux in the upper 1000 m to the whole 8000 km BIOSOPE transect. Comparison between the large particulate material (LPM) abundance and the estimated fluxes from both UVP and sediment traps showed different patterns in different regions. On the western end of the BIOSOPE section the standing stock of particles in the surface layer was high but the export between 150 and 250 m was low. Below this layer the flux values increased. High values of about 30% of the calculated UVP maximum surface zone flux were observed below 900 m at the HNLC station. The South Pacific Gyre exported about 2 mg m<SUP>-2</SUP> d<SUP>-1</SUP>. While off Chilean coast 95% of the surface mixed layer matter was disaggregated, remineralized or advected in the upper kilometer, 20% of the surface zone flux was observed below 900 m near the Chilean coast. These results suggest that the export to deep waters is spatially heterogeneous and related to the different biotic and abiotic factors.

Large aggregates commonly named ``marine snow'' are difficult to collect and study because of their fragile nature, but they make up the largest fraction of vertical carbon flux in the ocean. Developments in imaging sensors and computer systems have facilitated the development of in situ image acquisition systems that can be used to produce profiles of aggregate size distribution and abundance. However, it is difficult to collect information on the different properties of particles, such as their composition, from in situ images. In this paper, we relate sediment trap data to particle size (d) distributions to estimate the vertical fluxes (F) of mass, particulate organic carbon (POC), particulate inorganic carbon (PIC) and particulate organic nitrogen (PON) using simple power relationships (F = Ad Mean aggregate fractal dimension of 2.3 and a size-dependent settling speed are determined from the flux estimations. We have used these relationships to map the distribution of mass flux along 180 degrees W in the equatorial Pacific. Similar mass fluxes below the euphotic zone have been reported along 150 degrees W for the same period with conventional sediment traps, supporting the accuracy of these relationships. The high spatial resolution of sedimentation processes studied in situ with the Underwater Video Profiler allowed us to undertake a detailed study of the role of physical processes in vertical fluxes. (c) 2008 Elsevier Ltd. All rights reserved.

Planktonic cnidarians and ctenophores were sampled with a multiple opening-closing net (Multinet) as well as a non-quantitative plankton net along the northern Mid-Atlantic Ridge (MAR) between Iceland and the Azores. Sixty-four species or genera of planktonic cnidarians (38 siphonophora, 21 hydromedusae, 5 scyphomedusae) and one genus of ctenophore were collected. Of these, Leuckartiara adnata and Clausophyes laetmata were new records for the area. Multinet samples collected from depths of 0-100, 100-500, 500-1000, 1000-1500 and 1500-2500 m at 11 stations were compared. Multivariate analysis of the data indicated that species composition and abundance along the ridge varied with the dominant water masses, with changes in the cnidarian zooplankton assemblage observed with regard to geographic location as well as depth. The surface waters of the two northernmost stations characterized by modified North Atlantic Water (MNAW) as well as the three southernmost stations characterized by North Atlantic Central Water (NACW) exhibited relatively high abundances (3284-13,915 individuals . 1000 m(-3)) in the upper 100 m. No such peak was evident at the middle stations characterized by Subarctic Intermediate Water (SAIW), where the abundances in the upper three depth strata were consistently lower (57-863 individuals . 1000 m(-3)). Across the study area, the lowest abundances were found in the 1500-2500 m stratum (0-56 ind. . 1000 m(-3)) The main divergence in the species composition and abundance of planktonic cnidarians was observed at the Subpolar Front (SPF), which marked the boundary for the distribution of many species. The divergence at the SPF was strongest in the upper 500 m but observable down to 1500 m. Profoundly different epipelagic species assemblages were observed in SAIW and NACW on opposite sides of the SPF, with the distribution of several species of calycophoran siphonophores confined to the southern NACW. At mid-water depths, the species composition north of the SPF was possibly influenced by Labrador Sea Water (LSW). The highest diversity of planktonic cnidarians was observed in the surface waters south of the SPF and in the 100-1000 m range north of the SPF. (c) 2007 Elsevier Ltd. All rights reserved.

This study provides and discusses the spatial distributions of abundances and sizes of marine-snow aggregates across the Ligurian Sea frontal system. A cross-front transect was sampled 34 times between 1992 and 1996, using the Underwater Video Profiler (UVP). Atlantic Water flows parallel to the Ligurian coast in the NW Mediterranean Sea, where that current creates a quasi-permanent front that separates the central and coastal waters. The horizontal distribution of aggregates (> 150 mu m ESD, Equivalent Spherical Diameter) in the upper 1000 m shows two main features. First, the smaller aggregates (150 mu m <ESD< 1 mm) are more abundant in coastal waters, as a result of continental input, cross-slope export, and re-suspension along the slope. The layers that contain very high concentrations of small aggregates are observed from surface down to 1000 m, and extend from the continental slope to the front. Second, the concentrations of large aggregates (ESD > 1 mm) are highest in and under the frontal zone, probably as a result of physical coagulation, and/or biological transformations. The seasonal intensity of large aggregate accumulations in and under the frontal structure seems to be more related to the autumn-winter increase in sub-mesoscale and mesoscale activity of the current flow than to the surface phytoplankton biomass. Interestingly, the horizontal distribution of aggregates is affected not only in the frontal zone (0-300 m depth), but also deeper down to 1000 m, probably as a consequence of rapid sinking or vertical transport. Results suggest that the settling of large aggregates under the frontal zone may limit the cross-slope transport of fine-grained particles by coagulation due to differential settling between the small particles suspended in the continental nepheloid layer and the large aggregates. This process, which takes place in sub-mesoscale zones (5-10 km wide), was also observed in one other front in the Western Mediterranean Sea. This led us to hypothesize that the impact of frontal processes on particle and aggregate dynamics might be generalized. Since fronts exist in many other coastal regions, the vertical fluxes at sub-mesoscale may have consequences for the transport of continental particles to the ocean's interior. (C) 2007 Elsevier B.V. All rights reserved.

Mesopelagic gelatinous zooplankton fauna are insufficiently known because of inappropriate and infrequent sampling, but may have important trophic roles. In situ imaging systems and undersea vehicles have been used to investigate their diversity, distribution, and abundance. The use of different platforms, however, restricts the comparison of data from different regions. Starting in 2001, the underwater video profiler (UVP) was deployed during 12 cruises in six oceanic regimes (Mediterranean Sea, North Atlantic shelves, Mid-Atlantic Ridge, tropical Pacific Ocean, eastern Indian Ocean, and Subantarctic Ocean) to determine the vertical distribution of organisms in the upper 1000 m. Nine oceanic regions were identified based on the hydrological properties of the water column. They correspond to nine of the biogeochemical provinces defined by Longhurst. In all, 21 morphotypes were recognized: sarcodines (eight groups), ctenophores (two groups), siphonophores, medusae (five groups), crustaceans (one group), chaetognaths, appenclicularians, salps, and fish. The similarity in the community assemblages of zooplankton in the 100-1000 m layer was significantly greater within regions than between regions, in most cases. The regions with comparable composition were located in the North Atlantic with adjacent water masses, suggesting that the assemblages were either mixed by advective transport or that environmental conditions were similar in mesopelagic layers. The data suggest that the spatial structuring of mesopelagic macrozooplankton occurs on large scales (e.g. basin scales) but not necessarily on smaller scales (e.g. oceanic front).

Spatial and temporal variability in the distribution of marine aggregates (> 110 mu m) was studied using underwater video profilers in an area off the Iberian Peninsula and Azores Islands dominated by mesoscale and submesocale hydrodynamics in winter, spring, and summer 2001. In the 0-200-m layer, aggregates were most abundant in spring (100-120 mg dry weight [dry wt] m(-3)) and lowest during summer and winter (1-10 mg dry wt (-3)). In the deeper layers,(down to 1,000 m), the seasonal pattern was different, with concentrations highest in spring and summer, and lowest in winter (e.g., at 800 in, 5-10 mg dry wt m(-3) in spring and summer; 1-5 mg dry wt m(-3) in winter). The seasonal change in the abundance of aggregates in the upper 1,000 m was consistent with changes in the composition and intensity of the particulate flux recorded in sediment traps and with seasonal changes in the surface phytoplankton community. In an area dominated by eddies, surface accumulation of aggregates and export down to 1,000 in occur at mesoscale distances (< 100 km). The occurrence of a rich aggregate layer may be related to mesoscale activity in water flow that drives nutrient inputs, phytoplankton production, and the formation of large aggregates. Such spatially constrained zones of massive export may be typical of frontal open-sea systems, and may have been missed by conventional sediment trap moorings, which cannot resolve export at this mesoscale level.

The downward transport of surface particle production constitutes an important mechanism for carbon sequestration by the ocean. Only a small fraction (similar or equal to 10%) of the flux that leaves the euphotic zone reaches 1000 m depth because the particulate organic matter is consumed and transformed in the oceanic midwater column. The depth at which this transformation occurs is crucial to estimate carbon sequestration. Description of the particle flux and remineralization with depth below the euphotic zone has previously been limited to empirical relationships that neglect physical and biological mechanisms. Because several particle properties and functions (settling speed, rates of coagulation and consumption) are related to particle size, measurements of particle size spectra provide an important tool to understand particle dynamics. Most of the mechanisms affecting particle dynamics known for the surface layer should continue in the mesopelagic region. We review the different mechanisms and formulate equations describing changes in particle size distributions throughout the water column as a result of particle sinking, coagulation, disaggregation, and bacterial and zooplankton consumption. The resulting model describes the midwater particle population by its mass distribution for the size range I pm to I cm. Most of the particle data sets have a narrower size range but we suggest that model results are not greatly affected by the lack of data on particles smaller than 200 mum because most of the particle mass is in particles larger than 100 mum, as seen in a full size-range particle spectrum. The combination of this model with a unique particle size spectra data set, obtained during an inter-annual survey at the French JGOFS site in the NW Mediterranean Sea, give an insight into the key processes for particle dynamics in the unknown midwater layers. (C) 2004 Elsevier Ltd. All rights reserved.

The largest decrease in the particle vertical flux occurs in the mesopelagic zone where particles are transformed by biological and physical mechanisms. Particle size distributions provide important clues into those processes affecting particle transformations in this region. We have studied them using an inter-annual data set showing the evolution of particle size distributions between 100 and 1000 m, comparing them to results from a series of size-resolved models of particle dynamics that include physical coagulation and biological remineralization. The formulation that best fits the observations consists of a combination of settling, microbial activity and zooplankton feeding. The calculated particulate organic carbon losses to microbial activity and zooplankton feeding are consistent with independent estimates of these rates. The model shows that it is possible to predict the particle size distribution at 1000 m depth knowing the particle size distribution at 100 m depth and the rates of transformation in the mesopelagic. The mesozooplankton appears to be important in decreasing the high flux of large particles in the upper midwater zone, microbes becomes more important in the deeper midwater zone as zooplankton become rarer. The results suggest that the mesozooplankton have a much greater effect on particle flux than the macrozooplankton. Their importance requires the mesozooplankton to feed preferentially on large settling particles, probably using remote detection. The present work shows that using particle size spectra is a useful way to understand the transformation of the vertical flux of element in the midwater zone. However, most of the assumptions on particle properties and processes are based on surface studies and more data from the midwater zone are needed to confirm the hypotheses. The model allows us to formulate crucial questions regarding particle dynamics in the midwater zone. (C) 2004 Elsevier Ltd. All rights reserved.

Marine snow ( MS) distribution from the surface to 1000 m depth was determined in the equatorial Pacific using the underwater video profiler during the Etude du Broutage en Zone Equatoriale cruise in fall 1996. The latitudinal transect was carried out at 17 stations along the 180degrees meridian from 8 degreesS to 8 degreesN during a cold phase of El Nino-Southern Oscillation. Higher MS concentrations were found below the equatorial zone than poleward. At the equator the estimated integrated MS carbon m(-2) in the upper kilometer was 5.7 g m(-2), while both southward and northward (between 1degrees and 8degrees) the mean integrated MS carbon was about 2.7 g. m(-2). In the upper 50 m the MS carbon was twofold lower than the combined carbon of autotrophic and heterotrophic protists and four times lower than the mesozooplankton carbon biomass, both measured concurrently during the cruise. Different water bodies had different MS content. The highest concentrations were found in the South Equatorial Current, the South Equatorial Counter Current, and the North Equatorial Countercurrent. Tropical waters at the south in the South Subsurface Countercurrents and the warm northern superficial waters had the lowest MS biomass. Mechanistically, a latitudinal ``conveyor belt'', a poleward divergence of upwelled waters that return to the equator after being downwelled at north and south convergent zones, may partially explain the vertical distribution of particulate matter observed during the studied period.

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Data on large particles (LP; > 0.15 mm), phytoplankton communities, vertical fluxes, and hydrology were collected between January 1992 and June 1996 in the NW Mediterranean Sea, during DYFAMED, an interdisciplinary program part of JGOFS France. LP concentrations at the study sites were typical for values found in other open-ocean studies. LP temporal evolution showed an annual cycle. Concentrations were the highest in winter/spring (20-1201-1, 5280 mg m(-3)) and lowest in summer and autumn (0-201-1, 0.8-60 mg m(-3)). We estimated that LP accounted on average, for 2-30% of the total particulate (> 0.7 mum) dry weight (DW). LP temporal evolution between 0-200 m was correlated with total Chl a and facoxanthin (diatoms), and inversely correlated to zeaxanthin (cyanobacteria and prochlorophytes). Although diatoms were clearly associated to LP, prymnesiophytes were associated to the two highest accumulation of particles > 1 mm. The DW fraction of particle > 0.5 mm to total LP increased from 10% in regenerated systems dominated by picoplankton to 50% during spring blooms. LP concentrations in the upper 200 m were correlated to mass flux recorded in sediment trap at 200 and 1000m. We defined three main periods for LP downward export related to physical stratification. (1) The major LP export occurred in winter and may be affected by deep vertical mixing; (2) in spring, at the onset of the thermal stratification LP downward export decreased, although pulses of phytoplanktonic production may have enhanced LP sedimentation over short time scales; (3) during the summer stratification, the deep water was generally depleted in LP. (C) 2002 Elsevier Science Ltd. All rights reserved.

The relationship between mesoscale hydrodynamics and the distribution of large particulate matter (LPM, particles larger than 200 mum) in the first 1000 m of the Western Mediterranean basin was studied with a microprocessor-driven CTD-video package, the Underwater Video Profiler (UVP). Observations made during the last decade showed that, in late spring and summer, LPM concentration was high in the coastal part of the Western Mediterranean basin at the shelf break and near the continental slope (computed maximum: 149 mug C l(-1) between 0 and 100 m near the Spanish coast of the Gibraltar Strait). LPM concentration decreased further offshore into the central Mediterranean Sea where, below 100 m, it remained uniformly low, ranging from 2 to 4 mug C l(-1). However, a strong variability was observed in the different mesoscale structures such as the Almeria-Oran jet in the Alboran Sea or the Algerian eddies. LPM concentration was up to one order of magnitude higher in fronts and eddies than in the adjacent oligotrophic Mediterranean waters (i.e. 35 vs. 8 mug C l(-1) in the Alboran Sea or 16 vs. 3 mug C l(-1) in a small shear cyclonic eddy). Our observations suggest that LPM spatial heterogeneity generated by the upper layer mesoscale hydrodynamics extends into deeper layers. Consequently, the superficial mesoscale dynamics may significantly contribute to the biogeochemical cycling between the upper and meso-pelagic layers. (C) 2002 Elsevier Science B.V. All rights reserved.

Day/night variations in the size distribution of the particulate matter > 0.15 mm (PM) were studied in May 1995 during the DYNAPROC time-series cruise in the northwestern Mediterranean Sea. Data on vertical distributions of PM (>0.15 mm) and zooplankton were collected with the Underwater Video Profiler (UVP). The comparisons of the UVP data with plankton net data and POC data from water bottles indicated that more than 97% of the particles detected by the UVP were non-living particles (0.15 mm) and that the PM contributed 4-34% of the total dry weight measured on GF/F filters. Comparison of seven pairs of day and night vertical profiles performed during the cruise showed that in the upper 800 m, the mean size and the volume of particles was higher at night than during the day. During the night, the integrated volume of the Ph I increased on average by 32 +/- 20%. This increase corresponded to a shift of smaller size classes ( < 0.5 mm) towards the larger ones (> 0.5 mm). During the day, the pattern was reversed, and the quantity of PM > 0.5 mm decreased. During the study period, the standing stock of PM (60-800 m) decreased from 7.5 to less than 2gm(-2) but the diel variations persisted, except for two short periods in the superficial layer following a wind event. The cyclic feeding activity induced by the diel vertical migration of zooplankton could be the best candidate to explain the observed diel fluctuations in the size classes of PM in the water column. However, our results also suggest that in the upper layer additional driving forces such as the increase of the level of turbulence after a wind event or the modification of the zoo- and phytoplankton community can influence the PM temporal evolution. (C) 2000 Elsevier Science Ltd. All rights reserved.

The Underwater Video Profiler is a vertically deployed survey system designed for the quantification of particles >280 mu m and of large zooplankton in the 0-1000 m water column. Light reflected by undisturbed target objects forms a dark-field image, which is recorded at 25 Hz frequency. The recorded images are automatically digitized and analysed. The results are expressed as abundance or size distributions and they can be converted to volume or mass units. The system can be configured as a multi-instrument array and can simultaneously acquire biological and physical data. From May 1994 to April 1995 a monthly survey was performed across a frontal structure associated to the North Ligurian geostrophic current. In winter and spring 1995 the front, as well as the offshore dispersion limit of particles, were located near to the coast. In contrast, during autumn 1994, its position was open sea and the terrestrial matter was dispersed far from the coast. The continuous presence of intermediate nepheloid layers along the continental slope indicates that different processes may supply and transport the particulate matter to deeper layers, from where it can be diffused into the basin. (C) 2000 Academic Press.