Particles sinking from the surface to the deep ocean play a key role in the biological carbon pump, whose efficiency depends partly on sinking velocities. Over the last decade, in situ imaging has enabled critical advances in our understanding of particle dynamics in the ocean. Yet, in situ velocity measurements are scarce and often inferred only from the bulk population of particles. Here, we introduce the VisuTrap, a new tool to measure in situ velocities of marine particles. It consists of an Underwater Vision Profiler 6 (UVP6) camera inserted into different types of sediment traps, which isolate a volume of water. Continuous image acquisition during shortterm or long-term deployments enables reconstruction of particle tracks and estimation of their in situ vertical velocities. We detail the configuration and special UVP6 settings for this application, as well as the image processing and track analysis pipeline. Then, we present results from several experiments in the Mediterranean Sea to illustrate the VisuTrap's use as a new approach to understand the dynamical behavior of marine particles in situ. In light of the broad range of morphological data generated by the UVP6, we discuss technical additions to refine in situ velocity measurements and the possibility of integrating such data into carbon flux assessments.

The Northwestern Mediterranean Sea is undergoing rapid environmental changes driven by climate variability and intense anthropogenic pressure. To monitor and understand the long-term impacts on marine ecosystems, the Mediterranean Ocean Observing System for the Environment (MOOSE) program combines multidisciplinary observations, including physical, chemical, and biological data across temporal and spatial scales. This study presents a holistic assessment of planktonic communities across the Northwestern Mediterranean using integrated approaches—environmental genomics and high-resolution imaging—spanning all plankton size fractions and depths. Data collected during three MOOSE-GE cruises in 2017, 2018, and 2019 were analyzed to explore plankton diversity patterns in relation to oceanographic features. Plankton assemblages were primarily shaped by organism size and water column depth, with fractions of 0.2–3 and 3–180 µm in the surface and deep chlorophyll maximum layers showing the highest alpha diversity. Fractions > 64 µm were dominated by metazoans, particularly Arthropoda, whereas size classes collected by Niskin bottles were dominated by protists such as Syndiniales and Rhizaria. Differences among cruises and sampling periods were detected in Niskin bottle samples, especially for diatoms and dinoflagellates, while plankton tow samples exhibited less pronounced temporal variability. Physical clustering of stations revealed clear cross-shelf and basin-scale gradients, which aligned more closely with community structure at fine taxonomic resolution (OTU level) for small plankton. Integrating imaging with environmental genomic data enhanced the characterization of key taxa like Copepoda and Rhizaria, demonstrating the complementary strengths of each method. While imaging provided quantitative data, environmental genomics captured cryptic and morphologically indistinct taxa, emphasizing the value of molecular approaches for microbial plankton. This study highlights the critical importance of combining high-resolution molecular and imaging tools with detailed environmental context to unravel plankton biodiversity patterns. It demonstrates that depth, size, and taxonomic resolution are key dimensions for understanding community structure over time. The MOOSE program proves effective for ecosystem-scale monitoring, providing an essential foundation for future assessments of biogeochemical processes and ecosystem responses to climate change and human-induced alterations in the Mediterranean Sea.

<div><p>Climatic changes in the physical environment modulate biogeochemical cycles, biodiversity, and trophic interactions in the Central Arctic Ocean (CAO). Physical processes and sea-ice conditions are highly seasonal in the CAO and dependent on interactions that occur throughout the evolution of the upper ocean-sea ice-lower atmosphere system. Understanding these seasonal interactions is critical to comprehending and predicting the long-term trends as the CAO moves towards ice-free summers and to informing future policy decisions at the core of ongoing discussions concerning the CAO Fisheries agreement, e.g., at the Arctic Council and International Council for Exploration of the Sea working group on the CAO. Here, we review current knowledge of the physical environment, biogeochemical cycles, and biodiversity in the waters of the CAO, identify emerging research questions, and introduce the science plan for the first Tara Polaris drift onboard the Tara Polar Station to advance knowledge and address these questions. Despite increased observational programs in the CAO over the past years, e.g., the Nansen and Amundsen Basin Observational System (NABOS) and Multidisciplinary drifting Observatory for the Study of Arctic Climate (MOSAiC), extensive knowledge gaps remain in relation to ocean stratification, sea ice and lightscape, nitrogen fixation and nutrient fluxes, carbon export and transfer, sympagic-pelagic coupling, aerosol production, contaminant transport and transformation, chronobiology, and fish distribution. Further knowledge on overall CAO biodiversity, ecosystem functionality and interannual variability is also critically needed.</p><p>We describe a way forward to address these knowledge gaps using ice-tethered and profiling instruments coupled with multi-omics, culturing, and imagery approaches deployed from Tara Polar Station during the first of ten Tara Polaris drifts designed to facilitate detection of interannual variability and change over time.</p></div>

The mesopelagic zone, between 100 and 1000 meters depth, is a crucial layer, in which carbon preliminary coming down from the surface is transformed before a portion makes it into the deep ocean. While eddies and their fronts influence surface productivity and carbon export, their effects deeper in the water column remain poorly understood. Here we show the importance and contribution of dark carbon fixation—the conversion of inorganic into organic carbon by prokaryotes—across five contrasting hydrological features in the North Atlantic, using isotopic tracers and quantification of chemoautotrophy genes. The approach allows simultaneous assessment of dark carbon fixation and heterotrophic activity of prokaryotes living suspended in seawater and attached to gravitationally settling particles. Our results highlight that heterotrophic prokaryotes attached to sinking particles contribute up to 21% of the total organic carbon required to sustain prokaryotic metabolism under the influence of eddy fronts. In contrast, dark carbon fixation by suspended prokaryotes can contribute up to half of the total carbon input to the mesopelagic zone in the cyclonic eddy. Our findings challenge the idea that carbon cycling in the mid-depth ocean is uniform, and highlight the need to integrate microbial fractions and physical heterogeneity into ocean carbon models

The oceans buffer against climate change via biogeochemical cycles underpinned by microbial metabolic activities. While planetary-scale surveys provide baseline microbiome data, inferring metabolic and biogeochemical impacts remains challenging. Here, we constructed a model for each TARA Ocean metagenome or metatranscriptome representing heterotrophic prokaryotes and their viruses and assessed these as community-wide metabolic phenotypes. To validate, we showed that even with reaction-mappable genes only (∼1/4 of the total genes), the composition of these models revealed metabolism-inferred ecological zones that matched taxonomy-inferred zones. Model inferences include providing a new metric of community-wide metabolic cooperation and new insights into connections between microbial metabolism and organism diversity, and the ecological role of viruses. The latter suggests they genomically target community-critical metabolic reactions and estimates where viruses remineralize versus sink carbon. While this new constraints-based, agile, and mechanistic modeling framework is highly upgradable, it already begins to convert molecular-scale environmental omics data to ecological and even planetary-scale biogeochemical features that will better bring microbes and their viruses into earth system and climate models.

<div><p>While a rich history of patchiness research has explored spatial structure in the ocean, there is no consensus over the controls on biological patchiness and how physical-ecological-biogeochemical processes and patchiness relate. The prevailing thought is that physics structures biology, but this has not been tested at basin scale with consistent in situ measurements. Here we use the slope of the relationship between variance vs spatial scale to quantify patchiness and ~650,000 nearly continuous (dx ~200 m) measurements -representing the Atlantic, Pacific, and Southern Oceans -and find that patchiness of biological parameters and physical parameters are uncorrelated. We show variance slope is an emergent property with unique patterns in biogeochemical properties distinct from physical tracers, yet correlated with other biological tracers. These results provide context for decades of observations with different interpretations, suggest the use of spatial tests of biogeochemical model parameterizations, and open the way for studies into processes regulating the observed patterns.</p></div>

Earth system models (ESMs) highly simplify their representation of biological processes, leading to major uncertainty in the impacts of climate change. Despite a growing understanding of molecular networks from genomic data, describing how changing phytoplankton physiology affects biogeochemical processes remains elusive. Here, we embed genome-scale models within a state-of-the-art ESM to deliver an integrated understanding of how gradients of nutrients modulate the molecular physiology of various plankton. In particular, when applied to Prochlorococcus , we find that glycogen and lipid management can be interpreted in terms of acclimation to different environments. Generalized to other phytoplankton such as the diatom Thalassiosira , we estimate the production of 39 metabolites that constitute hot spots of dissolved organic carbon described by their amount of carbon produced and their diversity of associated metabolites in ESMs. This modeling approach shows how genome scale–enabled ESMs have the potential to advance our understanding of microbial ecosystem functioning in ocean biogeochemical processes.

Life history traits influence marine species dispersal and habitat colonization. Medusozoans (jellyfish and siphonophores) exhibit diverse life cycles, evolved from an ancestral cycle alternating between a benthic polyp and a pelagic medusa. Despite their ecological importance, factors shaping medusozoan distribution remain poorly understood. By integrating metabarcoding and environmental data from the Tara Oceans expedition with life history traits, we provide global evidence supporting the longstanding hypothesis that benthic polyp presence/absence is a key factor influencing the distribution and abundance of planktonic medusozoans in the surface ocean. We inferred on a time-calibrated phylogeny of Medusozoa multiple transitions to a fully planktonic (holoplanktonic) life cycle, either through polyp loss, acquisition of drifting polyps, or development of polyps parasitizing pelagic organisms. We could associate each transition with a shift toward offshore habitats and the emergence of globally dominant Operational Taxonomic Units (OTUs), whose abundance far exceeds that of any nonholoplanktonic medusozoans in the planktonic realm. The prevalence of holoplanktonic medusozoans in terms of abundance and diversity is broadly observed in coastal and offshore environments, peaking over greater bathymetric depths in tropical and subtropical regions. We show that holoplanktonic and nonholoplanktonic groups interact with distinct yet compositionally similar planktonic communities. Holoplanktonic OTUs occupy more peripheral positions in a plankton interactome, suggesting greater flexibility in biotic interactions, an adaptive trait in rapidly changing planktonic ecosystems. These findings highlight how life cycle evolution shaped the global distribution of medusozoans and suggest that variations in life history may significantly influence how medusozoans respond to global environmental changes.

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. 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.

Phytoplankton produce organic matter in the sunlit upper ocean, which forms particles of “marine snow” that sink and transfer carbon from the surface to the deep ocean. These particles sustain a vast carbon reservoir and are consumed to provide energy to ecosystems in the deep sea (1). Deciphering what controls carbon transfer by marine snow has been a central question in oceanography since the 1980s. However, the formation, sinking, and consumption of this particulate matter involve many physical, chemical, and biological processes. Thus, the overall impact of sinking particles on the ocean’s carbon cycle remains highly uncertain and poorly understood (2). On page 166 of this issue, Chajwa et al. (3) report mucus “comet tails” of marine snow that substantially affect the sinking speed and transfer of carbon in the upper ocean. These observations provide new insights into how the composition of marine particles alters ocean ecology and biogeochemistry.

Carbon fixation is a key metabolic function shaping marine life, but the underlying taxonomic and functional diversity involved is only partially understood. Using metagenomic resources targeted at marine piconanoplankton, we provide a reproducible machine learning framework to derive the potential biogeography of genomic functions through the multi-output regression of gene read counts on environmental climatologies. Leveraging the Marine Atlas of Tara Oceans Unigenes, we investigate the genomic potential of primary production in the global ocean. The latter is performed by ribulose-1,5-bisphosphate carboxylase/oxygenase (RUBISCO) and is often associated with carbon concentration mechanisms in piconanoplankton, major marine unicellular photosynthetic organisms. We show that the genomic potential supporting C 4 enzymes and RUBISCO exhibits strong functional redundancy and important affinity toward tropical oligotrophic waters. This redundancy is taxonomically structured by the dominance of Mamiellophyceae and Prymnesiophyceae in mid and high latitudes. These findings enhance our understanding of the relationship between functional and taxonomic diversity of microorganisms and environmental drivers of key biogeochemical cycles.

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.

The TechOceanS project is developing new remote ocean sensing technology supporting wider ocean measurement and a drive to net zero. The project will deliver 5 new sensor classes for biogeochemistry, biology and ecosystems addressing 10 of 19 EOVs, 31 of 73 subvariables, 6 of 9 MSFD targets together with microplastics and a range of biotoxins and contaminants. It will also develop a new image processing workflow for extracting EOVs (9) and MSFD (6) and litter measurements from images. These innovations concentrate on key capability gaps in ocean observing from non-ship systems with a focus on low-cost per measurement through minimised instrument and deployment costs. This paper gives a brief overview of the technologies, and were possible, because of progress or protection of intellectual property, details of our approaches and early results.

Abstract Primary production, performed by RUBISCO, and often associated with carbon concentration mechanisms, is of major importance in the oceans. Thanks to growing metagenomic resources (e.g., eukaryotic Metagenome-Assembled-Genomes; MAGs), we provide the first reproducible machine-learning-based framework to derive the potential biogeography of a given function, through the multi-output regression of the standardized number of reads of the associated genes on environmental climatologies. We use it to study the genomic potential of C4-photosynthesis of picoeukaryotes, a diverse and abundant group of marine unicellular photosynthetic organisms. We show that the genomic potential supporting C4-enzymes and RUBISCO exhibit strong functional redundancy and an important affinity towards tropical oligotrophic waters. This redundancy is then structured taxonomically by the dominance of Mamiellophyceae and Prymnesiophyceae in mid and high latitudes. Finally, unlike the genomic potential related to most C4-enzymes, the one of RUBISCO showed a clear pattern affinity for temperate waters.

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.

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.

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.

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.

Earth System Models (ESMs) highly simplify their representation of biological processes, leading to major uncertainty in climate change impacts. Despite a growing understanding of molecular networks from genomic data, describing how changing phytoplankton physiology affects the production of key metabolites remains elusive. Here we embed a genome-scale model within a state-of-the-art ESM to deliver an integrated understanding of how gradients of nutritional constraints modulate metabolic reactions and molecular physiology. Applied to the prevalent marine cyanobacteria Prochlorococcus , we find that glycogen and lipid storage can be understood as a consequence of acclimation to environmental gradients. Given the pressing need to assess how biological diversity influences biogeochemical functions, genome-enabled ESMs allow the quantification of the contribution of modeled organisms to the production of dissolved organic carbon and its molecular composition.

In marine environments, life cycle strategies strongly impact species dispersal and their ability to colonize new habitats. Pelagic medusozoans (jellyfish and siphonophores) exhibit various reproductive strategies, variations of meroplanktonic and holoplanktonic life cycles. In the ancestral meroplanktonic life cycle, a benthic polyp stage alternates with a pelagic medusa stage. During the course of evolution, some medusozoans lost their benthic stage, leading to a holoplanktonic life cycle. The ecological consequences of these losses have not been addressed at global scale. Here, integrating metabarcoding and environmental data from Tara Oceans into a phylogenetic framework, we show that each convergent transition toward a holoplanktonic life cycle is associated with a more offshore distribution compared to meroplanktonic medusozoans. Our analyses showed that holoplanktonic medusozoans are more globally distributed and relatively more abundant than meroplanktonic medusozoans, although they are less diversified and occupy a more peripheral position in a global plankton community interactome. This suggests that holoplanktonic medusozoans have acquired a greater tolerance to biotic and abiotic conditions. Overall, our results demonstrate the relationship between medusozoan life cycles, distribution, and biotic interactions, suggesting that the loss of the benthic stage promoted colonization of the open ocean.

The ocean contains about 40 times more carbon than the atmosphere, storing 38,000 Pg C as dissolved inorganic carbon (DIC) versus 900 Pg C as carbon dioxide (CO$_2$) in the present atmosphere. The biological carbon pump contributes to ocean carbon storage by moving organic carbon out of the surface ocean into deeper waters in sinking particles, vertically migrating organisms and physical circulation. Century-scale (≥100 years) storage of the resulting biogenic DIC is commonly assumed to occur exclusively in the deep ocean, typically below 1,000 m. However, recent work has shown that carbon can be sequestered at century scales above 1,000 m in many ocean regions, in what we call ‘continuous vertical sequestration’. Here we calculate the century-scale carbon sequestration flux driven by the biological pump throughout the water column by combining previously published estimates of organic carbon flux and modelled values of water-mass sequestration time distributions. We estimate that the flux of organic carbon that is sequestered for ≥100 years in the contemporary ocean by the combined action of various biological pump pathways is 0.9–2.6 Pg C yr$^{−1}$, which is up to six times larger than previous estimates based on the organic carbon flux reaching the deep ocean.

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.

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.

For more than a decade, high-throughput sequencing has transformed the study of marine planktonic communities and has highlighted the extent of protist diversity in these ecosystems. Nevertheless, little is known relative to their genomic diversity at the species-scale as well as their major speciation mechanisms. An increasing number of data obtained from global scale sampling campaigns is becoming publicly available, and we postulate that metagenomic data could contribute to deciphering the processes shaping protist genomic differentiation in the marine realm. As a proof of concept, we developed a findable, accessible, interoperable and reusable (FAIR) pipeline and focused on the Mediterranean Sea to study three a priori abundant protist species: Bathycoccus prasinos, Pelagomonas calceolata and Phaeocystis cordata. We compared the genomic differentiation of each species in light of geographic, environmental and oceanographic distances. We highlighted that isolation-byenvironment shapes the genomic differentiation of B. prasinos, whereas P. cordata is impacted by geographic distance (i.e. isolation-by-distance). At present time, the use of metagenomics to accurately estimate the genomic differentiation of protists remains challenging since coverages are lower compared to traditional population surveys. However, our approach sheds light on ecological and evolutionary processes occurring within natural marine populations and paves the way for future protist population metagenomic studies.

DNA viruses are increasingly recognized as influencing marine microbes and microbe-mediated biogeochemical cycling. However, little is known about global marine RNA virus diversity, ecology, and ecosystem roles. In this study, we uncover patterns and predictors of marine RNA virus community- and “species”-level diversity and contextualize their ecological impacts from pole to pole. Our analyses revealed four ecological zones, latitudinal and depth diversity patterns, and environmental correlates for RNA viruses. Our findings only partially parallel those of cosampled plankton and show unexpectedly high polar ecological interactions. The influence of RNA viruses on ecosystems appears to be large, as predicted hosts are ecologically important. Moreover, the occurrence of auxiliary metabolic genes indicates that RNA viruses cause reprogramming of diverse host metabolisms, including photosynthesis and carbon cycling, and that RNA virus abundances predict ocean carbon export.

Siliceous Rhizaria (polycystine radiolarians and phaeodarians) are significant contributors to carbon and silicon biogeochemical cycles. Considering their broad taxonomic diversity and their wide size range (from a few micrometres up to several millimetres), a comprehensive evaluation of the entire community to carbon and silicon cycles is challenging. Here, we assess the diversity and contribution of silicified Rhizaria to the global biogenic silica stocks in the upper 500 m of the oligotrophic North-Western Mediterranean Sea using both imaging (FlowCAM, Zooscan and Underwater Vision Profiler) and molecular tools and data. While imaging data (cells m -3 ) revealed that the most abundant organisms were the smallest, molecular results (number of reads) showed that the largest Rhizaria had the highest relative abundances. While this seems contradictory, relative abundance data obtained with molecular methods appear to be closer to the total biovolume data than to the total abundance data of the organisms. This result reflects a potential link between gene copies number and the volume of a given cell allowing reconciling molecular and imaging data. Using abundance data from imaging methods we estimate that siliceous Rhizaria accounted for up to 6% of the total biogenic silica biomass of the siliceous planktonic community in the upper 500m of the water column.

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.

Remote deep-ocean sediment (DOS) ecosystems are among the least explored biomes on Earth. Genomic assessments of their biodiversity have failed to separate indigenous benthic organisms from sinking plankton. Here, we compare global-scale eukaryotic DNA metabarcoding datasets (18 S -V9) from abyssal and lower bathyal surficial sediments and euphotic and aphotic ocean pelagic layers to distinguish plankton from benthic diversity in sediment material. Based on 1685 samples collected throughout the world ocean, we show that DOS diversity is at least threefold that in pelagic realms, with nearly two-thirds represented by abundant yet unknown eukaryotes. These benthic communities are spatially structured by ocean basins and particulate organic carbon (POC) flux from the upper ocean. Plankton DNA reaching the DOS originates from abundant species, with maximal deposition at high latitudes. Its seafloor DNA signature predicts variations in POC export from the surface and reveals previously overlooked taxa that may drive the biological carbon pump.

Functional traits are increasingly used to assess changes in phytoplankton community structure and to link individual characteristics to ecosystem functioning. However, they are usually inferred from taxonomic identification or manually measured for each organism, both time consuming approaches. Instead, we focus on high throughput imaging to describe the main temporal variations of morphological changes of phytoplankton in Narragansett Bay, a coastal time-series station. We analyzed a 2-yr dataset of morphological features automatically extracted from continuous imaging of individual phytoplankton images (~ 105 million images collected by an Imaging FlowCytobot). We identified synthetic morphological traits using multivariate analysis and revealed that morphological variations were mainly due to changes in length, width, shape regularity, and chain structure. Morphological changes were especially important in winter with successive peaks of larger cells with increasing complexity and chains more clearly connected. Small nanophytoplankton were present year-round and constituted the base of the community, especially apparent during the transitions between diatom blooms. High inter-annual variability was also observed. On a weekly timescale, increases in light were associated with more clearly connected chains while more complex shapes occurred at lower nitrogen concentrations. On an hourly timescale, temperature was the determinant variable constraining cell morphology, with a general negative influence on length and a positive one on width, shape regularity, and chain structure. These first insights into the phytoplankton morphology of Narragansett Bay highlight the possible morphological traits driving the phytoplankton succession in response to light, temperature, and nutrient changes.

The Southwest Atlantic Ocean (SWAO) is a spatially dynamic region with a remarkably high primary productivity. An exhaustive identification of the members of its phytoplankton community is a key step to understand the processes that sustain this ecosystem. Here, we provide a community composition analysis of eukaryotic phytoplankton in four SWAO sectors. We gathered 18S rRNA gene metabarcoding data and complemented it with confocal microscopy images, both from the TaraOceans expedition in late spring 2010. Our work showed local and regional variation across three different size fractions that reflect the complexity of this region. Diversity decreased along temperature and latitudinal gradients, but also showed intricate paterns of occurrences across samples, suggesting that multiple factors shape the community structure. Samples resembled communities from other temperate regions and showed an increasing influence by cold waters from the Southern Ocean towards higher latitudes. These results complement previous regional studies that used other methods such as microscopy or pigment analysis. Our study contributes to the beginning of genomic-based surveys of plankton communities in the SW Atlantic and calls for further work in the region to enhance ecosystem monitoring and projections in the context of global 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.

Biogeographical studies have traditionally focused on readily visible organisms, but recent technological advances are enabling analyses of the large-scale distribution of microscopic organisms, whose biogeographical patterns have long been debated1,2. The most prominent global biogeography of marine plankton was derived by Longhurst3 based on parameters principally associated with photosynthetic plankton. Localized studies of selected plankton taxa or specific organismal sizes1,4–7 have mapped community structure and begun to assess the roles of environment and ocean current transport in shaping these patterns2,8. Here we assess global plankton biogeography and its relation to the biological, chemical and physical context of the ocean (the ‘seascape’) by analyzing 24 terabases of metagenomic sequence data and 739 million metabarcodes from the Tara Oceans expedition in light of environmental data and simulated ocean current transport. In addition to significant local heterogeneity, viral, prokaryotic and eukaryotic plankton communities all display near steady-state, large-scale, size-dependent biogeographical patterns. Correlation analyses between plankto transport time and metagenomic or environmental dissimilarity reveal the existence of basin-scale biological and environmental continua emerging within the main current systems. Across oceans, there is a measurable, continuous change within communities and environmental factors up to an average of 1.5 years of travel time. Modulation of plankton communities during transport varies with organismal size, such that the distribution of smaller plankton best matches Longhurst biogeochemical provinces, whereas larger plankton group into larger provinces. Together these findings provide an integrated framework to interpret plankton community organization in its physico-chemical context, paving the way to a better understanding of oceanic ecosystem functioning in a changing global environment.

In the last decades, the Arctic Ocean has been affected by climate change, leading to alterations in the sea ice cover that influence the phytoplankton spring bloom, its associated food web, and therefore carbon sequestration. During the Green Edge 2016 expedition in the central Baffin Bay, the phytoplankton spring bloom and its development around the ice edge was followed along 7 transects from open water to the ice-pack interior. Here, we studied some of the processes driving phytoplankton aggregation, using aggregate and copepod distribution profiles obtained with an underwater vision profiler deployed at several stations along the transects. Our results revealed a sequential pattern during sea ice retreat in phytoplankton production and in aggregate production and distribution. First, under sea ice, phytoplankton started to grow, but aggregates were not formed. Second, after sea ice melting, phytoplankton (diatoms and Phaeocystis spp. as the dominant groups) benefited from the light availability and stratified environment to bloom, and aggregation began coincident with nutrient depletion at the surface. Third, maxima of phytoplankton aggregates deepened in the water column and phytoplankton cells at the surface began to degrade. At most stations, silicate limitation began first, triggering aggregation of the phytoplankton cells; nitrate limitation came later. Copepods followed aggregates at the end of the phytoplankton bloom, possibly because aggregates provided higher quality food than senescing phytoplankton cells at the surface. These observations suggest that aggregation is involved in 2 export pathways constituting the biological pump: the gravitational pathway through the sinking of aggregates and fecal pellets and the migration pathway when zooplankton follow aggregates during food foraging.

Stratified oceanic systems are characterized by the presence of a so-called Deep Chlorophyll a Maximum (DCM) not detectable by ocean color satellites. A DCM can either be a phytoplankton (carbon) biomass maximum (Deep Biomass Maximum, DBM), or the consequence of photoacclimation processes (Deep photoAcclimation Maximum, DAM) resulting in the increase of chlorophyll a per phytoplankton carbon. Even though these DCM (further qualified as either DBMs or DAMs) have long been studied, no global-scale assessment has yet been undertaken and large knowledge gaps still remain in relation to the environmental drivers responsible for their formation and maintenance. In order to investigate their spatial and temporal variability in the open ocean, we use a global data set acquired by more than 500 Biogeochemical-Argo floats given that DCMs can be detected from the comparative vertical distribution of chlorophyll a concentrations and particulate backscattering coefficients. Our findings show that the seasonal dynamics of the DCMs are clearly region-dependent. High-latitude environments are characterized by a low occurrence of intense DBMs, restricted to summer. Meanwhile, oligotrophic regions host permanent DAMs, occasionally replaced by DBMs in summer, while subequatorial waters are characterized by permanent DBMs benefiting from favorable conditions in terms of both light and nutrients. Overall, the appearance and depth of DCMs are primarily driven by light attenuation in the upper layer. Our present assessment of DCM occurrence and of environmental conditions prevailing in their development lay the basis for a better understanding and quantification of their role in carbon budgets (primary production and export).

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.

The biological carbon pump, in which carbon fixed by photosynthesis is exported to the deep ocean through sinking, is a major process in Earth's carbon cycle. The proportion of primary production that is exported is termed the carbon export efficiency (CEE). Based on in-lab or regional scale observations, viruses were previously suggested to affect the CEE (i.e., viral “shunt” and “shuttle”). In this study, we tested associations between viral community composition and CEE measured at a global scale. A regression model based on relative abundance of viral marker genes explained 67% of the variation in CEE. Viruses with high importance in the model were predicted to infect ecologically important hosts. These results are consistent with the view that the viral shunt and shuttle functions at a large scale and further imply that viruses likely act in this process in a way dependent on their hosts and ecosystem dynamics.

The goal of the EXport Processes in the Ocean from RemoTe Sensing (EXPORTS) field campaign is to develop a predictive understanding of the export, fate, and carbon cycle impacts of global ocean net primary production. To accomplish this goal, observations of export flux pathways, plankton community composition, food web processes, and optical, physical, and biogeochemical (BGC) properties are needed over a range of ecosystem states. Here we introduce the first EXPORTS field deployment to Ocean Station Papa in the Northeast Pacific Ocean during summer of 2018, providing context for other papers in this special collection. The experiment was conducted with two ships: a Process Ship, focused on ecological rates, BGC fluxes, temporal changes in food web, and BGC and optical properties, that followed an instrumented Lagrangian float; and a Survey Ship that sampled BGC and optical properties in spatial patterns around the Process Ship. An array of autonomous underwater assets provided measurements over a range of spatial and temporal scales, and partnering programs and remote sensing observations provided additional observational context. The oceanographic setting was typical of late-summer conditions at Ocean Station Papa: a shallow mixed layer, strong vertical and weak horizontal gradients in hydrographic properties, sluggish sub-inertial currents, elevated macronutrient concentrations and low phytoplankton abundances. Although nutrient concentrations were consistent with previous observations, mixed layer chlorophyll was lower than typically observed, resulting in a deeper euphotic zone. Analyses of surface layer temperature and salinity found three distinct surface water types, allowing for diagnosis of whether observed changes were spatial or temporal. The 2018 EXPORTS field deployment is among the most comprehensive biological pump studies ever conducted. A second deployment to the North Atlantic Ocean occurred in spring 2021, which will be followed by focused work on data synthesis and modeling using the entire EXPORTS data set.

Optical particle measurements are emerging as an important technique for understanding the ocean carbon cycle, including contributions to estimates of their downward flux, which sequesters carbon dioxide (CO2) in the deep sea. Optical instruments can be used from ships or installed on autonomous platforms, delivering much greater spatial and temporal coverage of particles in the mesopelagic zone of the ocean than traditional techniques, such as sediment traps. Technologies to image particles have advanced greatly over the last two decades, but the quantitative translation of these immense datasets into biogeochemical properties remains a challenge. In particular, advances are needed to enable the optimal translation of imaged objects into carbon content and sinking velocities. In addition, different devices often measure different optical properties, leading to difficulties in comparing results. Here we provide a practical overview of the challenges and potential of using these instruments, as a step toward improvement and expansion of their applications.

While Ocean modeling has made significant advances over the last decade, its complex biological component is still oversimplified. In particular, modeling organisms in the ocean system must integrate parameters to fit both physiological and ecological behaviors that are together very difficult to determine. Such difficulty occurs for modeling Pelagia noctiluca. This jellyfish has a high abundance in the Mediterranean Sea and could contribute to several biogeochemical processes. However, gelatinous zooplanktons remain poorly represented in biogeochemical models because uncertainties about their ecophysiology limit our understanding of their potential role and impact. To overcome this issue, we propose, for the first time, the use of the Statistical Model Checking Engine (SMCE), a probabilitybased computational framework that considers a set of parameters as a whole. Contrary to standard parameter inference techniques, SMCE identifies sets of parameters that fit both laboratory-culturing observations and in situ patterns while considering uncertainties. Doing so, we estimated the best parameter sets of the ecophysiological model that represents the jellyfish growth and degrowth in laboratory conditions as well as its size. Behind this application, SMCE remains a computational framework that supports the projection of a model with uncertainties in broader contexts such as biogeochemical processes to drive future studies.

Phytoplankton diversity is essential to understand the dynamics of marine ecosystems, global biogeochemical cycles and impacts of climate change. However, changes in phytoplankton communities are complex and occur at different time scales, from daily to decadal, thus making our understanding of the environmental processes driving them more difficult. Here, we focus on the morphological diversity; the individual morphological characteristics influencing the evolutionary success of organisms and the functioning of ecosystems, regardless of their taxonomic classification. We use high-resolution phytoplankton imagery generated by an Imaging FlowCytobot deployed in Narragansett Bay, United States, to detect the main morphological features of the local phytoplankton community, along with their seasonality and periodicities. We show that morphological analysis can uncover successions of communities and demonstrate significant changes with a 27.5 day and 24-hour periodicity related to the moon apogee-perigee cycle and the diel cycle. Building on these results we aim at linking morphology and taxonomy with multispectral backscattering, hyperspectral absorption and attenuation signals also coincidently recorded, moving towards the development of algorithms to retrieve phytoplankton groups from hyperspectral satellite data.

The European Marine Board is an independent and self-sustaining science policy interface organisation that currently represents 34 Member Organizations from 18 European countries. It was established in 1995 to facilitate enhanced cooperation between European marine science organizations towards the development of a common vision on the strategic research priorities for marine science in Europe. The EMB promotes and supports knowledge transfer for improved leadership in European marine research. Its membership includes major national marine or oceanographic institutes, research funding agencies and national consortia of universities with a strong marine research focus. Adopting a strategic role, the European Marine Board serves its member organizations by providing a forum within which marine research policy advice is developed and conveyed to national agencies and to the European Commission, with the objective of promoting the need for, and quality of, European marine research.

Due to its particular characteristics, the Mediterranean Sea is often viewed as a microcosm of the World Ocean. Its proportionally-reduced dimensions and peculiar hydrological circulation render it susceptible to environmental and climatic constraints, which are rapidly evolving. The Mediterranean is therefore an ideal site to examine, in order to better understand a number of key oceanographic phenomena. This is especially true of the Ligurian Sea where, due to its geology, oceanic conditions are found close to the coast. As such, 30 years ago, an offshore time-series site provided a fresh impetus to a long history of marine biology research, which has generated a very important body of data and knowledge. This is the second volume, in a two-volume series, that summarizes this research. Across these two books, the reader will find 13 chapters that examine the geology, physics, chemistry and biology of the Ligurian Sea ? always with the goal of providing key elements of oceanography in a changing world.

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.

Many coastal areas host rich marine ecosystems and are also centers of economic activities, including fishing, shipping and recreation. Due to the socioeconomic and ecological importance of these areas, predicting relevant indicators of the ecosystem state on sub-seasonal to interannual timescales is gaining increasing attention. Depending on the application, forecasts may be sought for variables and indicators spanning physics (e.g., sea level, temperature, currents), chemistry (e.g., nutrients, oxygen, pH), and biology (from viruses to top predators). Many components of the marine ecosystem are known to be influenced by leading modes of climate variability, which provide a physical basis for predictability. However, prediction capabilities remain limited by the lack of a clear understanding of the physical and biological processes involved, as well as by insufficient observations for forecast initialization and verification. The situation is further complicated by the influence of climate change on ocean conditions along coastal areas, including sea level rise, increased stratification, and shoaling of oxygen minimum zones. Observations are thus vital to all aspects of marine forecasting: statistical and/or dynamical model development, forecast initialization, and forecast validation, each of which has different observational requirements, which may be also specific to the study region. Here, we use examples from United States (U.S.) coastal applications to identify and describe the key requirements for an observational network that is needed to facilitate improved process understanding, as well as for sustaining operational ecosystem forecasting. We also describe new holistic observational approaches, e.g., approaches based on acoustics, inspired by Tara Oceans or by landscape ecology, which have the potential to support and expand ecosystem modeling and forecasting activities by bridging global and local observations.

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.

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.

Investigating Particle Size-Flux Relationships that the particle size-flux relationships may be different within the euphotic zone than in the shallow twilight zone and hypothesize that the changing nature of sinking particles with depth must be considered when investigating the remineralization length scale of sinking particles in the ocean.

Diatoms sustain the marine food web and contribute to the export of carbon from the surface ocean to depth. They account for about 40% of marine primary productivity and particulate carbon exported to depth as part of the biological pump. Diatoms have long been known to be abundant in turbulent, nutrient-rich waters, but observations and simulations indicate that they are dominant also in meso- and submesoscale structures such as fronts and filaments, and in the deep chlorophyll maximum. Diatoms vary widely in size, morphology and elemental composition, all of which control the quality, quantity and sinking speed of biogenic matter to depth. In particular, their silica shells provide ballast to marine snow and faecal pellets, and can help transport carbon to both the mesopelagic layer and deep ocean. Herein we show that the extent to which diatoms contribute to the export of carbon varies by diatom type, with carbon transfer modulated by the Si/C ratio of diatom cells, the thickness of the shells and their life strategies; for instance, the tendency to form aggregates or resting spores. Model simulations project a decline in the contribution of diatoms to primary production everywhere outside of the Southern Ocean. We argue that we need to understand changes in diatom diversity, life cycle and plankton interactions in a warmer and more acidic ocean in much more detail to fully assess any changes in their contribution to the biological pump.

We assessed the influence of the marine dia-zotrophic cyanobacterium Trichodesmium on the bio-optical properties of western tropical South Pacific (WTSP) waters (18–22 • S, 160 • E–160 • W) during the February–March 2015 OUTPACE cruise. We performed measurements of backscattering and absorption coefficients, irradiance, and radiance in the euphotic zone with a Satlantic MicroPro free-fall profiler and took Underwater Vision Profiler 5 (UPV5) pictures for counting the largest Trichodesmium spp. colonies. Pigment concentrations were determined by fluorimetry and high-performance liquid chromatography and picoplankton abundance by flow cytometry. Tri-chome concentration was estimated from pigment algorithms and validated by surface visual counts. The abundance of large colonies counted by the UVP5 (maximum 7093 colonies m −3) was well correlated to the trichome concentrations (maximum 2093 trichomes L −1) with an ag-gregation factor of 600. In the Melanesian archipelago, a maximum of 4715 trichomes L −1 was enumerated in pump samples (3.2 m) at 20 • S, 167 30 • E. High Trichodesmium abundance was always associated with absorption peaks of mycosporine-like amino acids (330, 360 nm) and high particulate backscattering, but not with high Chl a fluorescence or blue particulate absorption (440 nm). Along the west-to-east transect, Trichodesmium together with Prochlorococ-cus represented the major part of total chlorophyll concentration ; the contribution of other groups were relatively small or negligible. The Trichodesmium contribution to total chlorophyll concentration was the highest in the Melane-sian archipelago around New Caledonia and Vanuatu (60 %), progressively decreased to the vicinity of the islands of Fiji (30 %), and reached a minimum in the South Pacific Gyre where Prochlorococcus dominated chlorophyll concentration. The contribution of Trichodesmium to zeaxanthin was respectively 50, 40 and 20 % for these regions. During the OUTPACE cruise, the relationship between normalized water-leaving radiance (nL w) in the ultraviolet and visible and chlorophyll concentration was similar to that found during the BIOSOPE cruise in the eastern tropical Pacific. Principal component analysis (PCA) of OUTPACE data showed that nL w at 305, 325, 340, 380, 412 and 440 nm was strongly correlated to chlorophyll and zeaxanthin, while nL w at 490 Published by Copernicus Publications on behalf of the European Geosciences Union. 5250 C. Dupouy et al.: Trichodesmium impact on UV–Vis radiance and pigments and 565 nm exhibited lower correlations. These results, as well as differences in the PCA of BIOSOPE data, indicated that nL w variability in the greenish blue and yellowish green during OUTPACE was influenced by other variables associated with Trichodesmium presence, such as backscattering coefficient, phycoerythrin fluorescence and/or zeaxanthin absorption , suggesting that Trichodesmium detection should involve examination of nL w in this spectral domain.

While our knowledge about the roles of microbes and viruses in the ocean has increased tremendously due to recent advances in genomics and metagenomics, research on marine microbial eukaryotes and zooplankton has benefited much less from these new technologies because of their larger genomes, their enormous diversity, and largely unexplored physiologies. Here, we use a metatranscriptomics approach to capture expressed genes in open ocean Tara Oceans stations across four organismal size fractions. The individual sequence reads cluster into 116 million unigenes representing the largest reference collection of eukaryotic transcripts from any single biome. The catalog is used to unveil functions expressed by eukaryotic marine plankton, and to assess their functional biogeography. Almost half of the sequences have no similarity with known proteins, and a great number belong to new gene families with a restricted distribution in the ocean. Overall, the resource provides the foundations for exploring the roles of marine eukaryotes in ocean ecology and biogeochemistry.

Marine Synechococcus cyanobacteria are major contributors to global oceanic primary production and exhibit a unique diversity of photosynthetic pigments, allowing them to exploit a wide range of light niches. However, the relationship between pigment content and niche partitioning has remained largely undetermined due to the lack of a single-genetic marker resolving all pigment types (PTs). Here, we developed and employed a robust method based on three distinct marker genes (cpcBA, mpeBA, and mpeW) to estimate the relative abundance of all known Synechococcus PTs from metagenomes. Analysis of the Tara Oceans dataset allowed us to reveal the global distribution of Synechococcus PTs and to define their environmental niches. Green-light specialists (PT 3a) dominated in warm, green equatorial waters, whereas blue-light specialists (PT 3c) were particularly abundant in oligotrophic areas. Type IV chromatic acclimaters (CA4-A/B), which are able to dynamically modify their light absorption properties to maximally absorb green or blue light, were unexpectedly the most abundant PT in our dataset and predominated at depth and high latitudes. We also identified populations in which CA4 might be nonfunctional due to the lack of specific CA4 genes, notably in warm high-nutrient low-chlorophyll areas. Major ecotypes within clades I–IV and CRD1 were preferentially associated with a particular PT, while others exhibited a wide range of PTs. Altogether, this study provides important insights into the ecology of Synechococcus and highlights the complex interactions between vertical phylogeny, pigmentation, and environmental parameters that shape Synechococcus community structure and evolution.

With global climate change altering marine ecosystems, research on plankton ecology is likely to navigate uncharted seas. Yet, a staggering wealth of new plankton observations, integrated with recent advances in marine ecosystem modelling, may shed light on marine ecosystem structure and functioning. A EuroMarine foresight workshop on the “Impact of climate change on the distribution of plankton functional and phylogenetic diversity” (PlankDiv) identified five grand challenges for future plankton diversity and macroecology research: 1) What can we learn about plankton communities from the new wealth of high-throughput ‘omics’ data? 2) What is the link between plankton diversity and ecosystem function? 3) How can species distribution models be adapted to represent plankton biogeography? 4) How will plankton biogeography be altered due to anthropogenic climate change? and 5) Can a new unifying theory of macroecology be developed based on plankton ecology studies? In this review, we discuss potential future avenues to address these questions, and challenges that need to be tackled along the way.

The Gulf of Lions in the northwestern Mediterranean is one of the few sites around the world ocean exhibiting deep open‐ocean convection. Based on 6 year long (2009–2015) time series from a mooring in the convection region, shipborne measurements from repeated cruises, from 2012 to 2015, and glider measurements, we report evidence of bottom thick nepheloid layer formation, which is coincident with deep sediment resuspension induced by bottom‐reaching convection events. This bottom nepheloid layer, which presents a maximum thickness of more than 2000 m in the center of the convection region, probably results from the action of cyclonic eddies that are formed during the convection period and can persist within their core while they travel through the basin. The residence time of this bottom nepheloid layer appears to be less than a year. In situ measurements of suspended particle size further indicate that the bottom nepheloid layer is primarily composed of aggregates between 100 and 1000 µm in diameter, probably constituted of fine silts. Bottom‐reaching open ocean convection, as well as deep dense shelf water cascading that occurred concurrently some years, lead to recurring deep sediments resuspension episodes. They are key mechanisms that control the concentration and characteristics of the suspended particulate matter in the basin, and in turn affect the bathypelagic biological activity

During the SESAME EU FP6 project, all available particulate organic carbon (POC) data collected from drifting sediment trap and Underwater Vision Profiler deployments (INSU PROOF database, 1991–2011) were gathered in order to assess carbon export at the scale of the Mediterranean Sea. In this study, we observed that particle size, POC export, and the contribution of microphytoplankton to the phytoplankton community structure, all decreased following the west to east net primary production gradient. One the other hand, no clear longitudinal gradient was found regarding particle composition (C/N ratio or lipid content). The above longitudinal patterns were also observed at the seasonal scale from spring to summer in the northwestern subbasin. These observations suggest that particle size rather than organic matter composition controls fluxes of POC in the Mediterranean Sea. The comparison between POC and dissolved organic carbon (DOC) fluxes highlights the different time-scale of physicals vertical mechanisms and suggests that DOC flux can play an underestimated role in the supply of fresh carbon to the deep waters Mediterranean Sea. Indeed, DOC supply to deeper layers can be one order of magnitude larger than particle carbon flux but occurs in pulses when stratification breaks due to (i) deep-water formation, or (ii) winter mixing. In contrast, the vertical export of POC occurs throughout the year bringing weak, but almost continuous, energy to meso- and bathypelagic organisms.

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 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.

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.

Three vertical ocean carbon pumps have been known for almost three decades to sequester atmospheric carbon in the deep-water and sediment reservoirs, i.e. the solubility pump, the carbonate pump, and the soft-tissue (also known as organic, or biological) carbon pump (BCP). These three pumps maintain the vertical gradient in total dissolved inorganic carbon between the surface and deep waters. The more recently proposed microbial carbon pump (MCP) would maintain a gradient between short- and long-lived dissolved organic carbon (DOC; average lifetimes of <100 and >100 years, respectively). Long-lived DOC is an additional proposed reservoir of sequestered carbon in the ocean. This review: examines critically aspects of the vertical ocean carbon pumps and the MCP, in particular their physical dimensions and their potential roles in carbon sequestration; normalises the dimensions of the MCP to allow direct comparisons with the three vertical ocean carbon pumps; compares the MCP and vertical ocean carbon pumps; organises in a coherent framework the information available in the literature on refractory DOC; explores the potential effects of the globally changing ocean on the MCP; and identifies the assumptions that generally underlie the MCP studies, as bases for future research. The study: proposes definitions of terms, expressions and concepts related to the four ocean carbon pumps (i.e. three vertical pumps and MCP); defines the magnitude for the MCP as the rate of production of DOC with an average lifetime of >100 years and provides its first estimate for the World Ocean, i.e. 0.2 Pg C year−1; and introduces an operational “first-time-sequestration” criterion that prevents organic carbon fluxes from being assigned to both the BCP and the MCP. In our review of the potential effects of predicted climate-related changes in the ocean environment on the MCP, we found that three of the seven predicted changes could potentially enhance carbon sequestration by the MCP, and three could diminish it.

Agulhas rings provide the principal route for ocean waters to circulate from the Indo-Pacific to the Atlantic basin. Their influence on global ocean circulation is well known, but their role in plankton transport is largely unexplored. We show that, although the coarse taxonomic structure of plankton communities is continuous across the Agulhas choke point, South Atlantic plankton diversity is altered compared with Indian Ocean source populations. Modeling and in situ sampling of a young Agulhas ring indicate that strong vertical mixing drives complex nitrogen cycling, shaping community metabolism and biogeochemical signatures as the ring and associated plankton transit westward. The peculiar local environment inside Agulhas rings may provide a selective mechanism contributing to the limited dispersal of Indian Ocean plankton populations into the Atlantic.

Understanding interactions between microbial communities and their environment well enough to be able to predict diversity or biotic response on the basis of physicochemical parameters is a fundamental pursuit of microbial ecology that still eludes us. Networks have become a key approach to understanding systems of interacting objects, and network based analysis recently shown great promises to decipher microbial interactions. However, modeling microbial communities is a complicated task, because (i) communities are complex, (ii) most are described qualitatively, and (iii) quantitative understanding of the way communities interacts with their surroundings remains incomplete.We propose herein a network analysis that aims to overcome these points while focusing on one open biological question: revealing and analyzing plankton networks driving carbon export in the global ocean. The biological carbon pump is the process by which photosynthesis transforms CO2 to organic carbon sinking to the deep-ocean as particles where it is sequestered. While the intensity of the pump correlate to plankton community composition, the underlying ecosystem structure and interactions driving this process remain largely uncharacterized Here we use environmental and metagenomic data gathered during the Tara Oceans expedition to improve understanding of these drivers. We show that specific plankton communities correlate with carbon export and highlight unexpected and overlooked taxa such as Radiolaria, alveolate parasites and bacterial pathogens, as well as Synechococcus and their phages, as key players in the biological pump. Additionally, we show that the abundances of just a few bacterial and viral genes predict most of the global ocean carbon export’s variability. Together these findings help elucidate ecosystem drivers of the biological carbon pump and present a case study for scaling from genes-to-ecosystems.

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.

Mesoscale eddies may drive a significant component of cross-shelf transport important in the ecology of shelf ecosystems and adjacent boundary currents. The Leeuwin Current in the eastern Indian Ocean becomes unstable in the austral autumn triggering the formation of eddies. We hypothesized that eddy formation represented the major driver of cross-shelf transport during the autumn. Acoustic Doppler Current Profiler profiles confirmed periodic offshore movement of 2 Sv of shelf waters into the forming eddy from the shelf, carrying a load of organic particles (>0.06 mm). The gap between inflow and outflow then closed, such that the eddy became isolated from further direct input of shelf waters. Drifter tracks supported an anticyclonic surface flow peaking at the eddy perimeter and decreasing in velocity at the eddy center. Oxygen and nutrient profiles suggested rapid remineralization of nitrate mid-depth in the isolated water mass as it rotated, with a total drawdown of oxygen of 3.6 mol m 22 to 350 m. Depletion of oxygen, and release of nitrate, occurred on the timescale of 1 week. We suggest that N supply and N turnover are rapid in this system, such that nitrate is acting primarily as a regenerated nutrient rather than as a source of new nitrogen. We hypothesize that sources of eddy particulate C and N could include particles sourced from coastal primary producers within 500 km such as macrophytes and sea-grasses known to produce copious detritus, which is prone to resuspension and offshore transport.

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.

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.

Viruses influence ecosystems by modulating microbial population size, diversity, metabolic outputs, and gene flow. Here, we use quantitative double-stranded DNA (dsDNA) viral-fraction metagenomes (viromes) and whole viral community morphological data sets from 43 Tara Oceans expedition samples to assess viral community patterns and structure in the upper ocean. Protein cluster cataloging defined pelagic upper-ocean viral community pan and core gene sets and suggested that this sequence space is well-sampled. Analyses of viral protein clusters, populations, and morphology revealed biogeographic patterns whereby viral communities were passively transported on oceanic currents and locally structured by environmental conditions that affect host community structure. Together, these investigations establish a global ocean dsDNA viromic data set with analyses supporting the seed-bank hypothesis to explain how oceanic viral communities maintain high local diversity.

The goal of the Arabian Sea section of the TARA oceans expedition was to study large particulate matter (LPM > 100 μm) distributions and possible impact of associated midwater biological processes on vertical carbon export through the oxygen minimum zone (OMZ) of this region. We propose that observed spatial patterns in LPM distribution resulted from the timing and location of surface phytoplankton bloom, lateral transport, microbial processes in the core of the OMZ, and enhanced biological processes mediated by bacteria and zooplankton at the lower oxycline. Indeed, satellite-derived net primary production maps showed that the northern stations of the transect were under the influence of a previous major bloom event while the most southern stations were in a more oligotrophic situation. Lagrangian simulations of particle transport showed that deep particles of the northern stations could originate from the surface bloom while the southern stations could be considered as driven by 1-D vertical processes. In the first 200 m of the OMZ core, minima in nitrate concentrations and the intermediate nepheloid layer (INL) coincided with high concentrations of 100 μm < LPM < 200 μm. These particles could correspond to colonies of bacteria or detritus produced by anaerobic microbial activity. However, the calculated carbon flux through this layer was not affected. Vertical profiles of carbon flux indicate low flux attenuation in the OMZ, with a Martin model b exponent value of 0.22. At three stations, the lower oxycline was associated to a deep nepheloid layer, an increase of calculated carbon flux and an increase in mesozooplankton abundance. Enhanced bacterial activity and zooplankton feeding in the deep OMZ is proposed as a mechanism for the observed deep particle aggregation. Estimated lower flux attenuation in the upper OMZ and re-aggregation at the lower oxycline suggest that OMZ may be regions of enhanced carbon flux to the deep sea relative to non OMZ regions.

Ballast material (organic, opal, calcite, lithogenic) is suggested to affect sinking speed of aggregates in the ocean. Here, we tested this hypothesis by incubating appendicularians in suspensions of different algae or Saharan dust, and observing the sinking speed of the marine snow formed by their discarded houses. We show that calcite increases the sinking speeds of aggregates by ~100% and lithogenic material by ~150% while opal only has a minor effect. Furthermore the effect of ballast particle concentration was causing a 33 m d-1 increase in sinking speed for a 5×10 5 µm 3 ml-1 increase in particle concentration, near independent on ballast type. We finally compare our observations to the literature and stress the need to generate aggregates similar to those in nature in order to get realistic estimates of the impact of ballast particles on sinking speeds.

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 study of science-making is a growing discipline that builds largely on online publication and citation databases, while prepublication processes remain hidden. Here, we report on results from a large-scale survey of the submission process, covering 923 scientific journals from the biological sciences in years 2006 to 2008. Manuscript flows among journals revealed a modular submission network, with high-impact journals preferentially attracting submissions. However, about 75% of published articles were submitted first to the journal that would publish them, and high-impact journals published proportionally more articles that had been resubmitted from another journal. Submission history affected post-publication impact: Resubmissions from other journals received significantly more citations than first-intent submissions, and resubmissions between different journal communities received significantly fewer citations.

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.

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.

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.

The genus (Gastrotricha Chaetonotida) includes two species, and ; its morphological affinity with the genus has been pointed out. Here, new morphological data from light and electron microscopy and the description of the spermatozoon of are reported, with the aim of clarifying the phylogenetic position of the genus. The mouth cavity has a wreath of stout, protrusible processes. The two secondary furcal tubes are inserted ventrally and are covered with elongate scales. All the caudal tubes contain a duo-gland adhesive system. Three kinds of ciliated sensory receptors are described for the first time in . The filiform spermatozoon consists of an acrosome, a nuclear-mitochondrial complex, and a flagellum. The acrosome including two long and different cones, the single, giant mitochondrion surrounding the nuclear base, and the axoneme arising from a deep nuclear ‘fossa' appear as autapomorphic characters. The keeled, solid cuticular body scales and the spermatozoon with a supernumerary membrane are features shared with . The structure of the accessory fibres is a strong spermatological similarity between the families Muselliferidae and Xenotrichulidae. Thus morphological and spermatological characters support the inclusion of and into the family Muselliferidae recently described. The comparative spermatology also suggests that Xenotrichulidae may be the sister group of Muselliferidae.

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.

Agglomerative cluster analyses encompass many techniques, which have been widely used in various fields of science. In biology, and specifically ecology, datasets; are generally highly variable and may contain outliers, which increase the difficulty to identify the number of clusters. Here we present a new criterion to determine statistically the optimal level of partition in a classification tree. The criterion robustness is tested against perturbated data (outliers) using an observation or variable with values randomly generated. The technique, called Random Simulation Test (RST), is tested on (1) the well-known Iris dataset (Fisher, R.A., 1936. The use of multiple measurements in taxonomic problems. Ann. Eugenic. 7, 179-188], (2) simulated data with predetermined numbers of clusters following Milligan and Cooper [Milligan, G.W, Cooper, M.C., 1985. An examination of procedures for determining the number of clusters in a data set. Psychometrika SO, 159-1791 and finally (3) is applied on real copepod communities data previously analyzed in Beaugrand et al. (Beaugrand, G., Ibanez, F., Lindley, J.A., Reid, P.C., 2002. Diversity of calanoid copepods in the North Atlantic and adjacent seas: species associations and biogeography. Mar. Ecol. Prog. Ser. 232, 179-1951. The technique is compared to several standard techniques. RST performed generally better than existing algorithms on simulated data and proved to be especially efficient with highly variable datasets.

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).

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 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 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 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.

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.

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.

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.