French Research Institute for Exploitation of the Sea
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End-to-End Artificial Learning of Protection Gradient from Raw eDNA Sequences
No full textTo face the ever-increasing threats on ecosystems and their biodiversity, protected areas are expanding worldwide but assessing their effects requires advanced monitoring methods. Environmental DNA (eDNA) metabarcoding can reveal local biodiversity from genetic material released in the environment, offering ecosystem-health insights without invasive or destructive surveys. Yet, to harness the full potential of eDNA data in ecosystem assessment, robust and direct links between raw eDNA sequences and protection status remain to be learned with machine learning. Here, we present the first fully end-to-end framework learning and predicting a continuous protection gradient directly from raw eDNA sequences, bypassing taxonomic assignment or precomputed biodiversity indices. Our framework combines contrastive self-supervised pre-training to extract meaningful embeddings from eDNA sequences with a neural-network classifier to predict the level of protection. Applied to eDNA fish surveys on the Mediterranean coast, we show that raw sequences encode protection status along a gradient from unprotected to fully protected areas. This general framework can facilitate hypothesis testing on disturbance gradients and indicate whether a site is degraded or effectively protected, providing a scalable tool for ecosystem monitoring and adaptive management
Hydroacoustic observations of the 15 January 2022 Hunga Tonga-Hunga Ha‘apai eruption: The role of bathymetry along the path
No full textThe 15 January 2022 submarine volcanic eruption of Hunga Tonga-Hunga Ha`apai (HTHH) released immense energy throughout the ocean, solid Earth, and atmosphere. We analyze mid-oceanic column acoustic pressure recordings from 24 freely drifting \textsc{Mermaid} sensors, and from 11 moored hydrophones in the International Monitoring System. We focus on the pulsed hydroacoustic phase which propagated horizontally through the water column as a T 30-minute \textit{T}~wave with energy around 2.5--10~Hz. The records show high correlation between some receivers, significant variation among others, and varying amplitudes that cannot be explained by distance alone. We investigate the origin of this heterogeneity via the influence of bathymetric features that may block, or occlude, \textit{T}-wave propagation, affecting both shape and amplitude of the records received. We count the number of seafloor obstacles within the horizontal plane of the first (ray-theoretical) Fresnel zone at a depth of 1350~m, where the fundamental-mode \textit{T}-wave eigenfunction is maximum. Adjusted for geometric spreading, the cross-correlations and sound pressure level differences between receivers systematically relate to differences in occlusion count. Our model of signal loss due to seafloor interactions predicts a 5.6~dB reduction in sound pressure level per log of occlusion count. Beyond helping us understand the particulars of the HTHH eruption, our findings aid in correcting signal amplitudes to constrain volcanic or explosive yield estimates and earthquake magnitudes, and are useful to model detectability through various oceanic corridors when designing hydroacoustic monitoring networks of the future
Does the Environment “Filter” or “Select” Species? Bridging the Ecologies of Microbes and Macro-Organisms for a Common Niche Assembly Theory
No full textMore than five decades before the introduction of “environmental filtering” in plant and vegetation sciences, Baas Becking proposed that the “environment selects” for studies in microbial ecology. He coupled this with the ubiquity law that he proposed for microbes to obtain the tenet “everything is everywhere, but, the environment selects”. Nowadays, while this tenet is mostly used as a null hypothesis for studies of microbial biogeography, the latter part has large implications for niche assembly theories. In this respect, it is very similar to the idea of “environmental filtering”, although some minor differences exist regarding how both concepts have been applied in macrobial and microbial ecologies. During the second decade of the 21st century, the usefulness of the latter has been questioned due to difficulties in disentangling the roles of environmental (abiotic) and ecological interaction in community assembly. A new vision has emerged in the literature that considers the environmental filter as dynamic and continuously influenced by biotic communities. With a small modification, this scheme provides a solution that can accommodate the ecologies of both microbes and macro-organisms for a common niche assembly theory
Modelling water flow in presence of various obstructions: description and validation of a generic module for 2- and 3-dimensional simulations
No full textIn coastal areas, various types of biological and anthropogenic structures significantly influence the flow and related sediment dynamics. In this paper, we describe a new generic flow-obstruction module, designed to represent both upward or downward, rigid or flexible structures. This module provides a particularly accurate representation of flow velocities in the presence of flexible obstructions, due to a thorough description of their bending. The obstruction/flow interaction module can operate either in 3D or 2D mode. It also offers the possibility of incorporating multiple types of obstructions within a single mesh, which is invaluable when modeling realistic ecosystem dynamics. Module validation was carried out using flume experiments on seagrasses, as well as using numerical studies involving two anthropogenic structures: mussel long-lines and oyster tables. The coupled hydrodynamic/obstruction model yielded excellent results for 2D/3D velocity fields with minimal calibration efforts. This module can be integrated into any hydrodynamic coastal model and is aimed at being upscaled to a regional scale, offering the potential to explore future trajectories regarding the vulnerability of coastal systems in response to global change, or to identify restoration measures in engineered coastal systems
Sedimentary Architecture Prediction Using Facies Interpretation and Forward Seismic Modeling: Application to a Mediterranean Land–Sea Pliocene Infill (Roussillon Basin, France)
No full textThis study predicts sedimentary architectures and facies distribution within the Pliocene prograding prism of the Roussillon Basin (Gulf of Lion, France), developed along an onshore–offshore continuum. Boreholes and outcrops provide facies-scale observations onshore, while seismic data capture basin-scale structures offshore. Forward seismic modeling bridges spatial and scale gaps between these datasets, yielding characteristic synthetic seismic signatures for the sedimentary facies associations observed onshore, used as analogs for offshore deposits. These signatures are then identified in offshore seismic data, allowing seismic profiles to be populated with sedimentary facies without a well tie. Predicted offshore architectures are consistent with shoreline trajectories and facies successions observed onshore. The Roussillon prism records passive margin reconstruction in the Mediterranean Basin following the Messinian Salinity Crisis, through the following three successive depositional profiles marking the onset of infilling: (1) Gilbert deltas, (2) wave- and storm-reworked fan deltas, and (3) a wave-dominated delta. Offshore, transitions in clinoform type modify sedimentary architectures, influenced by inherited Messinian paleotopography. This autogenic control generates spatial variability in accommodation, driving changes in depositional style. Overall, this multi-scale and integrative approach provides a robust framework for predicting offshore sedimentary architectures and can be applied to other deltaic settings with limited land–sea data continuity
Medusae (Cnidaria) of Reunion Island (South West Indian Ocean): Diversity, Abundance and Distribution
No full textNumerous studies have been conducted on the benthic stages of Medusozoa in Reunion Island, but none on the pelagic stages. This study is the first to investigate the shallow waters of the island for the diversity, abundance, and spatio-temporal distribution of jellyfish. During a one-year survey, samples were collected with a plankton net weekly or biweekly at four sites (two reef/two non-reef) and two depths (10/50 m). Of the 267 samples, 3450 medusae were sorted and 56 species identified. The meroplanktonic Hydroidolina (Antho- and Leptomedusae) were the most diverse (38 species), while the holoplanktonic Trachylinae (13 species) were the most abundant. Hydromedusa species richness was higher at coastal stations than offshore, but similar between reef and non-reef sites. There was no significant variation in species richness or abundance between months or seasons. Including some other catches, the total number of species reached 62. Eight species are new records for the Indian Ocean (all Anthomedusae). Indian Ocean literature references are given in the species list, and some photographs are provided. This initial study, which greatly expands the local hydrozoan fauna knowledge, will serve as a reference for future research, especially regarding climate change and coastal management in Reunion Island
Expertise relative aux causes des mortalités conchylicoles constatées lors de l’épisode de canicule de juin et juillet 2025 dans l’Hérault.
No full textExpertise n°25-041 relative aux causes des mortalités conchylicoles constatées lors de l’épisode de canicule de juin et juillet 2025 dans l’Hérault
Quasi-geostrophic vortex merger over bathymetry
No full textWe investigate interactions between two like-signed vortices over either an isolated seamount or a basin (a depression in the bathymetry), using a quasi-geostrophic, two-layer model on the -plane. When the vortex pair is centred over the seamount, the vortices are pushed together by the secondary flow generated in the bottom layer, facilitating their merger. Over a basin, the deep anomalies are much stronger and their interaction strains out the surface vortices. The results are supported by an analytical estimation of the initial potential vorticity anomalies in the lower layer and by analysis of the linear stability of a single vortex over the bathymetry. Similar phenomena are observed when the vortex pair is displaced from the bathymetric centre and when the initial vortices are initially compensated. Sub-deformation-scale vortices are less influenced by bathymetry than larger vortices. The results help explain asymmetries noted previously in turbulence simulations over bathymetry