French Research Institute for Exploitation of the Sea
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Climate change, stock productivity and demersal fisheries management: a central Mediterranean case study
No full textStock-recruitment (S-R) relationships are critical for assessing stock productivity and guiding fisheries management. In the Mediterranean Sea, the estimation of accurate S-R relationships is challenging due to limited data. The Adriatic Sea, a highly productive but overfished Mediterranean region, is particularly vulnerable to climate change. Over the past two decades, significant declines in long-lived demersal (e.g. European hake) stocks in the Adriatic and Western Ionian seas have prompted targeted management measures. However, recent positive trends in medium- and short-lived stocks (e.g shrimps) suggest that reduced coastal fishing pressure and favorable environmental conditions are driving partial stock recovery. The relative influence of these factors, and whether favorable environmental impacts will persist, remains uncertain. This study is the first to estimate environmentally mediated S-R relationships (EMSRR) for key stocks in the investigated region. Using the BEMTOOL simulation model, we assess the biological and economic impacts of various management and climate scenarios. Results highlight the importance of integrating climate factors into mixed fisheries management to ensure the robustness of measures preventing stocks from falling below safe biological limits
Characteristics of Mesoscale to Submesoscale Eddies in the Labrador Sea: Insights from Ship Observations
No full textCharacterization of coherent eddies is often based on gridded satellite altimetry products. In subpolar regions, these products face limitations due to their low spatial resolution, and the decreasing Rossby radius of deformation at higher latitudes, making in-situ observations indispensable for eddy characterization. Here, we present a census of mesoscale to submesoscale eddy characteristics in the Labrador Sea - a region where eddies play an important role in winter deep convection and subsequent restratification. Using ship-based observations, we fit an idealized eddy solution to horizontal velocity measurements acquired along ship tracks, determining an optimal eddy center and other key eddy properties. Based on three research cruises, we reconstructed 40 eddies ranging from 3 to 39 km in radius (mean 15 km) and azimuthal velocity between 7 and 58 cm s−1 (mean 26 cm s−1). The azimuthal velocity structure implies to a large extent solid-body rotation in the eddy’s inner core, while opposite signs of vorticity in the outer ring suggest strong vorticity shields. When compared to ship-based observations, the eddy field representation in gridded altimetry products is significantly distorted, with many eddies being underrepresented or undetected. This is even the case for larger-scale features despite having an eddy signature in the along-track altimetry product, which appears to be suppressed in the subsequent mapping methodology. Finally, comparisons with submesoscale-permitting numerical simulation output shows favorable agreement giving confidence in both the ship-based reconstruction and the numerical model’s realism in representing high-latitude eddy dynamics
An ecosystem modelling approach to assess potential impacts of offshore wind farms
No full textOffshore wind energy is in great expansion around the world. Considerable gaps in scientific knowledge on ecological impacts of offshore wind farms (OWFs), including the lack of standardized operational tools to conduct cumulative impact assessment, could lead to delays in the consent process. Ecosystem models are useful tools for cumulative impact assessments because they consider various ecosystem components and their interactions, and therefore are able to provide integrative evaluations. In this study, we improved an existing individual-based ecosystem model (OSMOSE), aiming to assess the cumulative effects of OWFs on various biological groups and fishing activities in the Eastern English Channel (EEC). This work presents substantial technical developments on the existing OSMOSE model application, enhancing its capability to evaluate OWF effects. Technical model improvements included new species, a better representation of the fishing process, prey field forcing updates to include climate change projections, and inter-annual calibration over the period 2002–2021. These developments were essential for improving the depiction of OWFs cumulative impacts, encompassing effects from underwater noise emission, sediment resuspension, and fishing access restriction. We simulated the EEC ecosystem during construction and operational phases under a factorial plan combining OWFs deployment and fishing regulation scenarios. At the scale of the entire EEC ecosystem, total fish biomass and catch were slightly reduced under all scenarios. The most significant biomass declines were observed for cuttlefish, herring, and red mullet, primarily driven by changes in predation and fishing pressure, especially during the construction phase. However, at the local scale (model grid resolution), these changes appear to be OWF-specific, as no consistent spatial patterns in fish biomass were observed across OWFs deployment sites. The differences among scenarios suggest a trade-off between energy production, fishery resource exploitation, and environmental protection goals. The most probable OWF spatial deployment scenario that balanced on regulatory and socio-economic considerations also represented a balance of ecological factors
Endocrine effects of Imazalil on aromatase expression, vitellogenesis and ovarian histology using cyp19a1a-eGFP-casper transgenic zebrafish
No full textConsidering the hazards and risks posed by endocrine disrupting chemicals (EDC) to organisms, there is a need to study their effects. To that end, transgenic fish are powerful models that can provide mechanistic information regarding the endocrine activity of test chemicals. In this study, we used a newly developed transgenic zebrafish line (cyp19a1a-eGFP-casper) in the OECD 21-day fish assay (OECD TG 230) to provide additional mechanistic insight on Imazalil (IMZ; 1.9; 9.9 and 140.7 µg/L). After 21 days of exposure to IMZ, the circulating concentrations of 17-β-estradiol (E2) and vitellogenin decreased in females, reflecting the aromatase activities inhibition. Exposure to 140.7 µg/L of IMZ for 21 days also resulted in a change in the proportion of the different oocyte stages in the ovaries, with an accumulation of large oocytes in exposed females. In addition to the classical endpoints, in vivo GFP fluorescence was quantified in the ovaries during the time course of the exposure to follow gonadal aromatase expression. After seven days of exposure, ovarian aromatase expression increased in females exposed to medium and high concentrations of IMZ, persisting over the 21-day of exposure in fish from the highest concentration group and reflecting a compensatory response to the aromatase enzymatic activities inhibition. Results from the present study provided valuable information on the mode of action and the effects of IMZ in zebrafish. Transgenic zebrafish exposure to IMZ caused a cascade of responses consistent with effects reported for wild-type fish exposed to azole fungicides, both qualitatively and quantitatively. The cyp19a1a-eGFP(-casper) transgenic zebrafish lines, allowed in vivo monitoring of gonadal aromatase expression in a time- and concentration-dependent manner thereby demonstrating their relevance to provide complementary mechanistic information on aromatase in regulatory assays such as OECD TG 230
Offshore Record of Explosive Volcanic Eruptions in the Southern Part of the Panamá Basin During the Past 10 Myr: 1. Tephrostratigraphy, Cross‐Correlations and Geochemical Characterization
No full textNorthern Andean volcanism is characterized by an intense Quaternary activity, whose onshore deposits have partly covered Mio‐Pliocene products associated with the early development of the arc, making it difficult to obtain an exhaustive catalog of past eruptions. To improve our knowledge of the largest eruptions that occurred in the Northern Andean arc, we analyzed several cores from drilling sites off Ecuador to seek tephra records. We characterize for the first time the mineralogical and geochemical characteristics of tephra beds recorded in the southern part of the Panamá Basin in the sediments of DSDP and ODP drilling Sites 504, 677, 678, 1238, 1239 and 1240. We show that products of at least 27 major eruptions from the Northern Andes have reached the Pacific Ocean since the Early Pliocene, and we have correlated 11 of them between several drilling sites. Products of the oldest volcanism had mainly rhyolitic compositions belonging to a High‐K calc‐alkaline magmatic series, whereas magmas display more heterogeneous SiO2 and K2O contents from the beginning of the Pleistocene. Correlations established in this work allow us to provide new temporal constraints to age models of sedimentary sequences of Sites 677, 1238 and 1240 constructed based on biostratigraphy. In addition, we show that sediments of ODP Site 1240, the closest to the Galápagos islands, recorded several Pleistocene rhyolitic eruptions associated with the hotspot's activity, possibly revealing past oceanic ridge‐hotspot interactions
Chromosome-level assembly and annotation of the grey reef shark (Carcharhinus amblyrhynchos) genome
No full textTo date less than 5% of shark species have nuclear reference genomes, despite next-generation sequencing advances. Particularly for threatened shark species, there is a lack of reliable genomes which are crucial in facilitating research and conservation applications. We assembled the first nuclear reference genome of the endangered grey reef shark (Carcharhinus amblyrhynchos) using long-read PacBio HiFi and Omni-C sequencing to reach chromosome-level contiguity (36 pseudo chromosomes; 2.9 Gbp) and high completeness (94% complete BUSCOs). BRAKER3 annotated 16,522 protein-coding genes after masking repetitive elements which accounted for 59% of the genome. We identified potential X and Y sex chromosomes on pseudochromosomes 36 and 57, respectively. The quality and completeness of the draft genome of C. amblyrhynchos will enable researchers to investigate genetic variations and adaptations specific to this species as well as across other Charcharhinus spp., opening new venues for comparative genomics and advancing conservation genetic applications
A simplified semi-empirical model for multifrequency seafloor backscattering angular response (ESAB)
No full textA new approach to seafloor acoustic backscatter prediction and inversion is presented here and applied to an experimental dataset. Based on a frequency-dependent semi-empirical geometrical-physical description, the Extended Seabed Acoustic Backscatter (ESAB) model addresses the seabed backscatter angular response over a wide frequency range, a key issue today in seafloor-mapping operations using multibeam echosounders. Starting from classical backscatter models, ESAB considers three main physical parameters corresponding to acoustical properties prevalent in seabed scattering phenomena: acoustical impedance, roughness facet-slope variance and sediment-volume scattering index. Classical theories are applied to describe the main backscatter components, for interface roughness (facets and Bragg) and sediment volume, modified to explicitly account for frequency. A special effort was applied for introducing an objective frequency dependence in the classical facets method using developments involving various aspects of the roughness properties, building on previous classical works. The interface and volume components are completed by geoacoustical relationships constraining the range of input parameters, as well as by connection terms that ensure numerical stability. The model proved effective across a frequency range corresponding at least to our available angle/frequency field data. Beyond its wide applicability domain, a key advantage of ESAB is its ability to maintain mathematical simplicity and numerical versatility, akin to its predecessor GSAB while providing a direct physical interpretation of parameters, requiring limited assumptions about the sediment physical nature and accounting for frequency dependence. The model effectiveness is demonstrated by the analysis of a comprehensive dataset from the Concarneau Bay (France), providing backscatter measurements acquired by a calibrated EK80 split-beam echosounder across wide incidence angle (0°–70°) and frequency (35–440 kHz) ranges for seven distinct geological facies. The inversion was performed through a simulated annealing algorithm, providing the three main seafloor parameters together with intermediate results. It provided stable and consistent results over the whole frequency range, confirming ESAB’s capability to accurately fit different angular and frequency response patterns while providing quantified and physically meaningful insights into seafloor characteristics. This dual capability of numerical versatility and physical interpretability makes ESAB particularly valuable for seafloor characterization applications involving multifrequency multibeam echosounders for backscatter angular response measurements
The QuatreA initiative: Acquiring, administering, analysing and applying data products derived from underwater optical imagery
No full textThis report summarizes the activities and outcomes of the QuatreA Working Group from February 2019. The QuatreA is a collaborative initiative between scientists in marine ecology and fisheries science from the Commonwealth Scientific and Industrial Research Organisation (CSIRO, Oceans and Atmosphere business unit), the University of Tasmania (UTAS) and the French Institute for the Exploitation of the Sea (IFREMER). The QuatreA Working Group (4AWG) stems from a willingness to share experiences in marine imagery between data producers and data analysts working in different spaces and with distinct protocols. Delivery of robust and reliable evidence-based science, particularly for monitoring purposes, must rely on clearly established workflows linking data collection to derived products aimed at end-users of science, e.g. managers and policy-makers. This is all the more needed because marine imaging is a rapidly developing domain with flourishing propositions in terms of field protocols and image annotation. The 4AWG is thus addressing the entire life cycle of imaging data: image Acquisition, image Annotation, Analysis of derived-data, and Administration of all data. This report is constructed as a chronological compilation of the documentation of the meeting and workshop listed in the Table (timeline) above, presented as Chapters
Delayed mode analysis of salinity data acquired by Argo floats deployed in 2017-2018
No full textDelayed Mode analysis was carried out for the Argo floats deployed on the RREX 2017 cruise and by two Autonomous Systems For Argo floats Release (ASFAR) moored on Reykjanes Ridge. Salinity and temperature profiles were visually checked and compared with nearby reference profiles. Real-time QC flags were reviewed. The OWC method was then applied to assess potential salinity offsets and/or drifts, using historical Argo and/or CTD profiles as reference
Persistent Coastal Temperature Biases in km‐Scale Climate Models Due To Unresolved Oceanic Tidal Mixing
No full textRecent advances in numerical modeling have enabled km‐scale climate simulations, improving global climate representation and local‐scale projections, critical to climate adaptation strategies. In this context, the present study assesses the performance of such models over coastal shelf seas—key climate‐sensitive regions—in their ability to represent the sea surface temperature (SST) and air temperature. Compared to satellite and reanalysis data, the models exhibit systematic warm biases (3°C in SST, 1.5°C in air temperature) in summer across several shelf seas: the European shelf, the Gulf of Maine, the Yellow sea, the Arctic and Patagonian shelves. These biases strongly correlate with tidal mixing fronts, driven by the dissipation of the barotropic tide and identified by the Simpson‐Hunter parameter. These findings suggest that missing tidal mixing is a significant error source on coastal shelves, highlighting the need for improved ocean mixing representations to enhance model accuracy