<div><p>The Western Tropical South Pacific has recently been identified as a global hotspot for microbial dinitrogen fixation and shallow hydrothermal activity, yet the dynamics of dissolved organic matter (DOM) in this ecosystem remains understudied. During the TONGA cruise (2019), we investigated the distribution of dissolved organic carbon (DOC), chromophoric DOM (CDOM) and fluorescent DOM (FDOM) from Melanesian waters to the South Pacific Gyre, including the Lau Basin/Tonga-Kermadec Volcanic Arc. DOC concentration, CDOM absorption [aCDOM(254)],</p><p>the CDOM spectral slope (S275-295) and tyrosine-like fluorescence decreased from surface to deep waters across subregions. In contrast, apparent oxygen utilization (AOU), nutrients, aCDOM(350), specific UV absorbance (SUVA254), humic-like fluorescence, humification (HIX) and combustion (COX) indices increased with depth. These distributions reveal 1) the production of labile, low molecular weight DOM by phytoplankton, and photobleaching in the photic layer, and 2) the production of higher molecular weight, bio-refractory DOM from the remineralization of sinking particulate organic carbon and DOC in deeper waters. Also, the tryptophan-like fluorescence peaks at depth could be associated with the presence of sinking Trichodesmium spp. Regional variations in DOM characteristics were less pronounced than water-mass-related differences but revealed subtle trends along the west-east gradient, with overall higher DOC, CDOM and FDOM levels in the Melanesian and Lau Basin/Arc subregions compared to the South Pacific Gyre. At 200-m depth near the Arc, the release of hydrothermal fluids altered the DOM composition close to the vent, with significant increases in aCDOM(254) and tyrosine-like material, and significant decreases in HIX and COX indices. We further show an indirect, large-scale impact of shallow hydrothermal vents on the DOM stock in the 0-50-m surface layer, driven by the iron fertilization-induced stimulation of planktonic activity in the photic zone. The increased DOM stocks were observed mostly in the Lau Basin/Arc subregion but extending to Melanesian waters and the western edge of South Pacific Gyre. Collectively, these processes shape the optical 3 properties and biogeochemical behavior of DOM, highlighting the importance of hydrothermal systems in the oceanic carbon cycle.</p></div>

Abstract. Phytoplankton community composition is a key determinant of ocean biogeochemical cycles, yet its observation from 20 autonomous platforms remains challenging. In this study, we assessed the potential of in situ multispectral excitation fluorescence (MXF) to discriminate phytoplankton assemblages in the Northwestern Mediterranean Sea, with a view toward applications on Biogeochemical-Argo (BGC-Argo) profiling floats. Laboratory measurements on ten phytoplankton strains confirmed that MXF ratios at 440, 470, and 532 nm provide taxon-specific signatures, especially for picocyanobacteria and green algae. Field observations of phytoplankton pigments were clustered into four ecologically distinct phytoplankton communities along the seasonal cycle. A machine learning model was then trained to classify these clusters using MXF and additional bio-optical indices. Results show that existing BGC-Argo configurations (single-wavelength fluorescence, particulate backscattering and beam attenuation coefficients) reliably distinguish broad community structures such as pico- versus microphytoplankton dominance, but resolving finer pigment-based differences requires the added spectral information of MXF. The different excitation channels contributed unequally: 440 and 470 nm provided robust pigment sensitivity across communities, while 532 nm was particularly informative for detecting phycoerythrin- and chlorophyll b–rich taxa. Overall, combining MXF with bio-optical proxies improved classification performance by integrating pigment-specific and size-structure information, demonstrating the potential of MXF to enhance autonomous monitoring of phytoplankton community dynamics and their role in ocean biogeochemical cycles.

Le réseau Argo est un programme d'observation international qui coordonne la mesure de variables océaniques essentielles à l'aide de flotteurs profileurs, des plateformes d'observation autonomes et dérivantes. Aujourd'hui, plus de 4000 profileurs Argo sillonnent les océans du monde et fournissent en accès libre des données in situ uniques à la communauté scientifique : température, salinité, irradiance, concentration en chlorophylle a, etc. Vingt-cinq ans après le déploiement des premiers flotteurs les progrès en matière de détection ouvrent de nouvelles perspectives d'innovation, en particulier pour les capteurs mesurant la concentration en chlorophylle a. Dans le cadre du projet PIANO, financé par l'Ifremer, le Laboratoire d'Océanographie de Villefranche (LOV) étudie et test de nouveaux fluorimètres et développent un capteur inédit en collaboration étroite avec NKE Instrumentation.

Abstract. Particles of marine origin may act as ice nuclei when clouds form and therefore influence cloud properties and lifetime. Here we investigate the abundance of Ice Nuclei Particles in bulk seawater (INPSW) collected in natural seawater of the Western Tropical South Pacific and in sea spray aerosol (INPSSA) artificially generated from the surface seawater. The study area was separated into two oligotrophic zones (the Melanesian Basin and the Western South Pacific Gyre), and a mesotrophic one (the Lau basin), characterized by high plankton biomass due iron fertilization by underwater hydrothermal activity of the Tonga volcanic arc. Our results show that INPSW were on average 80 % heat labile, strongly suggesting a biological origin. INPSW concentrations were two-fold higher in the Lau basin as compared to both oligotrophic areas at all freezing temperatures. This trend is consistent with a higher abundance of planktonic microorganisms, pigments and particulate organic carbon (POC) concentrations in the Lau basin. Over the whole cruise transect, medium to strong correlations were found between INPSW concentrations and pigments (notably with bacteriochlorophyll-a and carotene), bacterial abundance and POC. The heat stable fraction of INPSW exhibited correlations with Dissolved Organic Carbon (DOC) concentrations and were not as variable as the heat labile INPSW. In the nascent sea spray, INPSSA were also mostly heat labile in coherence with the INPSW. INPSSA were predominantly (60 %), submicron in size (presumed originating from film drops), but the supermicron INPSSA constituted 40 % of the INPSSA and were all heat labile (presumably originating from jet drops). Supermicron INPSSA were between 60 to 80 % heat stable with a high variability between samples, indicating different nature of the two fractions of INPs. Supermicron INPSSA were generally more abundant in the Lau basin, while submicron INPSSA did not exhibit any significant difference between the three regions. We report a transfer function of seawater INPs to SSA INPs of 1.70 m-2.LSW and 3.3 m-2.LSW for heat stable INPs, hinting that heat stable INPs were more efficiently transferred to the SSA. Our results suggest that hydrothermal activity indirectly enhances the INP concentration of surface waters, through boosting the biological activity, which results in increases of the ice forming ability of supermicron sea spray particle. Given the extent of hydrothermal activity throughout the global Ocean, its impact on cloud properties should be considered in future ocean-atmosphere interaction studies.

The recent roadmap IndOOS-2 has stressed the need to expand the biogeochemical-Argo observing system in the Indian Ocean. The Monaco Explorations Indian Ocean expedition offered a unique opportunity to meet this goal in the southwestern sector which was, in this regard and at that time, one of the least covered oceanic regions. We designed a deployment strategy for the biogeochemical float array grounded on past experiences, existing knowledge, and the analysis of historical datasets to cover the contrasting biophysical regimes from the Seychelles Chagos Thermocline Ridge to the subtropical gyre. Aligning with IndOOS-2 recommendations, a denser float distribution was set in the tropical band to enhance biogeochemical observations in upwelling zones. Following this strategy, a fleet of seventeen biogeochemical floats was successfully deployed during the expe- dition in October–November 2022. After two years of operations, the spatio-temporal distribution covered by the fleet confirmed that the goals of the deployment strategy have been reached, revealing seasonal modulations of the meridional trophic gradient with respect to phytoplankton biomass from tropical mesotrophy to subtropical oligotrophy

Seasonality in light, temperature, and nutrient availability are well-known to regulate phytoplankton blooms and the bacterioplankton community. During the spring bloom, phytoplankton release biomolecules as part of the dissolved organic matter (DOM) pool exploited by the bacterioplankton. Here, we investigated the seasonal variability of phytoplankton biomass, enantiomers of dissolved hydrolyzable amino acids (DHAA), bacterioplankton abundances and community composition at the Microbial Observatory Laboratory Arago (MOLA) in the NW Mediterranean Sea from 2019 to 2021. Phytoplankton biomass estimated from pigment biomarkers suggests a spring bloom succession from cryptophytes, haptophytes, and prasinophytes in March to diatoms in April. The spring bloom coincided with a 50% increase in L-enantiomers of DHAA and an increase in bacterial abundance. After the spring bloom, elevated concentrations of D-enantiomers of DHAA and gamma-aminobutyric acid suggest bacterial processing of labile biomolecules contributed to the seasonal accumulation of dissolved organic carbon (DOC). Linking organic molecules with the free-living bacterioplankton community showed a seasonal succession of niches and substrate regimes. The parallel analysis of DOM and bacterioplankton community provides an important baseline for bacteria-substrate relationships over the seasonal cycle in the northwestern Mediterranean Sea.

Phytoplankton community composition significantly influences important biogeochemical processes, particularly the biological carbon pump. Assessing the global distribution and dynamics of main phytoplankton groups is therefore of the utmost importance. Taking advantage of the synoptic view of satellite ocean color and altimetry observations combined with vertically-resolved proles of chlorophyll fluorescence collected by the global BioGeoChemical-Argo (BGC-Argo) fleet, we previously developed a neural network-based approach to infer a global tridimensional (3D) gridded product of chlorophyll a (Chla), i.e. the SOCA-Chla method. Expanding upon SOCA-Chla, we introduce SOCA-PFT, a novel method for deriving a global 3D product of phytoplankton functional types (PFT). SOCA-PFT follows the same principle as SOCA-Chla but requires an initial step to enrich the training BGC-Argo database with the PFT information that would not otherwise be available. This step involves developing a neural network trained on a large-scale database of concurrent shipborne measurements of vertical proles of pigments determined by High Performance Liquid Chromatography (HPLC), fluorescence and temperature/salinity (T/S). Applied to the BGC-Argo database, this intermediate method yields a PFT-enriched BGC-Argo database, which is further matched up with satellite observations to train the SOCA-PFT method. The resulting global PFT product provides depth-resolved Chla associated with pico-, nano-, and microphytoplankton as well as concentrations of pigment biomarkers representing major phytoplankton groups. This new product is expected to be useful for various applications, from understanding the response of phytoplankton communities to environmental conditions, to improving the quantification of biogeochemical budgets or validating biogeochemical models that explicitly incorporate multiple phytoplankton groups.

Abstract The Southern Ocean (SO) is known for its atypical bio‐optical regime. This complicates the interpretation of proxies measured from satellite and in situ platforms equipped with optical sensors, which occupy an important niche for monitoring the vast and remote SO. A ship‐based field study in concert with time series observations from BioGeoChemical‐Argo (BGC‐Argo) profiling floats were used to investigate spatial and temporal variations in bio‐optical relationships in the open ocean waters surrounding the Kerguelen Plateau in the Indian sector of the SO. Compared to other regions with similar chlorophyll concentrations, chlorophyll‐specific phytoplankton absorption in the blue waveband presented a consistent negative anomaly. The anomaly was uniform over deep mixed layers and correlated with phytoplankton size, photoacclimation and atypically high concentrations of fucoxanthin. The BGC‐Argo observation‐based proxies revealed that the blue absorption anomaly increased with chlorophyll concentration both spatially and temporally and, while particularly pronounced in the naturally iron‐fertilized waters, was also found in the High Nutrient Low Chlorophyll region. While phytoplankton size was an important driver of the anomaly, photoacclimation associated with self‐shading of phytoplankton cells was also involved during intense booms. The backscattering coefficient exhibited negative and positive anomalies in the low and high biomass regimes, respectively. The large positive anomaly in high biomass regimes was attributed to the variable non‐algal particles characteristics associated with a relatively high production of bloom by‐products. With clear understanding of the bio‐optical anomalies, BGC‐Argo floats stand as unique tools for monitoring the bio‐optical spatio‐temporal complexity of the SO.

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

the Tara Pacific expedition (2016-2018) sampled coral ecosystems around 32 islands in the Pacific Ocean and the ocean surface waters at 249 locations, resulting in the collection of nearly 58 000 samples. The expedition was designed to systematically study warm-water coral reefs and included the collection of corals, fish, plankton, and seawater samples for advanced biogeochemical, molecular, and imaging analysis. Here we provide a complete description of the sampling methodology, and we explain how to explore and access the different datasets generated by the expedition. Environmental context data were obtained from taxonomic registries, gazetteers, almanacs, climatologies, operational biogeochemical models, and satellite observations. The quality of the different environmental measures has been validated not only by various quality control steps, but also through a global analysis allowing the comparison with known environmental large-scale structures. Such publicly released datasets open the perspective to address a wide range of scientific questions.

The objective of the TONGA oceanographic expedition was to study the control of productivity and carbon sequestration by micronutrients of shallow hydrothermal origin in the Western Tropical South Pacific (WTSP) Ocean. The 37-day oceanographic survey took place on board the R/V L’Atalante in 2019 between Oct. 31 to Dec. 6 (Nouméa-Nouméa). Over a large area of the WTSP the team acquired numerous results on both the entire water column (up to the sediment) and the atmosphere. Specific task are represented on figure 1: (task 1) to characterize chemically and optically shallow hydrothermal fluids and to compare the source from below (shallow hydrothermal fluids) with the source from above (atmospheric deposition); (task 2) to quantify the dynamical dispersion of the fluids at small and regional scale; (task 3) to investigate the impact of the shallow hydrothermal sources on the biological activity and diversity, and the feedback to the atmosphere via the oceanic emissions of primary and secondary aerosols. (Task 4) to communicate about the campaign (see for example our Tweeter account (https://twitter.com/tongaproject) and the movie (26’) both in French (https://www.youtube.com/watch?v=e5kAd0i6Dck) and English (https://www.youtube.com/watch?v=UeABf-cVR-k). A long west to east (up to the blue waters of the gyre) transect allowed to characterize the different biogeochemical provinces crossed and a focus in the region of the Lau Basin allowed to investigate the impact of shallow hydrothermal sources. A series of short and long stations allowed to fully characterize the stocks and the fluxes in the different provinces. Short-term (up to 10 days) processes studies have been conducted (drifting moorings and minicosms experiments). Part of these results will feed into important modeling work. A fixed mooring line launched at the end of the campaign and recovered in Nov. 2020 as well as the 7 ARGO floats and 20 drifting buoys that were dropped during the campaign provide a broader temporal context of the acquisitions done during the campaign. An important focus of the campaign was the trace metal characterization of the entire water column. For this, TONGA has been labeled by the international program GEOTRACES (https://www.geotraces.org/). The impact on biological communities of fluids is supported by the international IMBER program (https://imber.info/). The TONGA project is also part of the LEFE program (funding by LEFE-CYBER and LEFE-GMMC), the ANR (Appel à projets génériques) and the Fondation A-MIDeX of the Aix-Marseille Université.

Diazotrophs are widespread microorganisms that alleviate nitrogen limitation in 60% of our oceans, thereby regulating marine productivity. Yet, the group-specific contribution of diazotrophs to organic matter export has not been quantified, which so far has impeded an accurate assessment of their impact on the biological carbon pump. Here, we examine the fate of five groups of globally-distributed diazotrophs by using an original combination of mesopelagic particle sampling devices across the subtropical South Pacific Ocean. We demonstrate that cyanobacterial and non-cyanobacterial diazotrophs are exported down to 1000 m depth. Surprisingly, group-specific export turnover rates point to a more efficient export of small unicellular cyanobacterial diazotrophs (UCYN) relative to the larger and filamentous Trichodesmium. Phycoerythrin-containing UCYN-B and UCYN-C-like cells were recurrently found embedded in large (>50 µm) organic aggregates or organized into clusters of tens to hundreds of cells linked by an extracellular matrix, presumably facilitating their export. Beyond the South Pacific, our data are supported by analysis of the Tara Oceans metagenomes collected in other ocean basins, extending the scope of our results globally. We show that, when diazotrophs are found in the euphotic zone, they are also systematically present in mesopelagic waters, suggesting their transport to the deep ocean. We thus conclude that diazotrophs are a significant part of the carbon sequestered in the deep ocean and, therefore, they need to be accounted in regional and global estimates of export.

Abstract. The Green Edge project was designed to investigate the onset, life and fate of a phytoplankton spring bloom (PSB) in the Arctic Ocean. The lengthening of the ice-free period and the warming of seawater, amongst other factors, have induced major changes in arctic ocean biology over the last decades. Because the PSB is at the base of the Arctic Ocean food chain, it is crucial to understand how changes in the arctic environment will affect it. Green Edge was a large multidisciplinary collaborative project bringing researchers and technicians from 28 different institutions in seven countries, together aiming at understanding these changes and their impacts into the future. The fieldwork for the Green Edge project took place over two years (2015 and 2016) and was carried out from both an ice-camp and a research vessel in the Baffin Bay, canadian arctic. This paper describes the sampling strategy and the data set obtained from the research cruise, which took place aboard the Canadian Coast Guard Ship (CCGS) Amundsen in spring 2016. The dataset is available at https://doi.org/10.17882/59892 (Massicotte et al., 2019a).

Influence of the phytoplankton community composition on the in situ fluorescence signal: Implication for an improved estimation of the chlorophyll-a concentration from BiogeoChemical-Argo profiling floats.

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.

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

The Green Edge project was designed to investigate the onset, life, and fate of a phytoplankton spring bloom (PSB) in the Arctic Ocean. The lengthening of the ice-free period and the warming of seawater, amongst other factors, have induced major changes in Arctic Ocean biology over the last decades. Because the PSB is at the base of the Arctic Ocean food chain, it is crucial to understand how changes in the Arctic environment will affect it. Green Edge was a large multidisciplinary, collaborative project bringing researchers and technicians from 28 different institutions in seven countries together, aiming at understanding these changes and their impacts on the future. The fieldwork for the Green Edge project took place over two years (2015 and 2016) and was carried out from both an ice camp and a research vessel in Baffin Bay, in the Canadian Arctic. This paper describes the sampling strategy and the dataset obtained from the research cruise, which took place aboard the Canadian Coast Guard ship (CCGS) Amundsen in late spring and early summer 2016. The sampling strategy was designed around the repetitive, perpendicular crossing of the marginal ice zone (MIZ), using not only ship-based station discrete sampling but also high-resolution measurements from autonomous platforms (Gliders, BGC-Argo floats …) and under-way monitoring systems. The dataset is available at https://doi.org/10.17882/86417 (Bruyant et al., 2022).

The Green Edge initiative was developed to investigate the processes controlling the primary productivity and the fate of organic matter produced during the Arctic phytoplankton spring bloom (PSB) and to determine its role in the ecosystem. Two field campaigns were conducted in 2015 and 2016 at an ice camp located on landfast sea ice southeast of Qikiqtarjuaq Island in Baffin Bay (67.4797N, 63.7895W). During both expeditions, a large suite of physical, chemical and biological variables was measured beneath a consolidated sea ice cover from the surface to the bottom at 360 m depth to better understand the factors driving the PSB. Key variables such as temperature, salinity, radiance, irradiance, nutrient concentrations, chlorophyll-a concentration, bacteria, phytoplankton and zooplankton abundance and taxonomy, carbon stocks and fluxes were routinely measured at the ice camp. Here, we present the results of a joint effort to tidy and standardize the collected data sets that will facilitate their reuse in other Arctic studies. The dataset is available at http://www.seanoe.org/data/00487/59892/ (Massicotte et al., 2019a).

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

Graphical Abstract Highlights d A catalog of 47 million genes was generated from 370 globally distributed metagenomes d Meta-omics data integration disentangled the mechanisms of changes in transcript pools d Transcript pool changes of metabolic marker genes show distinct mechanistic patterns d Community turnover as a response to ocean warming may be strongest in polar regions

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.

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

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.

Dinoflagellates (Alveolata) are one of the ecologically most important groups of modern phytoplankton. Their biological complexity makes assessment of their global diversity and community structure difficult. We used massive V9 18S rDNA sequencing from 106 size-fractionated plankton communities collected across the world's surface oceans during the Tara Oceans expedition (2009-2012) to assess patterns of pelagic dinoflagellate diversity and community structuring over global taxonomic and ecological scales. Our data and analyses suggest that dinoflagellate diversity has been largely underestimated, representing overall approximate to 1/2 of protistan rDNA metabarcode richness assigned at 90% to a reference sequence in the world's surface oceans. Dinoflagellate metabarcode diversity and abundance display regular patterns across the global scale, with different order-level taxonomic compositions across organismal size fractions. While the pico to nano-planktonic communities are composed of an extreme diversity of metabarcodes assigned to Gymnodiniales or are simply undetermined, most micro-dinoflagellate metabarcodes relate to the well-referenced Gonyaulacales and Peridiniales orders, and a lower abundance and diversity of essentially symbiotic Peridiniales is unveiled in the meso-plankton. Our analyses could help future development of biogeochemical models of pelagic systems integrating the separation of dinoflagellates into functional groups according to plankton size classes.

Ocean microbes drive biogeochemical cycling on a global scale. However, this cycling is constrained by viruses that affect community composition, metabolic activity, and evolutionary trajectories. Owing to challenges with the sampling and cultivation of viruses, genome-level viral diversity remains poorly described and grossly understudied, with less than 1% of observed surface-ocean viruses known. Here we assemble complete genomes and large genomic fragments from both surface- and deep-ocean viruses sampled during the Tara Oceans and Malaspina research expeditions, and analyse the resulting ‘global ocean virome’ dataset to present a global map of abundant, double-stranded DNA viruses complete with genomic and ecological contexts. A total of 15,222 epipelagic and mesopelagic viral populations were identified, comprising 867 viral clusters (defined as approximately genus-level groups. This roughly triples the number of known ocean viral populations and doubles the number of candidate bacterial and archaeal virus genera, providing a near-complete sampling of epipelagic communities at both the population and viral-cluster level. We found that 38 of the 867 viral clusters were locally or globally abundant, together accounting for nearly half of the viral populations in any global ocean virome sample. While two-thirds of these clusters represent newly described viruses lacking any cultivated representative, most could be computationally linked to dominant, ecologically relevant microbial hosts. Moreover, we identified 243 viral-encoded auxiliary metabolic genes, of which only 95 were previously known. Deeper analyses of four of these auxiliary metabolic genes (dsrC, soxYZ, P-II (also known as glnB) and amoC) revealed that abundant viruses may directly manipulate sulfur and nitrogen cycling throughout the epipelagic ocean. This viral catalog and functional analyses provide a necessary foundation for the meaningful integration of viruses into ecosystem models where they act as key players in nutrient cycling and trophic networks.

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.

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

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.

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.

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.

Diazotrophic cyanobacteria play an important role in biogeochemical cycles of carbon and nitrogen and, hence, in oceanic productivity in the tropical and subtropical regions of the ocean. Although many studies have examined the impact of iron (Fe) limitation on particulate primary production and dinitrogen (N₂) fixation in the colonial cyanobacterium Trichodesmium, none have looked at the impact of Fe limitation on the percentage extracellular release (PER) and secondary production (SP) in Fe-limited cultures of this cyanobacterium. Here, we present the results of a series of culture experiments during which we examined the impact of 3 concentrations of dissolved iron (DFe) on total primary production (TPP = dissolved + particulate primary production, i.e. DPP + PPP), PER and on SP. Under severe Fe limitation (5 nM DFe), biomass, growth rates, TPP and N₂ fixation were strongly reduced, while PER increased relative to the rates ob served at the highest Fe concentration. Moreover, reducing Fe concentration induced an increase in the percentage of photosynthetically fixed C used for algal growth, while the percentage of C used to support algal respiration decreased. Reduced Fe concentrations also induced a decrease in SP and in the SP:DPP ratio, indicating that the efficiency of transfer of fixed carbon from autotrophic to heterotrophic processes is reduced. This suggests that Fe, either directly through influencing cellular processes or indirectly through influencing organic matter structure or nitrogen availability, is controlling SP and, thus, microbial carbon utilization. These results suggest that the amount of carbon entering into the microbial loop may be reduced under Fe limitation, thus leading to an accumulation of dissolved organic carbon with potentially important impacts on microbial carbon cycling and, ultimately, on the biological carbon pump

We investigated the link between iron (Fe) limitation and intracellular dimethylsulfoniopropionate (DMSP) concentration in two oceanic phytoplankton species, the diatom Thalassiosira oceanica and the diazotrophic cyanobacterium Trichodesmium erythraeum. Dimethylsulfoxide (DMSO) concentrations were also measured in Fe-replete and Fe-limited T. oceanica. Fe limitation decreased the growth rates of T. oceanica and T. erythraeum by 33-fold and 3.5-fold, respectively and increased intracellular DMSP (DMSPp) concentrations by 12-fold (from 2.8 to 33.7 mmol Lcell−1) and by 45-fold (from 0.05 to 2.27 mmol Ltrichome−1), respectively. Intracellular dimethylsulfoxide (DMSOp) concentrations in T. oceanica increased by 5-fold under severe Fe limitation, from 0.78 mmol Lcell−1 in Fe-replete cells to 3.86 mmol Lcell−1. The increase in DMSPp and DMSOp under Fe limitation provides support for the role of these sulfur compounds as antioxidants. Under severe Fe limitation, the large increase in DMSPp : C and DMSP : chlorophyll a (Chl a) ratios for both T. oceanica (by 16- and 40-fold, respectively) and T. erythraeum (by 18- and 145-fold, respectively) places these species above the range of values generally attributed to diatoms and cyanophytes. Comparison of these values with in situ results, such as those from Fe fertilization experiments, suggests that the decrease in DMSPp : Chl a and DMSOp : Chl a that is generally observed with alleviation of Fe limitation may be partly related to decreases in DMSPp and DMSOp in individual species. The role of diatoms and diazotrophic cyanobacteria in the biogeochemical cycle of dimethylsulfide and associated sulfur compounds in Fe-limited oceanic environments should not be overlooked.

The ecophysiology of the photoprotective xanthophyll cycle (XC) was compared in six chlorophyll c-containing pico- and nano- phytoplankton species. Different accessory pigment combinations and ecological properties characterize the six studied species, Bolidomonas mediterranea, Pelagomonas calceolata, Phaeocystis cordata, Phaeocystis sp.(strain RCC186), Mesopedinella arctica and Ochromonas sp. The first experimental set consisted in the study of the activity of the xanthophyll cycle and non-photochemical quenching (NPQ) during two gradual light increases, with photon flux density (PFD) ranging from 40 to 400 mu mol photons m(-2) s(-1). Pigments, absorption spectra, flow cytometry measurements for cell counts and chlorophyll a autofluorescence and Electron Transport Rate (ETR) vs. light curves were determined at different times during the experiment. The second set of experiments consisted in using two inhibitors: carotenogenesis inhibitor (norflurazon) and deepoxidation step (occurring in the xanthophyll cycle) inhibitor (dithiotreitol) during high-light shift, to compare the functioning of the xanthophyll cycle among the different species. Results highlighted a large diversity in the xanthophyll cycle functioning, possibly related to the ecological traits of the species. In view of the results, three groups of species have been identified as (i) highlight-adapted, (ii) low light-adapted and (iii) variable light-adapted species. (C) 2009 Elsevier GmbH. All rights reserved.

Growth, photosynthesis, and photoacclimation properties of batch cultures of Pelagomonas calceolata (Pelagophyceae) were compared for 1 week under three different fluctuating light regimes with the same total daily amount of light. Treatments consisted of a sinusoidal diurnal light cycle or a high-frequency fluctuating light simulating two different regimes of vertical mixing (highly fluctuating light [HFL] or fluctuating light [FL]). Three to five samples were taken every day for analysis of pigments, absorption spectrum, variable fluorescence, nonphotochemical quenching (NPQ), electron transport rate vs. light curves, and cell concentration. Pelagomonas achieved the same growth rate during the exponential growth phase under all three light conditions, revealing a high degree of acclimation to light and also suggesting that the daily light dose is the main factor regulating growth and division. Photophysiological adjustments occurred in the cells in response to the three light regimes. Pelagomonas seems to adopt the n-type photoacclimation in HFL, whereas the s-type photoacclimation is applied in FL. The cells rapidly trigger photoprotective mechanisms such as the xanthophyll cycle and NPQ, even though these do not appear to be able to fully prevent photoinhibition. The enhanced costs for maintenance and repair associated with HFL may have limited the allocation of energy to growth, thus explaining the shorter duration of the exponential growth phase in this regime with respect to the two others.

The photophysiological properties of strain RCC 237 belonging to the marine picoplanktonic genus Picochlorum, first described by Henley et al., were investigated under different photon flux densities (PFD), ranging from 40 to 400 mu mol photons. m(-2).s(-1), mainly focusing on the development of the xanthophyll cycle and its relationship with the nonphotochemical quenching of fluorescence (NPQ). The functioning of the xanthophyll cycle and its photoprotective role was investigated by applying a progressive increase of PFD and using dithiotreitol and norflurazon to block specific enzymatic reactions in order to study in depth the relationship between xanthophyll cycle and NPQ. These two processes were significantly related only during the gradually increasing light periods and not during stable light periods, where NPQ and zeaxanthin were decoupled. This result reveals that NPQ is a photoprotective process developed by algae only when cells are experiencing increasing PFD or in response to stressful light variations, for instance after a sudden light shift. Results showed that the photobiological properties of Picochlorum strain RCC 237 seem to be well related to the surface water characteristics, as it is able to maintain its photosynthetic characteristics under different PFDs and to quickly activate the xanthophyll cycle under high light.

Light is one of the most important factors affecting marine phytoplankton growth, and its variability in time and space strongly influences algal performance and success. The hypothesis tested in this work is that the activity of the xanthophyll cycle and the development of nonphotochemical quenching could be considered a functional trait of algal diversity. If this hypothesis is true, a relationship must exist between fast-activated pigment variations linked to photoprotective behavior and the ecology of the species. This assumption was tested on three diatoms: Skeletonema marinoi Sarno et Zingone, Thalassiosira rotula Meunier, and Chaetoceros socialis Lauder. These three diatoms occupy different ecological niches. Strains of these diatoms were subjected to five changes in irradiance. Xanthophyll-cycle activity, quantum yield of fluorescence, and electron transport rate were the main parameters determined. There were marked interspecific differences in xanthophyll-cycle activity, and these differences were dependent on the light history of the cells. Chaetoceros socialis responded efficiently to changing irradiance, which might relate to its dominance during the spring bloom in some coastal areas. In contrast, T. rotula responded with a slower photoprotection activation, which seems to reflect its more offshore ecological distribution. The photoresponse of S. marinoi (a late-winter coastal species blooming in the Adriatic Sea) was light-history dependent, becoming photoinhibited under high light when acclimated to low light, but capable of reaching a high photoprotection level when acclimated to moderate light. Our hypothesis on the photoprotection capacity as a functional trait in microalgae seems to be validated given the results of this study.