Search

A planetary-scale understanding of the ocean ecosystem, particularly in light of climate change, is crucial. Here, we review the work of TaraOceans, an international, multidisciplinary project to assess the complexity of ocean life across comprehensive taxonomic and spatial scales. Using a modified sailing boat, the team sampled plankton at 210 globally distributed sites at depths down to 1,000 m. We describe publicly available resources of molecular, morphological and environmental data, and discuss how an ecosystems biology approach has expanded our understanding of plankton diversity and ecology in the ocean as a planetary, interconnected ecosystem. These efforts illustrate how global-scale concepts and data can help to integrate biological complexity into models and serve as a baseline for assessing ecosystem changes and the future habitability of our planet in the Anthropocene epoch.

Subpolar Mode Water (SPMW) is an important water mass originating in the eastern North Atlantic. Its formation, subject to modification through oceanic interior mixing, can directly influence the volume of water contributing to the Atlantic meridional overturning circulation. Utilizing observation‐based data sets spanning from 1993 to 2018, we estimated the formation rates and volume of SPMW within isopycnal layers and examined its temporal variability. Two complementary approaches were used to estimate the formation rate: a thermodynamic approach focusing on the air‐sea interactions and a kinematic approach involving volume transport from the mixed layer to the ocean's interior, including the entrainment/detrainment of the mixed layer itself. This is the first time that thermodynamic and kinematic approaches are applied to observation‐based data in the North Atlantic. Our results suggest a substantial role of diapycnal mixing in diluting the dense waters formed by air‐sea fluxes toward the range of SPMW densities. The study reveals a complex interplay of processes, with entrainment being the primary driver of subduction/obduction rates, while advection contributes to the overall small‐scale dynamics. Variations in the volume and location of SPMW formation are observed from year to year. Notably, when SPMW forms extensively in lighter isopycnal layers, the volume occupied by denser isopycnals decreases and vice versa. We attributed this compensation effect to a propagation signal, where formation in the lightest isopycnal bins influences the formation in denser isopycnal bins with a delay of a few years, emphasizing the circulation's role in shaping the SPMW distribution. We present an analysis of one important type of water mass, the Subpolar Mode Water (SPMW) located in the North Atlantic Ocean. We looked at data collected over a period of 26 years from 1993 to 2018, to understand how SPMW forms and how its volume changes over time. We used two different methods to calculate how much SPMW forms each year to have the best possible picture. One method looked at air‐water interactions, and the other at how the water moves from the top layer of the ocean to deeper parts. This is the first time these methods are applied to observation‐based data in the North Atlantic. Our findings highlight the important role of water mixing in changing the density of SPMW. We also found that one of the main reasons how the SPMW leaves the top layer of the ocean is through the shoaling/deepening of the mixed layer itself over time, modulated horizontally by the small‐scale dynamics of the ocean. Additionally, the volume of SPMW and location where it forms can vary from year to year. Notably, when SPMW forms in larger amounts in the upper part of the ocean, there is less SPMW in the denser water. Subduction of water below the mixed layer is driven by entrainment with advection modulating the small‐scale dynamicsVolume and formation of Subpolar Mode Water changes every year in size and locationThe difference between the formation rate from the thermodynamic and kinematic approaches suggests a large role of diapycnal mixing Subduction of water below the mixed layer is driven by entrainment with advection modulating the small‐scale dynamics Volume and formation of Subpolar Mode Water changes every year in size and location The difference between the formation rate from the thermodynamic and kinematic approaches suggests a large role of diapycnal mixing

The water mass transformation (WMT) framework weaves together circulation, thermodynamics, and biogeochemistry into a description of the ocean that complements traditional Eulerian and Lagrangian methods. In so doing, a WMT analysis renders novel insights and predictive capabilities for studies of ocean physics and biogeochemistry. In this review, we describe fundamentals of the WMT framework and illustrate its practical analysis capabilities. We show how it provides a robust methodology to characterize and quantify the impact of physical processes on buoyancy and other thermodynamic fields. We also detail how to extend WMT to insightful analysis of biogeochemical cycles.

Water mass transformation quantifies transport of matter between different density classes of the World Ocean. We present the first observationally based quantification of transformation rates due to air‐sea buoyancy fluxes, which considers different parameterizations of shortwave radiation depth penetration, including the influence of albedo and the Chlorophyll aconcentration. The results provide a range of solutions that can be used to compare model‐based transformation rates against. We compared two air‐sea flux products with limited representation of ice dynamics at high latitudes. We find that variations in the air‐sea heat fluxes due to Chlorophyll aand its horizontal distribution are as important for water mass transformation rates than differences between the freshwater flux products. An accurate representation of the effects and spatial distribution of Chlorophyll ais required to obtain realistic transformation rates. Air‐sea fluxes of heat and freshwater (precipitation, evaporation, warming by the sun, etc.) are difficult to measure accurately. Yet they influence the ocean circulation and, for example, how and how much heat and anthropogenic carbon are absorbed by the ocean. In this study, we measure variations of the effect of air‐sea fluxes on ocean dynamics. We found that Chlorophyll ain the ocean (a measure for very small biology), changes both the amount of incoming sunlight (through reflection) and how deep the sunlight can reach. Through this effect, Chlorophyll amay indirectly affect the climate system. Scientist predicting future climates should therefore include this effect carefully in their numerical ocean models. First observationally based quantification of shortwave radiation depth penetration parameterizations effects on water mass transformationThe effect of Chl aon water mass transformation is as important as that due to differences between freshwater flux productsWater mass transformation suggest errors in air‐sea fluxes in models propagate into mixing parameterizations and the ocean T&S structure

Vertical velocities at the ocean mesoscale are several orders of magnitude smaller than corresponding horizontal flows, making their direct monitoring a still unsolved challenge. Vertical motion is generally retrieved indirectly by applying diagnostic equations to observation‐based fields. The most common approach relies on the solution of an adiabatic version of the Omega equation, neglecting the ageostrophic secondary circulation driven by frictional effects and turbulent mixing in the boundary layers. Here we apply a diabatic semigeostrophic diagnostic model to two different 3‐D reconstructions covering the Southern Ocean during the period 2010–2012. We incorporate the effect of vertical mixing through a modified K‐profile parameterization and using ERA‐interim data, and perform an indirect validation of the ageostrophic circulation with independent drifter observations. Even if horizontal gradients and associated vertical flow are likely underestimated at 1/4° × 1/4° resolution, the exercise provides an unprecedented relative quantification of the contribution of vertical mixing and adiabatic internal dynamics on the vertical exchanges along the Antarctic Circumpolar Current. Kinematic estimates of subduction rates show the destruction of poleward flowing waters lighter than 26.6 kg/m3(14 ÷ 15 Sv) and two main positive bands associated with the Antarctic Intermediate Water (7 ÷ 11 Sv) and Sub‐Antarctic Mode Waters (4 ÷ 7 Sv) formation, while Circumpolar Deep Water upwelling attains around 3 ÷ 6 Sv. Diabatic and adiabatic terms force distinct spatial responses and vertical velocity magnitudes along the water column and the restratifying effect of adiabatic internal dynamics due to mesoscale eddies is shown to at least partly compensate the contribution of wind‐driven vertical exchanges to net subduction. 3‐D ageostrophic motions are retrieved by applying Omega equation to observation‐based reconstructions of the Southern OceanDiabatic and adiabatic terms force distinct spatial responses and vertical velocity intensity changes along the water columnA kinematic approach is used to provide an observation‐based analysis of water mass subduction driven by each forcing term

The depth of the upper ocean mixed layer provides fundamental information on the amount of seawater that directly interacts with the atmosphere. Its space‐time variability modulates water mass formation and carbon sequestration processes related to both the physical and biological pumps. These processes are particularly relevant in the Southern Ocean, where surface mixed‐layer depth estimates are generally obtained either as climatological fields derived from in situ observations or through numerical simulations. Here we demonstrate that weekly observation‐based reconstructions can be used to describe the variations of the mixed‐layer depth in the upper ocean over a range of space and time scales. We compare and validate four different products obtained by combining satellite measurements of the sea surface temperature, salinity, and dynamic topography and in situ Argo profiles. We also compute an ensemble mean and use the corresponding spread to estimate mixed‐layer depth uncertainties and to identify the more reliable products. The analysis points out the advantage of synergistic approaches that include in input the sea surface salinity observations obtained through a multivariate optimal interpolation. Corresponding data allow to assess mixed‐layer depth seasonal and interannual variability. Specifically, the maximum correlations between mixed‐layer anomalies and the Southern Annular Mode are found at different time lags, related to distinct summer/winter responses in the Antarctic Intermediate Water and Sub‐Antarctic Mode Waters main formation areas. The Southern Ocean mixed‐layer depth seasonal and interannual variability is retrieved from different observation‐based 3‐D reconstructionsSynergistic techniques that ingest sea surface salinity obtained through multivariate interpolation provide the most accurate estimatesThe nonzonal response of the mixed‐layer anomalies to the Southern Annual Mode is related to distinct seasonal patterns

In mid- and high-latitude oceans, winter surface cooling and strong winds drive turbulent mixing that carries phytoplankton to depths of several hundred metres, well below the sunlit layer. This downward mixing, in combination with low solar radiation, drastically limits phytoplankton growth during the winter, especially that of the diatoms and other species that are involved in seeding the spring bloom. Here we present observational evidence for widespread winter phytoplankton blooms in a large part of the North Atlantic subpolar gyre from autonomous profiling floats equipped with biogeochemical sensors. These blooms were triggered by intermittent restratification of the mixed layer when mixed-layer eddies led to a horizontal transport of lighter water over denser layers. Combining a bio-optical index with complementary chemotaxonomic and modelling approaches, we show that these restratification events increase phytoplankton residence time in the sunlight zone, resulting in greater light interception and the emergence of winter blooms. Restratification also caused a phytoplankton community shift from pico- and nanophytoplankton to phototrophic diatoms. We conclude that transient winter blooms can maintain active diatom populations throughout the winter months, directly seeding the spring bloom and potentially making a significant contribution to over-winter carbon export.

Relatively rapid reemergence of anthropogenic carbon (Cant) in the Equatorial Pacific is of potential importance for its impact on the carbonate buffering capacity of surface seawater and thereby impeding the ocean's ability to further absorb Cantfrom the atmosphere. We explore the mechanisms sustaining Cantreemergence (upwelling) from the thermocline to surface layers by applying water mass transformation diagnostics to a global ocean/sea ice/biogeochemistry model. We find that the upwelling rate of Cant(0.4 PgC yr−1) from the thermocline to the surface layer is almost twice as large as air‐sea Cantfluxes (0.203 PgC yr−1). The upwelling of Cantfrom the thermocline to the surface layer can be understood as a two‐step process: The first being due to diapycnal diffusive transformation fluxes and the second due to surface buoyancy fluxes. We also find that this reemergence of Cantdecreases dramatically during the 1982/1983 and 1997/1998 El Niño events. The upwelling rate of anthropogenic carbon from the thermocline to the surface layer is almost twice as large as air‐sea fluxesDiffusion has a major impact on reemergence of anthropogenic carbon in the Equatorial PacificReemergence of anthropogenic carbon decreases dramatically during the El Niño events

Genes encoding reverse transcriptases (RTs) are found in most eukaryotes, often as a component of retrotransposons, as well as in retroviruses and in prokaryotic retroelements. We investigated the abundance, classification and transcriptional status of RTs based on Tara Oceans marine metagenomes and metatranscriptomes encompassing a wide organism size range. Our analyses revealed that RTs predominate large-size fraction metagenomes (>5 μm), where they reached a maximum of 13.5% of the total gene abundance. Metagenomic RTs were widely distributed across the phylogeny of known RTs, but many belonged to previously uncharacterized clades. Metatranscriptomic RTs showed distinct abundance patterns across samples compared with metagenomic RTs. The relative abundances of viral and bacterial RTs among identified RT sequences were higher in metatranscriptomes than in metagenomes and these sequences were detected in all metatranscriptome size fractions. Overall, these observations suggest an active proliferation of various RT-assisted elements, which could be involved in genome evolution or adaptive processes of plankton assemblage.

We analyze 12 years of mesoscale vertical motion derived from an observation‐based product in the top 1000 m of the North West Atlantic Ocean. Vertical velocities (O(10 m d−1)) associated with Gulf Stream instabilities consist of alternating cells of upwelling and downwelling. Here we show that the magnitude of the vertical motions decays exponentially southward with an e‐folding length scale that is informative on the dynamics of the system. We further investigate the impact of the vertical supply of nutrients about phytoplankton growth with a conceptual model incorporating the mean effect of nutrient distribution, quasi‐geostrophic dynamics, and Ekman suction/pumping. Results confirm that the mean effect of mesoscale vertical velocity variability alone can sustain observed levels of net primary production in the immediate vicinity of the Gulf Stream, while other mechanisms, including horizontal advection and submesoscale dynamics, need to be considered when moving toward the subtropical gyre. New estimation of vertical velocity derived from an observational‐based approachQG‐vertical velocities can sustain net primary production in the Gulf StreamThe same methodology can be applied to other regions of the Global Ocean

ABSTRACTThe ability to detect HIV-2 and to discriminate between HIV-1 and HIV-2 infections was evaluated in 46 serum samples from Guinea-Bissau (GB) and Guinea-Conakry (GC) using serological tests and commercial (HIV-1) and in-house (HIV-2) real-time PCR assays. Samples were first identified as HIV-2 positive by Genie I/II assay in GB and GC. HIV positivity was detected in 44 of 46 samples by all screening and confirmatory assays. A diagnostic strategy based on Inno-LIA and HIV-1/2 RNA detection assays allowed accurate discrimination between HIV-1 and HIV-2 in 84% of single infections and confirmed 32% of double infections. In samples with double reactivity in the Inno-LIA test and no detection of both genomes, cross-reactivity likely hampered the identification of true double infections. In conclusion, the implementation of a diagnostic strategy, based on multiple specific serological tests and highly sensitive quantitative PCR assays, is recommended to ensure accurate HIV-2 diagnosis and appropriate therapy for individuals from areas in which the virus is endemic.