French Research Institute for Exploitation of the Sea
ArchiMer - Institutional Archive of IfremerNot a member yet
27944 research outputs found
Sort by
The influence of habitat heterogeneity and disturbance on benthic community structure in deep-sea polymetallic nodule environments and management implications for seabed mining
No full textHabitat heterogeneity is known to influence faunal community structure, but its influence on deep-sea benthic communities remains understudied, particularly for polymetallic nodule environments in abyssal waters. As nodules are currently of interest for mining, understanding the potential impact of this disturbance on habitat heterogeneity, and the subsequent effect on faunal communities, becomes critical for developing environmental management plans. Although some aspects of the influence of habitat heterogeneity on the nodule-associated fauna have been studied, the influence on multiple size components of the benthic community across varying spatial scales has not yet been fully assessed, and the current metrics by which habitat heterogeneity is measured may be insufficient. This review synthesizes existing research regarding habitat heterogeneity, the influence of disturbance on habitat heterogeneity, and the influence of this heterogeneity on metazoan fauna (megafauna, macrofauna, and meiofauna) in polymetallic nodule environments across spatial scales. Current gaps in knowledge and the implications of this knowledge for the management of proposed deep-seabed mining are also discussed
Working Group on Spatial Fisheries Data (WGSFD; outputs from 2024 meeting)
No full textThe ICES Working Group on Spatial Fisheries Data (WGSFD) develops standardised methods for collecting, processing, and analysing vessel monitoring system (VMS) and logbook data to support fisheries management and marine spatial planning across European waters. The group maintains the annual ICES VMS data call workflow and produces spatial fishing activity datasets that inform ICES advice on fishing pressure, benthic impacts, and marine ecosystem protection. Under its current terms of reference, the group has considered: • Habitat Integration: the group successfully incorporated habitat and bathymetry data into the VMS and logbooks data call. Using the Marine Strategy Framework Directive Broad Benthic Habitat Types (MSFD-BBHT) layer, WGSFD can now identify fishing ef-fort by specific habitat types or depth strata within each c-square grid cell, enabling more refined fishing pressure analysis. • Enhanced Data Processing: WGSFD proposed implementing a benchmark process for the VMS data call workflow and updated critical functions for assigning logbook infor-mation to VMS records, particularly improving handling of multi-gear trips. Swept area calculations were moved to national-level preparation, enhancing quality control and transparency. • Small-Scale Fisheries Protocols: Comprehensive protocols were developed for analys-ing high-resolution spatial data from vessels under 12 metres. Through case studies across eight countries, the group established that vessel position data must be acquired at least every 30 seconds for adequate representation, with machine learning approaches showing significant improvements over traditional methods. • Improved Temporal Resolution: Analysis of VMS polling frequency demonstrated that current two-hourly intervals still limit advice precision. Most member states now report data at frequencies between one and two hours, with some achieving 10-minute inter-vals. WGSFD established pathways for continued development including standardised workflows for high-resolution data processing, explored potential web-based API development, and continued refinement of habitat-specific fishing impact assessments. The group emphasised increased col-laboration between scientists and industry to validate analytical methods. These achievements position ICES to provide more precise, habitat-aware, and scientifically ro-bust advice on fishing activities' spatial distribution and environmental impacts across European waters
Genetic Differentiation in a Wide‐Ranging Tropical Seabird in the Indian Ocean Is Linked With Oceanographic Factors
No full textAim Knowledge of the main drivers of population differentiation is crucial for understanding evolutionary processes and preserving biodiversity. While primarily studied in terrestrial habitats, the mechanisms operating in the marine realm are less well understood. This study reconstructed the phylogeographic history of a tropical seabird to identify relevant marine barriers promoting intraspecific diversity in the Western Indian Ocean. Location Western Indian Ocean. Taxon Three subspecies of tropical shearwater : Puffinus bailloni bailloni , P. b. nicolae, P. b. colstoni. Methods We used restriction site‐associated DNA sequencing and applied population genomics to birds from six breeding colonies to assess intraspecific diversity, population genetic structure and connectivity in the tropical shearwater. Results were complemented with data from six oceanographic variables and effective migration surfaces to evaluate the role of oceanographic factors in driving population differentiation. Results All analyses consistently separated the birds from the northern colonies (subsp. nicolae and colstoni ) from those of the southern islands (subsp. bailloni ), but failed to assign the colstoni birds as a different taxon. Results revealed remarkable levels of genetic differentiation within an ocean basin in a highly vagile species and suggested higher levels of gene flow at the northern limit of the species' distribution compared to the southern range. Main Conclusions Our study suggests that ocean surfaces and sea surface temperature may constitute an important barrier to gene flow for the tropical shearwater and potentially other marine species in the region. This study does not support the colstoni form as a different subspecies, highlighting the need for further taxonomic reassessment. Ultimately, the results allowed us to identify Europa and Aldabra as the most threatened management units and propose conservation strategies directly applicable to these most at‐risk colonies
PlanktonFlow : hands-on deep-learning classification of plankton images for biologists
No full textHigh-resolution biodiversity monitoring is crucial to understand the complex dynamics of ecosystems. High throughput image-acquisition devices now provide biologists with a wealth of data, but mainstream, automated image-classification workflows are still lagging behind, while high-performance classification models remain hardly manageable by most biologists. To fill this gap, we developed PlanktonFlow, an end-to-end, fully automated deep-learning pipeline for plankton imagery intended for biologists having minimal technical expertise with machine learning. PlanktonFlow automates image pre-processing, model training and calculation of performance metrics for four different convolution neural network architectures (ResNet, DenseNet, EfficientNet, and YOLOv11), as well as inference on novel datasets. We highlight the potentialities of PlanktonFlow by comparing the relative performances of the four models and of the web-service EcoTaxa on classifying images from freshwater samples including 76 classes of both living and non-living objects. EfficientNet-B5 achieved the highest macro-averaged F1 score, outperforming Eco-Taxa as well as other models. Despite class imbalance and morphological complexity, all models generalized well across frequent and rare taxa, highlighting the relevancy of the pre-processing routine. Error analyses stressed that classification challenges arose from high intra-class variability and high inter-class similarity. To ease an appropriation and further developments by the community, PlanktonFlow is open source and has a modular structure. We foresee that future work could leverage semi-supervised learning, test the pipeline on other imaging systems, and expand its applicability to other biological systems
No longer polar opposites? Similarities in recent Arctic and Antarctic sea ice change
No full textUntil recently, trends in sea-ice cover in the Arctic and Antarctic seemed to follow opposite pathways. While Arctic sea ice showed a strong and prolonged decrease, Antarctic sea ice displayed a small but significant increase. Yet, in 2015, Antarctic sea ice experienced a sharp decline to an unprecedented summertime low in 2016 and a subsequent year-round minimum in 2023. These series of events have suggested the start of a sustained decline in Antarctic sea ice, similar to that in the Arctic. Meanwhile, the Arctic sea ice is transitioning towards a seasonal regime that resembles that of the Antarctic sea ice. These ongoing changes motivated the workshop on {\it The Role of Sea Ice and its Variability in the Climate System}, which brought together the Arctic and Antarctic research communities in July 2024 at the Abdus Salam International Centre for Theoretical Physics (ICTP) in Trieste, Italy. Here, we synthesize the discussions that took place during the workshop on changes in sea-ice properties as well as on oceanic and atmospheric drivers of these changes. We acknowledged that understanding these drivers requires enhanced observations of sea-ice parameters, such as thickness, improved process representation in models, such as ocean mesoscale eddies, and a more integrated approach to studying both polar regions. Our ability to predict sea ice changes, and hence assess future climate risks, depends on this refined understanding
Caractérisation génomique et transcriptomique du cycle de vie de l'herpèsvirus OsHV-1 chez son hôte, Magallana gigas
No full textSince the 1990s, the Pacific oyster Magallana gigas (formerly Crassostrea gigas) has experienced significant mortalities at larval and juvenile stages, associated with the Ostreid herpesvirus type 1 (OsHV- 1). This double-stranded DNA virus belongs to the order Herpesvirales and the family Malacoherpesviridae. The OsHV-1 life cycle consists of two phases: a lytic phase, responsible for massive seed mortalities and the release of large amounts of viral particles into the water, and a potential persistence phase, during which the virus may be maintained in an as-yet undetermined form within an unidentified reservoir. The structure of OsHV-1 viral particles is similar to that of the Orthoherpesviridae, while its genomic organization, comparable to that of the Alphaherpesvirinae, includes two unique regions flanked by inverted repeat sequences capable of recombining to form genomic isomers. Due to this genomic complexity, short-read sequencing approaches cannot provide a complete assembly of the viral genome nor accurately identify its isomers. In this context, this work aimed to: (i) evaluate the performance of Oxford Nanopore Technologies (ONT) long-read sequencing; (ii) characterize the plasticity of genomic architecture and the transcriptional dynamics of OsHV-1 during the lytic phase in M. gigas; and (iii) identify potential reservoirs of OsHV-1 during its persistence phase and characterize its underlying molecular mechanisms. The results demonstrate that ONT technology is a powerful tool to overcome the limitations of short-read sequencing. They also reveal a gene expression dynamic during the lytic phase similar to that of other herpesviruses and provide evidence supporting viral persistence in a latent form within M. gigas spat. Overall, this work represents an important step forward in understanding the interactions between OsHV-1 and M. gigas, and paves the way for new approaches to managing viral diseases in oyster farming.Depuis les années 1990, l’huître creuse Magallana gigas (anciennement Crassostrea gigas) connaît d’importantes mortalités aux stades larvaire et juvénile, associées à l’Ostreid herpesvirus de type 1 (OsHV-1). Ce virus à ADN double brin, appartenant à l’ordre des Herpesvirales et à la famille des Malacoherpesviridae. Le cycle de vie du virus OsHV-1 comporte deux phases : une phase lytique, responsable de mortalités massives du naissain et d’une forte excrétion de particules virales dans l’eau, et une potentielle phase de persistance, durant laquelle il se maintiendrait sous une forme encore indéterminée dans un réservoir non identifié. La structure des particules virales du virus OsHV-1 est similaire à celle des Orthoherpesviridae, et son organisation génomique, comparable à celle des Alphaherpesvirinae, comporte deux régions uniques encadrées de séquences répétées et inversées pouvant permuter et former des isomères génomiques. En raison de cette complexité génomique, les approches de séquençage à lectures courtes ne permettent pas un assemblage complet du génome viral ni l’identification précise des isomères. Dans ce contexte, cette thèse visait à : (i) évaluer les performances du séquençage à longues lectures Oxford Nanopore Technologies (ONT), (ii) caractériser la plasticité de l’architecture génomique et la dynamique transcriptionnelle du virus OsHV-1 en phase lytique M. gigas, et (iii) d’identifier les réservoirs potentiels du virus OsHV-1 durant sa phase de persistance et d’en caractériser les mécanismes moléculaires. Les résultats obtenus démontrent que la technologie ONT constitue un outil performant pour surmonter les limites du séquençage à lectures courtes. Ils révèlent également une dynamique d’expression génique en phase lytique similaire à celle d’autres herpèsvirus et apportent des élèments en faveur d’une persistance du virus sous forme latente dans le naissain de M. gigas. Ces travaux représentent une avancée importante dans la compréhension des interactions entre OsHV-1 et M. gigas, et ouvrent la voie à de nouvelles approches de gestion des maladies virales en ostréiculture
EGO gliders NetCDF format reference manual
No full textThis document specifies the NetCDF file format of EGO-gliders that is used to distribute glider data, metadata and technical data. It documents the standards used therein; this includes naming conventions as well as metadata content. It was initiated in October 2012, based on OceanSITES, Argo and ANFOG user's manuals. Everyone’s Gliding Observatories - EGO is dedicated to the promotion of the glider technology and its applications. The EGO group promotes glider applications through coordination, training, liaison between providers and users, advocacy, and provision of expert advice. We intend to favor oceanographic experiments and the operational monitoring of the oceans with gliders through scientific and international collaboration. We provide news, support, information about glider projects and glider data management, as well as resources related to gliders. All EGO data are publicly available. More information about the project is available at: http://www.ego-network.or
Evaluation and homogenization of a marine gravity database from shipborne and satellite altimetry-derived gravity data over the coastal region of Nigeria
No full textAccurate geoid modelling in marine areas requires the integration of gravity data from multiple sources including shipborne gravity measurements, global geopotential models, and satellite altimetry-derived gravity data. This study aims to develop homogenized gravity data for the coastal region of Nigeria to improve geoid modelling accuracy. Residual linear drifts in the shipborne gravity dataset from the Bureau Gravimétrique International (BGI) were corrected using crossover adjustments for each survey leg. We eliminated gross errors for each survey leg by using the 2-sigma method. Outliers in the historical shipborne gravity data were identified and removed using the leave-one-out cross-validation technique, resulting in a refined shipborne gravity dataset. The refined shipborne data were compared with the gravity data predicted by DTU21GRA, SSv29.1, SGG-UGM-2, XGM2019e_2159, GECO, EIGEN-6C4, and EGM2008. Our findings show that DTU21GRA outperformed the other models in the same region when compared with shipborne gravity data. The refined shipborne gravity data were merged with the DTU21GRA data using Least-Squares Collocation (LSC) to create a combined gravity dataset. The results of comparison between the complete refined shipborne gravity data and DTU21GRA before and after the integration process, shows that both the mean offset and the SD values decreased from 0.43 to −0.02 mGal and 3.14 to 2.69 mGal, respectively, which reveal an improvement in the final combined data. The geoid model constructed using the combined gravity data before and after the integration process showed an improvement in the SD values, decreasing from 0.023 m to 0.016 m when evaluated against the CNES-CLS22 MDT
Quality Information Document. In Situ TAC INSITU_GLO_BGC_DISCRETE_MY_013_046. And Synthetic Quality Overview document (SQO)
No full textThe quality of the INSITU_GLO_BGC_DISCRETE_MY_013_046 product from the Copernicus Marine Service distribution is assessed through overall quality and spatial coverage of the following variables: Chlorophyll FLU2 (chlorophyll-a fluorescence; [mg m-3]) CPHL (chlorophyll-a concentration [mg m-3]) Oxygen DOXY (dissolved oxygen [mmol m-3]) DOX1 (dissolved oxygen [ml l-1]) DOX2 (dissolved oxygen [μmol kg-1]) Nutrients NTRA (nitrate [mmol m-3]) NTAW (nitrate [μmol kg-1]) SLCA (silicate [mmol m-3]) PHOS (phosphate [mmol m-3]) The particularity of any oceanographic in-situ measurements dataset is that the horizontal and vertical coverage of the dataset varies strongly along time following the technological developments and the international cooperation on observations networks. One should thus ensure that both the vertical coverage and the horizontal coverage fit his needs in terms of sampled ocean variability scales before using the data. Therefore, the horizontal coverage of the dataset for chlorophyll, oxygen, nitrate, silicate, and phosphate variables are shown. As a measure of the overall quality of the data, the amount of data flagged as “good data” and “bad data”, respectively, during the quality control procedure is shown and discussed. For additional information regarding the in-depth validation of this product, the calculation of the assessment metrics presented in this product other detailed information in quality and noticeable events please refer to the reference quid document CMEMC-INS-QUID-013_046. Important notice: The contents of this document are an assessment based on the best set of observations available for evaluation at the time the operational system was validated. The validation methodology was defined and agreed within Copernicus Marine Service, inheriting the long experience of MyOcean and MERSEA series of projects (Hernandez et al., 2018) The results presented in this report and derived estimated accuracy numbers (EAN) are representative of average error levels over large areas of the ocean. These numbers might be used as a mean error in one given point of the area, but in order to refine error estimates locally, the reader is invited to use complementary information from reference QUIDs (error maps for instance, when available)
Quality Information Document. In Situ TAC multiparameter products: INSITU_GLO_PHYBGCWAV_DISCRETE_MYNRT_013_030 INSITU_ARC_PHYBGCWAV_DISCRETE_MYNRT_013_031 INSITU_BAL_PHYBGCWAV_DISCRETE_MYNRT_013_032 INSITU_IBI_PHYBGCWAV_DISCRETE_MYNRT_013_033 INSITU_BLK_PHYBGCWAV_DISCRETE_MYNRT_013_034 INSITU_MED_PHYBGCWAV_DISCRETE_MYNRT_013_035 INSITU_NWS_PHYBGCWAV_DISCRETE_MYNRT_013_036. And Synthetic Quality Overview document (SQO)
No full textThe INSITU_*_PHYBGCWAV_DISCRETE_MYNRT_013_030-036 products are based on in situ observations collected in real-time and revisited in delayed mode by data providers and the In Situ TAC 7 regions. The data validation is carried out by automatic quality control tests both in real time and delayed mode (Copernicus Marine In Situ Team, 2020). Moreover, data is visualized by experts to detect spikes and anomalous behaviour of the sensors and additionally, comparison with other sources is performed to detect possible wrong data. It is important to note that this product is providing data from global, regional, national or institutional observing systems. They are responsible for the data transmission and the equipment maintenance. The temporal coverage ranges from the beginning of the 20th century to now. It is presented with histograms. The metric is the platform-day (one platform, one day, one or many observations = +1) for temperature and salinity (T&S) observations and platform-month (one platform, one month, one or many observations = +1) for the rest of variables. The results show a continuous increase along the years and especially in the last two decades. The spatial coverage is presented through maps with the distribution of observations on the current year (2023) for all the variables. For underway data, measuring T&S and Oxygen, the coverage is rather homogeneous, while for fixed platforms like buoys, HF radars or tide gauges, measuring the rest of variables, the coverage is diverse with most of the stations concentrated in the Northern Hemisphere and more specifically in the coast of Europe and North America. For additional information regarding the in-depth validation of this product, the calculation of the assessment metrics presented in this product and other detailed information in quality and remarkable events please refer to the reference quid document CMEMS-INS-QUID-013_030-036. Important notice: The contents of this document are an assessment based on the best set of observations available for evaluation at the time the operational system was validated. The validation methodology was defined and agreed within Copernicus Marine Service, inheriting the long experience of MyOcean and MERSEA series of projects (Hernandez et al., 2018). The results presented in this report and derived estimated accuracy numbers (EAN) are representative of average error levels over large areas of the ocean. These numbers might be used as a mean error in one given point of the area, but in order to refine error estimates locally, the reader is invited to use complementary information from reference QUIDs (error maps for instance, when available)