Laboratoire d'Océanographie Microbienne

Abstract Ocean plastic can persist in sea surface waters, eventually accumulating in remote areas of the world’s oceans. Here we characterise and quantify a major ocean plastic accumulation zone formed in subtropical waters between California and Hawaii: The Great Pacific Garbage Patch (GPGP). Our model, calibrated with data from multi-vessel and aircraft surveys, predicted at least 79 (45–129) thousand tonnes of ocean plastic are floating inside an area of 1.6 million km 2 ; a figure four to sixteen times higher than previously reported. We explain this difference through the use of more robust methods to quantify larger debris. Over three-quarters of the GPGP mass was carried by debris larger than 5 cm and at least 46% was comprised of fishing nets. Microplastics accounted for 8% of the total mass but 94% of the estimated 1.8 (1.1–3.6) trillion pieces floating in the area. Plastic collected during our study has specific characteristics such as small surface-to-volume ratio, indicating that only certain types of debris have the capacity to persist and accumulate at the surface of the GPGP. Finally, our results suggest that ocean plastic pollution within the GPGP is increasing exponentially and at a faster rate than in surrounding waters.

Phytoplankton blooms over Arctic Ocean continental shelves are thought to be restricted to waters free of sea ice. Here, we document a massive phytoplankton bloom beneath fully consolidated pack ice far from the ice edge in the Chukchi Sea, where light transmission has increased in recent decades because of thinning ice cover and proliferation of melt ponds. The bloom was characterized by high diatom biomass and rates of growth and primary production. Evidence suggests that under-ice phytoplankton blooms may be more widespread over nutrient-rich Arctic continental shelves and that satellite-based estimates of annual primary production in these waters may be underestimated by up to 10-fold.

Understanding the role of microbes in the oceans has focused on taxa that occur in high abundance; yet most of the marine microbial diversity is largely determined by a long tail of low-abundance taxa. This rare biosphere may have a cosmopolitan distribution because of high dispersal and low loss rates, and possibly represents a source of phylotypes that become abundant when environmental conditions change. However, the true ecological role of rare marine microorganisms is still not known. Here, we use pyrosequencing to describe the structure and composition of the rare biosphere and to test whether it represents cosmopolitan taxa or whether, similar to abundant phylotypes, the rare community has a biogeography. Our examination of 740,353 16S rRNA gene sequences from 32 bacterial and archaeal communities from various locations of the Arctic Ocean showed that rare phylotypes did not have a cosmopolitan distribution but, rather, followed patterns similar to those of the most abundant members of the community and of the entire community. The abundance distributions of rare and abundant phylotypes were different, following a log-series and log-normal model, respectively, and the taxonomic composition of the rare biosphere was similar to the composition of the abundant phylotypes. We conclude that the rare biosphere has a biogeography and that its tremendous diversity is most likely subjected to ecological processes such as selection, speciation, and extinction.

Chitin is one the most abundant polymers in nature and interacts with both carbon and nitrogen cycles. Processes controlling chitin degradation are summarized in reviews published some 20 years ago, but the recent use of culture-independent molecular methods has led to a revised understanding of the ecology and biochemistry of this process and the organisms involved. This review summarizes different mechanisms and the principal steps involved in chitin degradation at a molecular level while also discussing the coupling of community composition to measured chitin hydrolysis activities and substrate uptake. Ecological consequences are then highlighted and discussed with a focus on the cross feeding associated with the different habitats that arise because of the need for extracellular hydrolysis of the chitin polymer prior to metabolic use. Principal environmental drivers of chitin degradation are identified which are likely to influence both community composition of chitin degrading bacteria and measured chitin hydrolysis activities.

Observations have shown that large areas of the world ocean are characterized by lower than expected chlorophyll concentrations given the ambient phosphate and nitrate levels. In these High Nutrient‐Low Chlorophyll regions, limitations of phytoplankton growth by other nutrients like silicate or iron have been hypothesized and further evidenced by in situ experiments. To explore these limitations, a nine‐component ecosystem model has been embedded in the Hamburg model of the oceanic carbon cycle (HAMOCC5). This model includes phosphate, silicate, dissolved iron, two phytoplankton size fractions (nanophytoplankton and diatoms), two zooplankton size fractions (microzooplankton and mesozooplankton), one detritus and semilabile dissolved organic matter. The model is able to reproduce the main characteristics of two of the three main HNLC areas, i.e., the Southern Ocean and the equatorial Pacific. In the subarctic Pacific, silicate and phosphate surface concentrations are largely underestimated because of deficiencies in ocean dynamics. The low chlorophyll concentrations in HNLC areas are explained by the traditional hypothesis of a simultaneous iron‐grazing limitation: Diatoms are limited by iron whereas nanophytoplankton is controlled by very efficient grazing by microzooplankton. Phytoplankton assimilates 18 × 10 9 mol Fe yr −1 of which 73% is supplied by regeneration within the euphotic zone. The model predicts that the ocean carries with it about 75% of the phytoplankton demand for new iron, assuming a 1% solubility for atmospheric iron. Finally, it is shown that a higher supply of iron to surface water leads to a higher export production but paradoxically to a lower primary productivity.

Over the last decades, it has become clear that plastic pollution presents a global societal and environmental challenge given its increasing presence in the oceans. A growing literature has focused on the microbial life growing on the surfaces of these pollutants called the "plastisphere," but the general concepts of microbial ecotoxicology have only rarely been integrated. Microbial ecotoxicology deals with (i) the impact of pollutants on microbial communities and inversely (ii) how much microbes can influence their biodegradation. The goal of this review is to enlighten the growing literature of the last 15 years on microbial ecotoxicology related to plastic pollution in the oceans. First, we focus on the impact of plastic on marine microbial life and on the various functions it ensures in the ecosystems. In this part, we also discuss the driving factors influencing biofilm development on plastic surfaces and the potential role of plastic debris as vector for dispersal of harmful pathogen species. Second, we give a critical view of the extent to which marine microorganisms can participate in the decomposition of plastic in the oceans and of the relevance of current standard tests for plastic biodegradability at sea. We highlight some examples of metabolic pathways of polymer biodegradation. We conclude with several questions regarding gaps in current knowledge of plastic biodegradation by marine microorganisms and the identification of possible directions for future research.

Using a protocol of numerical experiments where horizontal resolution is progressively increased, we show that small-scale (or sub-mesoscale) physics has a strong impact on both mesoscale physics and phytoplankton production/subduction.Mesoscale and sub-mesoscale physics result from the nonlinear equilibration of an unstable baroclinic jet. The biogeochemical context is oligotrophy. The explicitly resolved sub-mesoscales, at least smaller than one fifth of the internal Rossby radius of deformation, reinforce the mesoscale eddy field and contribute to double the primary production and phytoplankton subduction budgets. This enhancement is due to the reinforced mesoscale physics and is also achieved by the small-scale frontal dynamics. This sub-mesoscale physics is associated with density and vorticity gradients around and between the eddies. It triggers a significant small-scale nutrient injection in the surface layers, leading to a phytoplankton field mostly dominated by fine spatial structures. It is believed that, depending on wind forcings, this scenario should work alternately with that of Abraham (1998) which invokes horizontal stirring of nutrient injected at large scales. Results also reveal a strong relationship between new production and negative vorticity, in the absence of wind forcing and during the period of formation of the eddies.

Three-dimensional monthly velocity fields from an ocean general circulation model are used to study the annual mean mass balance of the Pacific Equatorial Undercurrent (EUC). Eulerian diagnostics are used to evaluate the various meridional, vertical, and zonal mass fluxes related to the EUC. There are several distinct regimes along the equator, showing clear asymmetries between the western and eastern parts of the basin, and between the northern and southern edges of the EUC. Meridional fluxes are decomposed into pure Ekman divergence and geostrophic convergence, and it is shown that the asymmetries are mainly related to the spatial structure of the Ekman divergence, and thus to that of the trade winds. Lagrangian calculations are used to evaluate accurately the mass transfers between various sections of the EUC and between the EUC domain and the Tropics. The authors show that geostrophic convergence only ventilates the upper layers of the EUC and that the EUC really is a tongue of water flowing from the western Pacific to the Galapagos Islands and beyond. Finally, Lagrangian integrations extended to extratropical regions show that the EUC contributes to an exchange of water between the southern and northern Pacific (and the Indian Ocean through the Indonesian Throughflow): The equatorial zonal pressure gradient draws water from the western boundary currents that originate mostly in the south subtropical gyre. The poleward Ekman divergence associated with the equatorial upwelling distributes EUC water over the surface, with significant recirculation within the EUC (more than 15% of the total transport at 150°W).

The nucleic acid contents of individual bacterial cells as determined with three different nucleic acid-specific fluorescent dyes (SYBR I, SYBR II, and SYTO 13) and flow cytometry were compared for different seawater samples. Similar fluorescence patterns were observed, and bacteria with high apparent nucleic acid contents (HNA) could be discriminated from bacteria with low nucleic acid contents (LNA). The best discrimination between HNA and LNA cells was found when cells were stained with SYBR II. Bacteria in different water samples collected from seven freshwater, brackish water, and seawater ecosystems were prelabeled with tritiated leucine and then stained with SYBR II. After labeling and staining, HNA, LNA, and total cells were sorted by flow cytometry, and the specific activity of each cellular category was determined from leucine incorporation rates. The HNA cells were responsible for most of the total bacterial production, and the specific activities of cells in the HNA population varied between samples by a factor of seven. We suggest that nucleic acid content alone can be a better indicator of the fraction of growing cells than total counts and that this approach should be combined with other fluorescent physiological probes to improve detection of the most active cells in aquatic systems.

Abstract An important element of a data assimilation system is the statistical model used for representing the correlations of background error. This paper describes a practical algorithm that can be used to model a large class of two‐ and three‐dimensional, univariate correlation functions on the sphere. Application of the algorithm involves a numerical integration of a generalized diffusion‐type equation (GDE). The GDE is formed by replacing the Laplacian operator in the classical diffusion equation by a polynomial in the Laplacian. The integral solution of the GDE defines, after appropriate normalization, a correlation operator on the sphere. The kernel of the correlation operator is an isotropic correlation function. The free parameters controlling the shape and length‐scale of the correlation function are the products kpT, p = 1, 2, …, where (‐1) p kp is a weighting (‘diffusion’) coefficient (kp > 0) attached to the Laplacian with exponent p, and T is the total integration ‘time’. For the classical diffusion equation (a special case of the GDE with kp = 0 for all p > 1) the correlation function is shown to be well approximated by a Gaussian with length‐scale equal to (2k1T) 1/2 . The Laplacian‐based correlation model is particularly well suited for ocean models as it can be easily generalized to account for complex boundaries imposed by coastlines. Furthermore, a one‐dimensional analogue of the GDE can be used to model a family of vertical correlation functions, which in combination with the two‐dimensional GDE forms the basis of a three‐dimensional, (generally) non‐separable correlation model. Generalizations to account for anisotropic correlations are also possible by stretching and/or rotating the computational coordinates via a ‘diffusion’ tensor. Examples are presented from a variational assimilation system currently under development for the OPA ocean general‐circulation model of the Laboratoire d'Oceanographie Dynamique et de Climatologie.

Plastic floating at the ocean surface, estimated at tens to hundreds of thousands of metric tons, represents only a small fraction of the estimated several million metric tons annually discharged by rivers. Such an imbalance promoted the search for a missing plastic sink that could explain the rapid removal of river-sourced plastics from the ocean surface. On the basis of an in-depth statistical reanalysis of updated data on microplastics-a size fraction for which both ocean and river sampling rely on equal techniques-we demonstrate that current river flux assessments are overestimated by two to three orders of magnitude. Accordingly, the average residence time of microplastics at the ocean surface rises from a few days to several years, strongly reducing the theoretical need for a missing sink.

Plastics are ubiquitous in the oceans and constitute suitable matrices for bacterial attachment and growth. Understanding biofouling mechanisms is a key issue to assessing the ecological impacts and fate of plastics in marine environment. In this study, we investigated the different steps of plastic colonization of polyolefin-based plastics, on the first one hand, including conventional low-density polyethylene (PE), additivated PE with pro-oxidant (OXO), and artificially aged OXO (AA-OXO); and of a polyester, poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV), on the other hand. We combined measurements of physical surface properties of polymers (hydrophobicity and roughness) with microbiological characterization of the biofilm (cell counts, taxonomic composition, and heterotrophic activity) using a wide range of techniques, with some of them used for the first time on plastics. Our experimental setup using aquariums with natural circulating seawater during 6 weeks allowed us to characterize the successive phases of primo-colonization, growing, and maturation of the biofilms. We highlighted different trends between polymer types with distinct surface properties and composition, the biodegradable AA-OXO and PHBV presenting higher colonization by active and specific bacteria compared to non-biodegradable polymers (PE and OXO). Succession of bacterial population occurred during the three colonization phases, with hydrocarbonoclastic bacteria being highly abundant on all plastic types. This study brings original data that provide new insights on the colonization of non-biodegradable and biodegradable polymers by marine microorganisms.

We have compared simulations of anthropogenic CO 2 in the four three‐dimensional ocean models that participated in the first phase of the Ocean Carbon‐Cycle Model Intercomparison Project (OCMIP), as a means to identify their major differences. Simulated global uptake agrees to within ±19%, giving a range of 1.85±0.35 Pg C yr −1 for the 1980–1989 average. Regionally, the Southern Ocean dominates the present‐day air‐sea flux of anthropogenic CO 2 in all models, with one third to one half of the global uptake occurring south of 30°S. The highest simulated total uptake in the Southern Ocean was 70% larger than the lowest. Comparison with recent data‐based estimates of anthropogenic CO 2 suggest that most of the models substantially overestimate storage in the Southern Ocean; elsewhere they generally underestimate storage by less than 20%. Globally, the OCMIP models appear to bracket the real ocean's present uptake, based on comparison of regional data‐based estimates of anthropogenic CO 2 and bomb 14 C. Column inventories of bomb 14 C have become more similar to those for anthropogenic CO 2 with the time that has elapsed between the Geochemical Ocean Sections Study (1970s) and World Ocean Circulation Experiment (1990s) global sampling campaigns. Our ability to evaluate simulated anthropogenic CO 2 would improve if systematic errors associated with the data‐based estimates could be provided regionally.

The Antarctic and Arctic regions offer a unique opportunity to test factors shaping biogeography of marine microbial communities because these regions are geographically far apart, yet share similar selection pressures. Here, we report a comprehensive comparison of bacterioplankton diversity between polar oceans, using standardized methods for pyrosequencing the V6 region of the small subunit ribosomal (SSU) rRNA gene. Bacterial communities from lower latitude oceans were included, providing a global perspective. A clear difference between Southern and Arctic Ocean surface communities was evident, with 78% of operational taxonomic units (OTUs) unique to the Southern Ocean and 70% unique to the Arctic Ocean. Although polar ocean bacterial communities were more similar to each other than to lower latitude pelagic communities, analyses of depths, seasons, and coastal vs. open waters, the Southern and Arctic Ocean bacterioplankton communities consistently clustered separately from each other. Coastal surface Southern and Arctic Ocean communities were more dissimilar from their respective open ocean communities. In contrast, deep ocean communities differed less between poles and lower latitude deep waters and displayed different diversity patterns compared with the surface. In addition, estimated diversity (Chao1) for surface and deep communities did not correlate significantly with latitude or temperature. Our results suggest differences in environmental conditions at the poles and different selection mechanisms controlling surface and deep ocean community structure and diversity. Surface bacterioplankton may be subjected to more short-term, variable conditions, whereas deep communities appear to be structured by longer water-mass residence time and connectivity through ocean circulation.

Dissolved organic matter (DOM) in the oceans is one of the largest pools of reduced carbon on Earth, comparable in size to the atmospheric CO2 reservoir. A vast number of compounds are present in DOM, and they play important roles in all major element cycles, contribute to the storage of atmospheric CO2 in the ocean, support marine ecosystems, and facilitate interactions between organisms. At the heart of the DOM cycle lie molecular-level relationships between the individual compounds in DOM and the members of the ocean microbiome that produce and consume them. In the past, these connections have eluded clear definition because of the sheer numerical complexity of both DOM molecules and microorganisms. Emerging tools in analytical chemistry, microbiology, and informatics are breaking down the barriers to a fuller appreciation of these connections. Here we highlight questions being addressed using recent methodological and technological developments in those fields and consider how these advances are transforming our understanding of some of the most important reactions of the marine carbon cycle.

An intraspecies phylogenetic grouping of 168 human commensal Escherichia coli strains isolated from the stools of three geographically distinct human populations (France, Croatia, Mali) was generated by triplex PCR. The distributions of seven known extraintestinal virulence determinants (ibeA, pap, sfa/foc, afa, hly, cnf1, aer) were also determined by PCR. The data from the three populations were compiled, which showed that strains from phylogenetic groups A (40%) and B1 (34%) were the most common, followed by phylogenetic group D strains (15%). Strains of the phylogenetic group B2 were rare (11%). However, a significant specific distribution for strains of groups A, B1 and B2 within each population was observed, which may indicate the influence of (i) geographic/climatic conditions, (ii) dietary factors and/or the use of antibiotics or (iii) host genetic factors on the commensal flora. Virulence determinants were rarely detected, with only 25.6% of the strains harbouring at least one of the virulence genes tested. The strains with virulence factors most frequently belonged to phylogenetic group B2. The commensal strains of phylogenetic groups A, B1 and D had fewer virulence determinants than pathogenic strains of the corresponding groups when these data were compared with those for previous collections of virulent extraintestinal infection strains studied using the same approach. However, the virulence patterns of commensal and pathogenic B2 phylogenetic group strains were the same. The data thus suggest that strains of the A, B1 and D phylogenetic groups predominate in the gut flora and that these strains must acquire virulence factors to become pathogenic. In contrast, commensal phylogenetic group B2 strains are rare but appear to be potentially virulent.

Flow cytometry has become a valuable tool in aquatic and environmental microbiology that combines direct and rapid assays to determine numbers, cell size distribution and additional biochemical and physiological characteristics of individual cells, revealing the heterogeneity present in a population or community. Flow cytometry exhibits three unique technical properties of high potential to study the microbiology of aquatic systems: (i) its tremendous velocity to obtain and process data; (ii) the sorting capacity of some cytometers, which allows the transfer of specific populations or even single cells to a determined location, thus allowing further physical, chemical, biological or molecular analysis; and (iii) high-speed multiparametric data acquisition and multivariate data analysis. Flow cytometry is now commonly used in aquatic microbiology, although the application of cell sorting to microbial ecology and quantification of heterotrophic nanoflagellates and viruses is still under development. The recent development of laser scanning cytometry also provides a new way to further analyse sorted cells or cells recovered on filter membranes or slides. The main infrastructure limitations of flow cytometry are: cost, need for skilled and well-trained operators, and adequate refrigeration systems for high-powered lasers and cell sorters. The selection and obtaining of the optimal fluorochromes, control microorganisms and validations for a specific application may sometimes be difficult to accomplish.

The onset of the monsoon system over West Africa is linked to the northward migration of the Inter‐Tropical Convergence Zone (ITCZ) during the northern spring and summer. By using daily gridded rainfall data and NCEP/NCAR wind reanalyses over the period 1968–1990, we show that this migration is characterised by an abrupt latitudinal shift of the ITCZ in late June from a quasi‐stationary location at 5N in May–June to another quasi‐stationary location at 10N in July–August. A composite analysis based on the shift dates shows that this northward shift is associated with the occurrence of a westward‐travelling monsoon depression pattern over the Sahel with characteristic periodicities of 20–40 days.

We assess the impact of high dust deposition rates on marine biota and atmospheric CO 2 using a state‐of‐the‐art ocean biogeochemistry model and observations. Our model includes an explicit representation of two groups of phytoplankton and colimitation by iron, silicate, and phosphate. When high dust deposition rates from the Last Glacial Maximum (LGM) are used as input, our model shows an increase in the relative abundance of diatoms in today's iron‐limited regions, causing a global increase in export production by 6% and an atmospheric CO 2 drawdown of 15 ppm. When the combined effects of changes in dust, temperature, ice cover, and circulation are included, the model reproduces roughly our reconstruction of regional changes in export production during the LGM based on several paleoceanographic indicators. In particular, the model reproduces the latitudinal dipole in the Southern Ocean, driven in our simulations by the conjunction of dust, sea ice, and circulation changes. In the North Pacific the limited open ocean data suggest that we correctly simulate the east‐west gradient in the open ocean, but more data are needed to confirm this result. From our model‐data comparison and from the timing of the dust record at Vostok, we argue that our model estimate of the role of dust is realistic and that the maximum impact of high dust deposition on atmospheric CO 2 must be <30 ppm.

A suite of standard ocean hydrographic and circulation metrics are applied to the equilibrium physical solutions from 13 global carbon models participating in phase 2 of the Ocean Carbon‐cycle Model Intercomparison Project (OCMIP‐2). Model‐data comparisons are presented for sea surface temperature and salinity, seasonal mixed layer depth, meridional heat and freshwater transport, 3‐D hydrographic fields, and meridional overturning. Considerable variation exists among the OCMIP‐2 simulations, with some of the solutions falling noticeably outside available observational constraints. For some cases, model‐model and model‐data differences can be related to variations in surface forcing, subgrid‐scale parameterizations, and model architecture. These errors in the physical metrics point to significant problems in the underlying model representations of ocean transport and dynamics, problems that directly affect the OCMIP predicted ocean tracer and carbon cycle variables (e.g., air‐sea CO 2 flux, chlorofluorocarbon and anthropogenic CO 2 uptake, and export production). A substantial fraction of the large model‐model ranges in OCMIP‐2 biogeochemical fields (±25–40%) represents the propagation of known errors in model physics. Therefore the model‐model spread likely overstates the uncertainty in our current understanding of the ocean carbon system, particularly for transport‐dominated fields such as the historical uptake of anthropogenic CO 2 . A full error assessment, however, would need to account for additional sources of uncertainty such as more complex biological‐chemical‐physical interactions, biases arising from poorly resolved or neglected physical processes, and climate change.