Laboratoire d’Océanologie et de Géosciences

An accurate description of the abundance and size distribution of lakes is critical to quantifying limnetic contributions to the global carbon cycle. However, estimates of global lake abundance are poorly constrained. We used high-resolution satellite imagery to produce a GLObal WAter BOdies database (GLOWABO), comprising all lakes greater than 0.002 km2. GLOWABO contains geographic and morphometric information for ~117 million lakes with a combined surface area of about 5 × 106 km2, which is 3.7% of the Earth's nonglaciated land area. Large and intermediate-sized lakes dominate the total lake surface area. Overall, lakes are less abundant but cover a greater total surface area relative to previous estimates based on statistical extrapolations. The GLOWABO allows for the global-scale evaluation of fundamental limnological problems, providing a foundation for improved quantification of limnetic contributions to the biogeochemical processes at large scales.

In this study, we evaluated accumulation and adverse effects of ingestion of microplastics in the monogonont rotifer (Brachionus koreanus). The dependence of microplastic toxicity on particle size was investigated by measuring several in vivo end points and studying the ingestion and egestion using 0.05-, 0.5-, and 6-μm nonfunctionalized polystyrene microbeads. To identify the defense mechanisms activated in response to microplastic exposure, the activities of several antioxidant-related enzymes and the phosphorylation status of mitogen-activated protein kinases (MAPKs) were determined. Exposure to polystyrene microbeads of all sizes led to significant size-dependent effects, including reduced growth rate, reduced fecundity, decreased lifespan and longer reproduction time. Rotifers exposed to 6-μm fluorescently labeled microbeads exhibited almost no fluorescence after 24 h, while rotifers exposed to 0.05- and 0.5-μm fluorescently labeled microbeads displayed fluorescence until 48 h, suggesting that 6-μm microbeads are more effectively egested from B. koreanus than 0.05- or 0.5-μm microbeads. This observation provides a potential explanation for our findings that microbead toxicity was size-dependent and smaller microbeads were more toxic. In vitro tests revealed that antioxidant-related enzymes and MAPK signaling pathways were significantly activated in response to microplastic exposure in a size-dependent manner.

Abstract. We present an overview of the plankton studies conducted during the last 25 years in the epipelagic offshore waters of the Mediterranean Sea. This quasi-enclosed sea is characterized by a rich and complex physical dynamics with distinctive traits, especially in regard to the thermohaline circulation. Recent investigations have basically confirmed the long-recognised oligotrophic nature of this sea, which increases along both the west-east and the north-south directions. Nutrient availability is low, especially for phosphorous (N:P up to 60), though this limitation may be buffered by inputs from highly populated coasts and from the atmosphere. Phytoplankton biomass, as chl a, generally displays low values (less than 0.2 μg chl a l−1) over large areas, with a modest late winter increase. A large bloom (up to 3 μg l−1) is observed throughout the late winter and spring exclusively in the NW area. Relatively high biomass values are recorded in fronts and cyclonic gyres. A deep chlorophyll maximum is a permanent feature for the whole basin, except during the late winter mixing. It is found at increasingly greater depths ranging from 30 m in the Alboran Sea to 120 m in the easternmost Levantine basin. Primary production reveals a west-east decreasing trend and ranges between 59 and 150 g C m−2 y−1 (in situ measurements). Overall, the basin is largely dominated by small autotrophs, microheterotrophs and egg-carrying copepod species. The microorganisms (phytoplankton, viruses, bacteria, flagellates and ciliates) and zooplankton components reveal a considerable diversity and variability over spatial and temporal scales, although the latter is poorly studied. Examples are the wide diversity of dinoflagellates and coccolithophores, the multifarious role of diatoms or picoeukaryotes, and the distinct seasonal or spatial patterns of the species-rich copepod genera or families which dominate the basin. Major dissimilarities between western and eastern basins have been highlighted in species composition of phytoplankton and mesozooplankton, but also in the heterotrophic microbial components and in their relationships. Superimposed to these longitudinal differences, a pronounced biological heterogeneity is also observed in areas hosting deep convection, fronts, cyclonic and anti-cyclonic gyres or eddies. In such areas, the intermittent nutrient enrichment promotes a switching between a small-sized microbial community and diatom-dominated populations. A classical food web readily substitutes the microbial food web in these cases. These switches, likely occurring within a continuum of trophic pathways, may greatly increase the flux towards higher trophic levels, in spite of the apparent heterotrophy. Basically, the microbial system seems to be both bottom-up and top-down controlled. A "multivorous web" is shown by the great variety of feeding modes and preferences and by the significant and simultaneous grazing impact on phytoplankton and ciliates by mesozooplankton.

Burial in sediments removes organic carbon (OC) from the short-term biosphere-atmosphere carbon (C) cycle, and therefore prevents greenhouse gas production in natural systems. Although OC burial in lakes and reservoirs is faster than in the ocean, the magnitude of inland water OC burial is not well constrained. Here we generate the first global-scale and regionally resolved estimate of modern OC burial in lakes and reservoirs, deriving from a comprehensive compilation of literature data. We coupled statistical models to inland water area inventories to estimate a yearly OC burial of 0.15 (range, 0.06-0.25) Pg C, of which ~40% is stored in reservoirs. Relatively higher OC burial rates are predicted for warm and dry regions. While we report lower burial than previously estimated, lake and reservoir OC burial corresponded to ~20% of their C emissions, making them an important C sink that is likely to increase with eutrophication and river damming.

Microplastic pollution causes a major concern in the marine environment due to their worldwide distribution, persistence, and adverse effects of these pollutants in the marine ecosystem. Despite its global presence, there is still a lack of information on the effect of microplastics on marine organisms at the molecular level. Herein we demonstrated ingestion and egestion of nano- (0.05 μm) and micro-sized (0.5 and 6 μm) polystyrene microbeads in the marine copepod Paracyclopina nana, and examined molecular responses to exposure to microbeads with in vivo endpoints such as growth rate and fecundity. Also, we proposed an adverse outcome pathway for microplastic exposure that covers molecular and individual levels. This study provides the first insight into the mode of action in terms of microplastic-induced oxidative stress and related signaling pathways in P. nana.

Ocean color measured from satellites provides daily, global estimates of marine inherent optical properties (IOPs). Semi-analytical algorithms (SAAs) provide one mechanism for inverting the color of the water observed by the satellite into IOPs. While numerous SAAs exist, most are similarly constructed and few are appropriately parameterized for all water masses for all seasons. To initiate community-wide discussion of these limitations, NASA organized two workshops that deconstructed SAAs to identify similarities and uniqueness and to progress toward consensus on a unified SAA. This effort resulted in the development of the generalized IOP (GIOP) model software that allows for the construction of different SAAs at runtime by selection from an assortment of model parameterizations. As such, GIOP permits isolation and evaluation of specific modeling assumptions, construction of SAAs, development of regionally tuned SAAs, and execution of ensemble inversion modeling. Working groups associated with the workshops proposed a preliminary default configuration for GIOP (GIOP-DC), with alternative model parameterizations and features defined for subsequent evaluation. In this paper, we: (1) describe the theoretical basis of GIOP; (2) present GIOP-DC and verify its comparable performance to other popular SAAs using both in situ and synthetic data sets; and, (3) quantify the sensitivities of their output to their parameterization. We use the latter to develop a hierarchical sensitivity of SAAs to various model parameterizations, to identify components of SAAs that merit focus in future research, and to provide material for discussion on algorithm uncertainties and future emsemble applications.

Boussinesq's hypothesis is at the heart of eddy viscosity models, which are used in many different fields to model turbulent flows. In its present time formulation, this hypothesis corresponds to an alignment between the Reynolds stress and mean strain tensors. We begin with historical remarks on Boussinesq's results and recall that he introduced a local averaging twenty years before Reynolds, but using an approach that prevented him from discovering Reynolds' stress tensor. We then introduce an indicator that characterizes the validity of this hypothesis. For experimental and numerical databases, when the tensors are known, this can be used to directly estimate the validity of this hypothesis. We show, using several different databases, that this hypothesis is almost never verified. We address, in conclusion, the analogy with kinetic theory, and the reason why this analogy cannot be applied, in general, for turbulent flows.

In this paper we review the technologies available to make globally quantitative observations of particles in general-and plankton in particular-in the world oceans, and for sizes varying from sub-microns to centimeters. Some of these technologies have been available for years while others have only recently emerged. Use of these technologies is critical to improve understanding of the processes that control abundances, distributions and composition of plankton, provide data necessary to constrain and improve ecosystem and biogeochemical models, and forecast changes in marine ecosystems in light of climate change. In this paper we begin by providing the motivation for plankton observations, quantification and diversity qualification on a global scale. We then expand on the state-of-the-art, detailing a variety of relevant and (mostly) mature technologies and measurements, including bulk measurements of plankton, pigment composition, uses of genomic, optical and acoustical methods as well Lombard et al.

Phytoplankton plays an important role in the global carbon cycle via the fixation of inorganic carbon during photosynthesis. However, the efficiency of this “biological pump of carbon” strongly depends on the nature of the phytoplankton. Monitoring spatial and temporal variations of the distribution of dominant phytoplankton groups at the global scale is thus of critical importance. Recently, an algorithm has been developed to detect the major dominant phytoplankton groups from anomalies of the marine signal measured by ocean color satellites. This method, called PHYSAT, allows to identify nanoeucaryotes, Prochlorococcus, Synechococcus and diatoms. In this paper, PHYSAT has been improved to detect an additional group, named phaeocystis‐like, by analyzing specific signal anomalies in the Southern Ocean during winter months. This new version of PHYSAT was then used to process daily global SeaWiFS GAC data between 1998 and 2006. The global distribution of major phytoplankton groups is presented in this study as a monthly climatology of the most frequent phytoplankton group. The contribution of nanoeucaryotes‐dominated waters to the global ocean varies from 45 to 70% depending on the season, whereas both diatoms and phaeocystis‐like contributions exhibit a stronger seasonal variability mostly due to the large blooms that occur during winter in the Southern Ocean. Three regions of particular interest are also studied in more details: the Southern Ocean, the North Atlantic, and the Equatorial Pacific. The North Atlantic diatom bloom shows a large interannual variability. Large blooms of both diatoms and phaeocystis‐like are observed during winter in the Southern Ocean, with a larger contribution from diatoms. Their respective geographical distribution is shown to be tightly related to the depth of the mixed‐layer, with diatoms prevailing in stratified waters. Synechococcus and Prochloroccocus prevail in the Equatorial Pacific, but our data show also sporadic diatoms contributions in this region during La Niña. The observed seasonal cycle and interannual variability of phytoplankton groups in the global ocean suggest that the PHYSAT archive is suitable to study the impact of climate variability on the structure of marine ecosystems.

Despite evidence from a number of Earth systems that abrupt temporal changes known as regime shifts are important, their nature, scale and mechanisms remain poorly documented and understood. Applying principal component analysis, change-point analysis and a sequential t-test analysis of regime shifts to 72 time series, we confirm that the 1980s regime shift represented a major change in the Earth's biophysical systems from the upper atmosphere to the depths of the ocean and from the Arctic to the Antarctic, and occurred at slightly different times around the world. Using historical climate model simulations from the Coupled Model Intercomparison Project Phase 5 (CMIP5) and statistical modelling of historical temperatures, we then demonstrate that this event was triggered by rapid global warming from anthropogenic plus natural forcing, the latter associated with the recovery from the El Chichón volcanic eruption. The shift in temperature that occurred at this time is hypothesized as the main forcing for a cascade of abrupt environmental changes. Within the context of the last century or more, the 1980s event was unique in terms of its global scope and scale; our observed consequences imply that if unavoidable natural events such as major volcanic eruptions interact with anthropogenic warming unforeseen multiplier effects may occur.

BACKGROUND: Given the polymicrobial nature of pulmonary infections in patients with cystic fibrosis (CF), it is essential to enhance our knowledge on the composition of the microbial community to improve patient management. In this study, we developed a pyrosequencing approach to extensively explore the diversity and dynamics of fungal and prokaryotic populations in CF lower airways. METHODOLOGY AND PRINCIPAL FINDINGS: Fungi and bacteria diversity in eight sputum samples collected from four adult CF patients was investigated using conventional microbiological culturing and high-throughput pyrosequencing approach targeting the ITS2 locus and the 16S rDNA gene. The unveiled microbial community structure was compared to the clinical profile of the CF patients. Pyrosequencing confirmed recently reported bacterial diversity and observed complex fungal communities, in which more than 60% of the species or genera were not detected by cultures. Strikingly, the diversity and species richness of fungal and bacterial communities was significantly lower in patients with decreased lung function and poor clinical status. Values of Chao1 richness estimator were statistically correlated with values of the Shwachman-Kulczycki score, body mass index, forced vital capacity, and forced expiratory volume in 1 s (p = 0.046, 0.047, 0.004, and 0.001, respectively for fungal Chao1 indices, and p = 0.010, 0.047, 0.002, and 0.0003, respectively for bacterial Chao1 values). Phylogenetic analysis showed high molecular diversities at the sub-species level for the main fungal and bacterial taxa identified in the present study. Anaerobes were isolated with Pseudomonas aeruginosa, which was more likely to be observed in association with Candida albicans than with Aspergillus fumigatus. CONCLUSIONS: In light of the recent concept of CF lung microbiota, we viewed the microbial community as a unique pathogenic entity. We thus interpreted our results to highlight the potential interactions between microorganisms and the role of fungi in the context of improving survival in CF.

The marine areas of South America (SA) include almost 30,000 km of coastline and encompass three different oceanic domains--the Caribbean, the Pacific, and the Atlantic--ranging in latitude from 12∘N to 55∘S. The 10 countries that border these coasts have different research capabilities and taxonomic traditions that affect taxonomic knowledge. This paper analyzes the status of knowledge of marine biodiversity in five subregions along the Atlantic and Pacific coasts of South America (SA): the Tropical East Pacific, the Humboldt Current,the Patagonian Shelf, the Brazilian Shelves, and the Tropical West Atlantic, and it provides a review of ecosystem threats and regional marine conservation strategies. South American marine biodiversity is least well known in the tropical subregions (with the exception of Costa Rica and Panama). Differences in total biodiversity were observed between the Atlantic and Pacific oceans at the same latitude. In the north of the continent, the Tropical East Pacific is richer in species than the Tropical West Atlantic, however, when standardized by coastal length, there is very little difference among them. In the south, the Humboldt Current system is much richer than the Patagonian Shelf. An analysis of endemism shows that 75% of the species are reported within only one of the SA regions, while about 22% of the species of SA are not reported elsewhere in the world. National and regional initiatives focusing on new exploration, especially to unknown areas and ecosystems, as well as collaboration among countries are fundamental to achieving the goal of completing inventories of species diversity and distribution.These inventories will allow accurate interpretation of the biogeography of its two oceanic coasts and latitudinal trends,and will also provide relevant information for science based policies.

Abstract Increased use and improved methodology of carbonate clumped isotope thermometry has greatly enhanced our ability to interrogate a suite of Earth‐system processes. However, interlaboratory discrepancies in quantifying carbonate clumped isotope (Δ 47 ) measurements persist, and their specific sources remain unclear. To address interlaboratory differences, we first provide consensus values from the clumped isotope community for four carbonate standards relative to heated and equilibrated gases with 1,819 individual analyses from 10 laboratories. Then we analyzed the four carbonate standards along with three additional standards, spanning a broad range of δ 47 and Δ 47 values, for a total of 5,329 analyses on 25 individual mass spectrometers from 22 different laboratories. Treating three of the materials as known standards and the other four as unknowns, we find that the use of carbonate reference materials is a robust method for standardization that yields interlaboratory discrepancies entirely consistent with intralaboratory analytical uncertainties. Carbonate reference materials, along with measurement and data processing practices described herein, provide the carbonate clumped isotope community with a robust approach to achieve interlaboratory agreement as we continue to use and improve this powerful geochemical tool. We propose that carbonate clumped isotope data normalized to the carbonate reference materials described in this publication should be reported as Δ 47 (I‐CDES) values for Intercarb‐Carbon Dioxide Equilibrium Scale.

The biogeochemical role of phytoplanktonic organisms strongly varies from one plankton type to another, and their relative abundance and distribution have fundamental consequences at the global and climatological scales. In situ observations find dominant types often associated to specific physical and chemical water properties. However, the mechanisms and spatiotemporal scales by which marine ecosystems are organized are largely not known. Here we investigate the spatiotemporal organization of phytoplankton communities by combining multisatellite data, notably high-resolution ocean-color maps of dominant types and altimetry-derived Lagrangian diagnostics of the surface transport. We find that the phytoplanktonic landscape is organized in (sub-)mesoscale patches (10-100 km) of dominant types separated by physical fronts induced by horizontal stirring. These physical fronts delimit niches supported by water masses of similar history and whose lifetimes are comparable with the timescale of the bloom onset (few weeks). The resonance between biological activity and physical processes suggest that the spatiotemporal (sub-)mesoscales associated to stirring are determinant in the observation and modeling of marine ecosystems.

Warming of the global climate is now unequivocal and its impact on Earth' functional units has become more apparent. Here, we show that marine ecosystems are not equally sensitive to climate change and reveal a critical thermal boundary where a small increase in temperature triggers abrupt ecosystem shifts seen across multiple trophic levels. This large-scale boundary is located in regions where abrupt ecosystem shifts have been reported in the North Atlantic sector and thereby allows us to link these shifts by a global common phenomenon. We show that these changes alter the biodiversity and carrying capacity of ecosystems and may, combined with fishing, precipitate the reduction of some stocks of Atlantic cod already severely impacted by exploitation. These findings offer a way to anticipate major ecosystem changes and to propose adaptive strategies for marine exploited resources such as cod in order to minimize social and economic consequences.

Abstract Global pollution by plastics derived from petroleum has fostered the development of carbon–neutral, biodegradable bioplastics synthesized from renewable resources such as modern biomass, yet knowledge on the impact of bioplastics on ecosystems is limited. Here we review the polylactic acid plastic with focus on synthesis, biodegradability tuning, environmental conversion to microplastics, and impact on microbes, algae, phytoplankton, zooplankton, annelids, mollusk and fish. Polylactic acid is a low weight semi-crystalline bioplastic used in agriculture, medicine, packaging and textile. Polylactic acid is one of the most widely used biopolymers, accounting for 33% of all bioplastics produced in 2021. Although biodegradable in vivo , polylactic acid is not completely degradable under natural environmental conditions, notably under aquatic conditions. Polylactic acid disintegrates into microplastics faster than petroleum-based plastics and may pose severe threats to the exposed biota.

Abstract Large‐scale biogeographical changes in the biodiversity of a key zooplankton group (calanoid copepods) were detected in the north‐eastern part of the North Atlantic Ocean and its adjacent seas over the period 1960–1999. These findings provided key empirical evidence for climate change impacts on marine ecosystems at the regional to oceanic scale. Since 1999, global temperatures have continued to rise in the region. Here, we extend the analysis to the period 1958–2005 using all calanoid copepod species assemblages (nine species assemblages based on an analysis including a total of 108 calanoid species or taxa) and show that this phenomenon has been reinforced in all regions. Our study reveals that the biodiversity of calanoid copepods are responding quickly to sea surface temperature (SST) rise by moving geographically northward at a rapid rate up to about 23.16 km yr −1 . Our analysis suggests that nearly half of the increase in sea temperature in the northeast Atlantic and adjacent seas is related to global temperature rises (46.35% of the total variance of temperature) while changes in both natural modes of atmospheric and oceanic circulation explain 26.45% of the total variance of temperature. Although some SST isotherms have moved northwards by an average rate of up to 21.75 km yr −1 (e.g. the North Sea), their movement cannot fully quantify all species assemblage shifts. Furthermore, the observed rates of biogeographical movements are far greater than those observed in the terrestrial realm. Here, we discuss the processes that may explain such a discrepancy and suggest that the differences are mainly explained by the fluid nature of the pelagic domain, the life cycle of the zooplankton and the lesser anthropogenic influence (e.g. exploitation, habitat fragmentation) on these organisms. We also hypothesize that despite changes in the path and intensity of the oceanic currents that may modify quickly and greatly pelagic zooplankton species, these organisms may reflect better the current impact of climate warming on ecosystems as terrestrial organisms are likely to significantly lag the current impact of climate change.

Although recent studies suggest that climate change may substantially accelerate the rate of species loss in the biosphere, only a few studies have focused on the potential consequences of a spatial reorganization of biodiversity with global warming. Here, we show a pronounced latitudinal increase in phytoplanktonic and zooplanktonic biodiversity in the extratropical North Atlantic Ocean in recent decades. We also show that this rise in biodiversity paralleled a decrease in the mean size of zooplanktonic copepods and that the reorganization of the planktonic ecosystem toward dominance by smaller organisms may influence the networks in which carbon flows, with negative effects on the downward biological carbon pump and demersal Atlantic cod (Gadus morhua). Our study suggests that, contrary to the usual interpretation of increasing biodiversity being a positive emergent property promoting the stability/resilience of ecosystems, the parallel decrease in sizes of planktonic organisms could be viewed in the North Atlantic as reducing some of the services provided by marine ecosystems to humans.

Using long‐term data of 149 warm alien species since 1924, we show that the introduction of warm and tropical alien species has been exacerbated by the observed warming of the eastern Mediterranean Sea. The phenomenon has accelerated after an abrupt shift in both regional and global temperatures that we detect around 1998, leading to a 150% increase in the annual mean rate of species entry after this date. Abrupt rising temperature since the end of the 1990s has modified the potential thermal habitat available for warm‐water species, facilitating their settlement at an unexpectedly rapid rate. The speed of alien species spreading and response to global warming is apparently much faster than temperature increase itself, presenting an important warning for the future of Mediterranean Sea biodiversity. In addition to the sea warming, other factors that enable and enhance biological invasions, such as salinity increase and oceanographic forcing, are also discussed.

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.