Laboratoire des Sciences de l'Environnement Marin

Plastics are persistent synthetic polymers that accumulate as waste in the marine environment. Microplastic (MP) particles are derived from the breakdown of larger debris or can enter the environment as microscopic fragments. Because filter-feeder organisms ingest MP while feeding, they are likely to be impacted by MP pollution. To assess the impact of polystyrene microspheres (micro-PS) on the physiology of the Pacific oyster, adult oysters were experimentally exposed to virgin micro-PS (2 and 6 µm in diameter; 0.023 mg·L(-1)) for 2 mo during a reproductive cycle. Effects were investigated on ecophysiological parameters; cellular, transcriptomic, and proteomic responses; fecundity; and offspring development. Oysters preferentially ingested the 6-µm micro-PS over the 2-µm-diameter particles. Consumption of microalgae and absorption efficiency were significantly higher in exposed oysters, suggesting compensatory and physical effects on both digestive parameters. After 2 mo, exposed oysters had significant decreases in oocyte number (-38%), diameter (-5%), and sperm velocity (-23%). The D-larval yield and larval development of offspring derived from exposed parents decreased by 41% and 18%, respectively, compared with control offspring. Dynamic energy budget modeling, supported by transcriptomic profiles, suggested a significant shift of energy allocation from reproduction to structural growth, and elevated maintenance costs in exposed oysters, which is thought to be caused by interference with energy uptake. Molecular signatures of endocrine disruption were also revealed, but no endocrine disruptors were found in the biological samples. This study provides evidence that micro-PS cause feeding modifications and reproductive disruption in oysters, with significant impacts on offspring.

Decadal fluctuations in salinity, nutrients, chlorophyll, a variety of zooplankton taxa, and fish stocks in the Northeast Pacific are often poorly correlated with the most widely‐used index of large‐scale climate variability in the region ‐ the Pacific Decadal Oscillation (PDO). We define a new pattern of climate change, the North Pacific Gyre Oscillation (NPGO) and show that its variability is significantly correlated with previously unexplained fluctuations of salinity, nutrients and chlorophyll. Fluctuations in the NPGO are driven by regional and basin‐scale variations in wind‐driven upwelling and horizontal advection – the fundamental processes controlling salinity and nutrient concentrations. Nutrient fluctuations drive concomitant changes in phytoplankton concentrations, and may force similar variability in higher trophic levels. The NPGO thus provides a strong indicator of fluctuations in the mechanisms driving planktonic ecosystem dynamics. The NPGO pattern extends beyond the North Pacific and is part of a global‐scale mode of climate variability that is evident in global sea level trends and sea surface temperature. Therefore the amplification of the NPGO variance found in observations and in global warming simulations implies that the NPGO may play an increasingly important role in forcing global‐scale decadal changes in marine ecosystems.

Over the past decade, a significant increase in the circulation of infectious agents was observed. With the spread and emergence of epizootics, zoonoses and epidemics, the risks of pandemics became more and more critical. Human and animal health has also been threatened by antimicrobial resistance, environmental pollution and the development of multifactorial and chronic diseases. This highlighted the increasing globalization of health risks and the importance of the human-animal-ecosystem interface in the evolution and emergence of pathogens. A better knowledge of causes and consequences of certain human activities, lifestyles and behaviors in ecosystems is crucial for a rigorous interpretation of disease dynamics and to drive public policies. As a global good, health security must be understood on a global scale and from a global and cross-cutting perspective, integrating human health, animal health, plant health, ecosystems health and biodiversity. In this paper, we discuss how crucial it is to consider ecological, evolutionary and environmental sciences in understanding the emergence and re-emergence of infectious diseases and in facing the challenges of antimicrobial resistance. We also discuss the application of the “One Health” concept to non-communicable chronic diseases linked to exposure to multiple stresses, including toxic stress, and new lifestyles. Finally, we draw up a list of barriers that need removing and the ambitions that we must nurture for the effective application of the “One Health” concept. We conclude that the success of this One Health concept now requires breaking down the interdisciplinary barriers that still separate human and veterinary medicine from ecological, evolutionary and environmental sciences. The development of integrative approaches should be promoted by linking the study of factors underlying stress responses to their consequences on ecosystem functioning and evolution. This knowledge is required for the development of novel control strategies inspired by environmental mechanisms leading to desired equilibrium and dynamics in healthy ecosystems and must provide in the near future a framework for more integrated operational initiatives.

Over the past few decades, we have realized that the silica cycle is strongly intertwined with other major biogeochemical cycles, like those of carbon and nitrogen, and as such is intimately related to marine primary production, the efficiency of carbon export to the deep sea, and the inventory of carbon dioxide in the atmosphere. For nearly 20 years, the marine silica budget compiled by Tréguer et al. (1995) , with its exploration of reservoirs, processes, sources, and sinks in the silica cycle, has provided context and information fundamental to study of the silica cycle. Today, the budget needs revisiting to incorporate advances that have notably changed estimates of river and groundwater inputs to the ocean of dissolved silicon and easily dissolvable amorphous silica, inputs from the dissolution of terrestrial lithogenic silica in ocean margin sediments, reverse weathering removal fluxes, and outputs of biogenic silica (especially on ocean margins and in the form of nondiatomaceous biogenic silica). The resulting budget recognizes significantly higher input and output fluxes and notes that the recycling of silicon occurs mostly at the sediment-water interface and not during the sinking of silica particles through deep waters.

Time series of environmental measurements are essential for detecting, measuring and understanding changes in the Earth system and its biological communities. Observational series have accumulated over the past 2-5 decades from measurements across the world's estuaries, bays, lagoons, inland seas and shelf waters influenced by runoff. We synthesize information contained in these time series to develop a global view of changes occurring in marine systems influenced by connectivity to land. Our review is organized around four themes: (i) human activities as drivers of change; (ii) variability of the climate system as a driver of change; (iii) successes, disappointments and challenges of managing change at the sea-land interface; and (iv) discoveries made from observations over time. Multidecadal time series reveal that many of the world's estuarine-coastal ecosystems are in a continuing state of change, and the pace of change is faster than we could have imagined a decade ago. Some have been transformed into novel ecosystems with habitats, biogeochemistry and biological communities outside the natural range of variability. Change takes many forms including linear and nonlinear trends, abrupt state changes and oscillations. The challenge of managing change is daunting in the coastal zone where diverse human pressures are concentrated and intersect with different responses to climate variability over land and over ocean basins. The pace of change in estuarine-coastal ecosystems will likely accelerate as the human population and economies continue to grow and as global climate change accelerates. Wise stewardship of the resources upon which we depend is critically dependent upon a continuing flow of information from observations to measure, understand and anticipate future changes along the world's coastlines.

In the EU, the mapping and assessment of ecosystems and their services, abbreviated to MAES, is seen as a key action for the advancement of biodiversity objectives, and also to inform the development and implementation of related policies on water, climate, agriculture, forest, marine and regional planning. In this study, we present the development of an analytical framework which ensures that consistent approaches are used throughout the EU. It is framed by a broad set of key policy questions and structured around a conceptual framework that links human societies and their well-being with the environment. Next, this framework is tested through four thematic pilot studies, including stakeholders and experts working at different scales and governance levels, which contributed indicators to assess the state of ecosystem services. Indicators were scored according to different criteria and assorted per ecosystem type and ecosystem services using the common international classification of ecosystem services (CICES) as typology. We concluded that there is potential to develop a first EU wide ecosystem assessment on the basis of existing data if they are combined in a creative way. However, substantial data gaps remain to be filled before a fully integrated and complete ecosystem assessment can be carried out.

A common dynamical paradigm is that turbulence in the upper ocean is dominated by three classes of motion: mesoscale geostrophic eddies, internal waves and microscale three‐dimensional turbulence. Close to the ocean surface, however, a fourth class of turbulent motion is important: submesoscale frontal dynamics. These have a horizontal scale of O(1–10) km, a vertical scale of O(100) m, and a time scale of O(1) day. Here we review the physical‐chemical‐biological dynamics of submesoscale features, and discuss strategies for sampling them. Submesoscale fronts arise dynamically through nonlinear instabilities of the mesoscale currents. They are ephemeral, lasting only a few days after they are formed. Strong submesoscale vertical velocities can drive episodic nutrient pulses to the euphotic zone, and subduct organic carbon into the ocean's interior. The reduction of vertical mixing at submesoscale fronts can locally increase the mean time that photosynthetic organisms spend in the well‐lit euphotic layer and promote primary production. Horizontal stirring can create intense patchiness in planktonic species. Submesoscale dynamics therefore can change not only primary and export production, but also the structure and the functioning of the planktonic ecosystem. Because of their short time and space scales, sampling of submesoscale features requires new technologies and approaches. This paper presents a critical overview of current knowledge to focus attention and hopefully interest on the pressing scientific questions concerning these dynamics.

Microplastics (MPs) are present throughout aquatic ecosystems, and can be ingested by a wide variety of organisms. At present, the physical and chemical effects of environmental MPs on aquatic organisms are poorly documented. This study aims to examine the physiological and behavioral effects caused by fish consuming environmental microplastics at different life stages. MP samples were collected from beaches on three islands (Easter Island, Guam and Hawaii) located near the North and South gyres of the Pacific Ocean. Larvae and juveniles of Japanese Medaka were fed for 30days with three doses of MPs (0.01, 0.1 and 1% w/w in fish food) approximate to the concentrations measured in moderately and heavily contaminated ocean areas. Ingestion of MPs by medaka larvae caused (variously) death, decreased head/body ratios, increased EROD activity and DNA breaks and, alterations to swimming behavior. A diet of 0.1% MPs was the most toxic. Two-month-old juveniles fed with 0.01% MPs did not exhibit any symptoms except an increase in DNA breaks. Our results demonstrate ingestion and mainly sublethal effects of environmental MPs in early life stages of fish at realistic MP concentrations. The toxicity of microplastics varies from one sample to another, depending on polymer composition, weathering and pollutant content. This study examines the ecological consequences microplastic build-up in aquatic ecosystems, more particularly in coastal marine areas, which serve as breeding and growing grounds for a number of aquatic species.

The GEOTRACES Intermediate Data Product 2017 (IDP2017) is the second publicly available data product of the international GEOTRACES programme, and contains data measured and quality controlled before the end of 2016. The IDP2017 includes data from the Atlantic, Pacific, Arctic, Southern and Indian oceans, with about twice the data volume of the previous IDP2014. For the first time, the IDP2017 contains data for a large suite of biogeochemical parameters as well asaerosol and rain data characterising atmospherictrace element and isotope (TEI) sources. The TEI data in the IDP2017 are quality controlled by careful assessment of intercalibration results and multi-laboratory data comparisons at crossover stations. The IDP2017 consists of two parts: (1) a compilation of digital data for more than 450 TEIs as well as standard hydrographic parameters, and (2) the eGEOTRACES Electronic Atlas providing an on-line atlas that includes more than 590 section plots and 130 animated 3D scenes. The digital data are provided in several formats, including ASCII, Excel spreadsheet, netCDF, and Ocean Data View collection. Users can download the full data packages or make their own custom selections with a new on-line data extraction service. In addition to the actual data values, the IDP2017 also contains data quality flags and 1-σ data error values where available. Quality flags and error values are useful for data filtering and for statistical analysis. Metadata about data originators, analytical methods and original publications related to the data are linked in an easily accessible way. The eGEOTRACES Electronic Atlas is the visual representation of the IDP2017 as section plots and rotating 3D scenes. The basin-wide 3D scenes combine data from many cruises and provide quick overviews of large-scale tracer distributions. These 3D scenes provide geographical and bathymetric context that is crucial for the interpretation and assessment of tracer plumes near ocean margins or along ridges. The IDP2017 is the result of a truly international effort involving 326 researchers from 25 countries. This publication provides the critical reference for unpublished data, as well as for studies that make use of a large cross-section of data from the IDP2017.

Lelong A., Hégaret H., Soudant P. and Bates S.S. 2012. Pseudo-nitzschia (Bacillariophyceae) species, domoic acid and amnesic shellfish poisoning: revisiting previous paradigms. Phycologia 51: 168–216. DOI: 10.2216/11-37Pseudo-nitzschia is a globally distributed diatom genus, some species of which produce domoic acid (DA), the neurotoxin that causes amnesic shellfish poisoning. This toxin killed at least three humans in 1987, launching numerous studies concerning the identification, distribution, ecology and physiology of Pseudo-nitzschia spp. Since previous reviews in 1998, knowledge has been gained about the fate of DA, including its accumulation by marine animals and its degradation by light and bacteria. Molecular techniques and more precise microscopy have enabled the description of new Pseudo-nitzschia species, 15 since 2002, including ones that are cryptic and pseudo-cryptic. An increasing number of the 37 identified species, including oceanic and coastal species, have been studied in laboratory culture. The sexual reproduction of 14 species has been documented. Fourteen species have now been shown to be toxigenic, although some strains are not always toxic under the testing conditions. The biotic and abiotic factors that modify DA production are reviewed, with a focus on how new discoveries have changed our original hypotheses about control mechanisms. Recent studies confirm that silicate and phosphate limitation trigger DA production. However, stress by low concentrations of iron or high concentrations of copper are newly discovered triggers, suggesting a trace-metal chelation role for DA. Organic sources of nitrogen (urea and glutamine), as well as changes in pH, CO2, salinity and bacterial concentration, also enhance DA production. Laboratory and field studies sometimes give divergent results for conditions that are conducive to toxin production. Gaps in knowledge include further information about the whole genome of Pseudo-nitzschia (including sexual stages), mechanisms of DA production and decline, presence or absence of a resting stage, heterotrophic ability, impact of viruses and fungi, and a more complete description of the ecological and physiological roles of DA.

Mixotrophic plankton, which combine the uptake of inorganic resources and the ingestion of living prey, are ubiquitous in marine ecosystems, but their integrated biogeochemical impacts remain unclear. We address this issue by removing the strict distinction between phytoplankton and zooplankton from a global model of the marine plankton food web. This simplification allows the emergence of a realistic trophic network with increased fidelity to empirical estimates of plankton community structure and elemental stoichiometry, relative to a system in which autotrophy and heterotrophy are mutually exclusive. Mixotrophy enhances the transfer of biomass to larger sizes classes further up the food chain, leading to an approximately threefold increase in global mean organism size and an ∼35% increase in sinking carbon flux.

This contribution documents widespread trawling damage to cold-water coral reefs at 840-1300 m depth along the West Ireland continental shelf break and at 200 m off West Norway. These reefs are spectacular but poorly known. By-catches from commercial trawls for deep-water fish off West Ireland included large pieces (up to 1 m(2)) of coral that had been broken from reefs and a diverse array of coral-associated benthos. Five azooxanthellate scleractinarian corals were identified in these by-catches, viz. Desmophyllum cristagalli, Enallopsammia rostrata, Lophelia pertusa, Madrepora oculata and Solenosmilia variabilis. Dating of carbonate skeletons using (14)C accelerator mass spectrometry showed that the trawled coral matrix was at least 4550 years old. Surveys by remotely operated vehicles in Norway showed extensive fishing damage to L. pertusa reefs. The urgent need for deep-water coral conservation measures is discussed in a Northeast Atlantic context.

Microplastic contamination was determined in sediments of the Southern North Sea and floating at the sea surface of North West Europe. Floating concentrations ranged between zero and 1.5 microplastic/m3, whereas microplastic concentrations in sediments ranged between zero and 3146 particles/kg dry weight sediment. In sediments, mainly fibers and spheres were found, whereas at the sea surface fragments were dominant. At the sea surface, concentrations of microplastics are lower and more variable than in sediments, meaning that larger sample sizes and water volumes are required to find detectable concentrations. We have calculated the widths of the confidence intervals (CI) for different sample sizes, to give a first indication of the necessary sample size for a microplastic survey at the water surface. Higher concentrations of floating microplastics were found near estuaries. In sediments, estuaries and areas with a high organic carbon content were likely hotspots. Standardization of monitoring methods within marine regions is recommended to compare and assess microplastics pollution over time.

The main microbial diseases affecting marine cultured bivalves have been revised on the basis of the etiologic agents, pathogenesis and pathogenicity. Several recent bivalve-interaction models have been studied, including Pecten larvae-Vibrio pectinicida, brown ring disease, juvenile oyster disease, Pacific oyster nocardiosis and summer mortalities of oysters. In addition, the taxonomy and phylogeny of new potential bivalve pathogens and their virulence factors have been established. Facing the difficulty of identifying bacterial strains associated with molluscan diseases (mainly vibriosis), polyphasic approaches have been developed to correlate the phenotype and genotype of potential pathogens. By evaluating likely virulence mechanisms, developing biotests to screen virulent strains and characterising the genes implicated in pathogenesis, a new generation of diagnostic tools, based on potential virulence, will be developed. Acquisition of pertinent diagnostic tools will be of major benefit in disease management, health surveillance and monitoring will contribute to maintaining sustainable aquaculture industries.

Infectious diseases are mostly explored using reductionist approaches despite repeated evidence showing them to be strongly influenced by numerous interacting host and environmental factors. Many diseases with a complex aetiology therefore remain misunderstood. By developing a holistic approach to tackle the complexity of interactions, we decipher the complex intra-host interactions underlying Pacific oyster mortality syndrome affecting juveniles of Crassostrea gigas, the main oyster species exploited worldwide. Using experimental infections reproducing the natural route of infection and combining thorough molecular analyses of oyster families with contrasted susceptibilities, we demonstrate that the disease is caused by multiple infection with an initial and necessary step of infection of oyster haemocytes by the Ostreid herpesvirus OsHV-1 µVar. Viral replication leads to the host entering an immune-compromised state, evolving towards subsequent bacteraemia by opportunistic bacteria. We propose the application of our integrative approach to decipher other multifactorial diseases that affect non-model species worldwide.

This review focuses on the analysis of temporal beta diversity, which is the variation in community composition along time in a study area. Temporal beta diversity is measured by the variance of the multivariate community composition time series and that variance can be partitioned using appropriate statistical methods. Some of these methods are classical, such as simple or canonical ordination, whereas others are recent, including the methods of temporal eigenfunction analysis developed for multiscale exploration (i.e. addressing several scales of variation) of univariate or multivariate response data, reviewed, to our knowledge for the first time in this review. These methods are illustrated with ecological data from 13 years of benthic surveys in Chesapeake Bay, USA. The following methods are applied to the Chesapeake data: distance-based Moran's eigenvector maps, asymmetric eigenvector maps, scalogram, variation partitioning, multivariate correlogram, multivariate regression tree, and two-way MANOVA to study temporal and space-time variability. Local (temporal) contributions to beta diversity (LCBD indices) are computed and analysed graphically and by regression against environmental variables, and the role of species in determining the LCBD values is analysed by correlation analysis. A tutorial detailing the analyses in the R language is provided in an appendix.

Our planet is changing, and one of the most pressing challenges facing the scientific community revolves around understanding how ecological communities respond to global changes. From coastal to deep-sea ecosystems, ecologists are exploring new areas of research to find model organisms that help predict the future of life on our planet. Among the different categories of organisms, meiofauna offer several advantages for the study of marine benthic ecosystems. This paper reviews the advances in the study of meiofauna with regard to climate change and anthropogenic impacts. Four taxonomic groups are valuable for predicting global changes: foraminifers (especially calcareous forms), nematodes, copepods and ostracods. Environmental variables are fundamental in the interpretation of meiofaunal patterns and multistressor experiments are more informative than single stressor ones, revealing complex ecological and biological interactions. Global change has a general negative effect on meiofauna, with important consequences on benthic food webs. However, some meiofaunal species can be favoured by the extreme conditions induced by global change, as they can exhibit remarkable physiological adaptations.

Abstract. The element silicon (Si) is required for the growth of silicified organisms in marine environments, such as diatoms. These organisms consume vast amounts of Si together with N, P, and C, connecting the biogeochemical cycles of these elements. Thus, understanding the Si cycle in the ocean is critical for understanding wider issues such as carbon sequestration by the ocean's biological pump. In this review, we show that recent advances in process studies indicate that total Si inputs and outputs, to and from the world ocean, are 57 % and 37 % higher, respectively, than previous estimates. We also update the total ocean silicic acid inventory value, which is about 24 % higher than previously estimated. These changes are significant, modifying factors such as the geochemical residence time of Si, which is now about 8000 years, 2 times faster than previously assumed. In addition, we present an updated value of the global annual pelagic biogenic silica production (255 Tmol Si yr−1) based on new data from 49 field studies and 18 model outputs, and we provide a first estimate of the global annual benthic biogenic silica production due to sponges (6 Tmol Si yr−1). Given these important modifications, we hypothesize that the modern ocean Si cycle is at approximately steady state with inputs =14.8(±2.6) Tmol Si yr−1 and outputs =15.6(±2.4) Tmol Si yr−1. Potential impacts of global change on the marine Si cycle are discussed.

The problem of understanding the effect of the environment on fish activities and performance, in any generalized way, remains intractable. Solving this issue is, however, a key to addressing contemporary environmental concerns. As suggested 20 years ago by W. H. Neill, the authors returned to the drawing board, using as a background the conceptual scheme initially proposed by F. E. J. Fry. They revisited the effect of ambient oxygen availability upon fish metabolism and clarified the definitions of limiting, critical and incipient lethal oxygen (ILO) levels. The concepts of oxy-conformer and oxy-regulator are revisited, and P. W. Hochachka's idea of scope for survival is explored. Finally, how the cardiovascular system contributes to the capacity of fishes to respond to the reduced oxygen availability is considered. Various hands-on recommendations and software (R scripts) are provided for researchers interested in investigating these concepts.

Abstract. Phytoplankton identification and abundance data are now commonly feeding plankton distribution databases worldwide. This study is a first attempt to compile the largest possible body of data available from different databases as well as from individual published or unpublished datasets regarding diatom distribution in the world ocean. The data obtained originate from time series studies as well as spatial studies. This effort is supported by the Marine Ecosystem Model Inter-Comparison Project (MAREMIP), which aims at building consistent datasets for the main plankton functional types (PFTs) in order to help validate biogeochemical ocean models by using carbon (C) biomass derived from abundance data. In this study we collected over 293 000 individual geo-referenced data points with diatom abundances from bottle and net sampling. Sampling site distribution was not homogeneous, with 58% of data in the Atlantic, 20% in the Arctic, 12% in the Pacific, 8% in the Indian and 1% in the Southern Ocean. A total of 136 different genera and 607 different species were identified after spell checking and name correction. Only a small fraction of these data were also documented for biovolumes and an even smaller fraction was converted to C biomass. As it is virtually impossible to reconstruct everyone's method for biovolume calculation, which is usually not indicated in the datasets, we decided to undertake the effort to document, for every distinct species, the minimum and maximum cell dimensions, and to convert all the available abundance data into biovolumes and C biomass using a single standardized method. Statistical correction of the database was also adopted to exclude potential outliers and suspicious data points. The final database contains 90 648 data points with converted C biomass. Diatom C biomass calculated from cell sizes spans over eight orders of magnitude. The mean diatom biomass for individual locations, dates and depths is 141.19 μg C l−1, while the median value is 11.16 μg C l−1. Regarding biomass distribution, 19% of data are in the range 0–1 μg C l−1, 29% in the range 1–10 μg C l−1, 31% in the range 10–100 μg C l−1, 18% in the range 100–1000 μg C l−1, and only 3% > 1000 μg C l−1. Interestingly, less than 50 species contributed to > 90% of global biomass, among which centric species were dominant. Thus, placing significant efforts on cell size measurements, process studies and C quota calculations of these species should considerably improve biomass estimates in the upcoming years. A first-order estimate of the diatom biomass for the global ocean ranges from 444 to 582 Tg C, which converts to 3 to 4 Tmol Si and to an average Si biomass turnover rate of 0.15 to 0.19 d−1. Link to the dataset: doi:10.1594/PANGAEA.777384.