French Research Institute for Exploitation of the Sea
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Seasonal Transition in the Dominance of Photoautotrophic and Heterotrophic Protists in the Photic Layer of a Subtropical Marine Ecosystem
No full textProtists are major functional players in the oceans. Time‐resolved protist diversity and succession patterns remain poorly described in subtropical ecosystems, limiting current understanding of food web dynamics and responses to environmental changes in these major world‐ocean regions. We used amplicon sequencing data and trait‐based annotation to examine the seasonality of planktonic protists in the subtropical Gulf of Aqaba (Red Sea). Temperature and nutrients were the major drivers of succession. We detected marked seasonal shifts in protists. Heterotrophs, including diverse parasitic functional groups, dominated the warm, stratified oligotrophic period spanning spring and summer. By contrast, nutrient influx during deep convective mixing in winter triggered a shift to photoautotrophic communities dominated by a few genera of chlorophytes. Deeper winter mixing resulted in larger blooms at the onset of stratification dominated by diatoms, relative to chlorophytes that prevailed during shallower blooms. This result illustrates the impact of mixing depth on bloom formation and composition. Comparisons with oceanwide rDNA datasets indicate that the oligotrophic protist assemblages from the Gulf resemble those from warm, open oceans. This work provides a detailed assessment of the seasonal switch in dominant trophic functions in protists in phase with nutrient levels in a subtropical planktonic ecosystem
A conservation priority index to rank fish species within IUCN Red List categories: a case study of marine fishes from Réunion Island
No full textAlthough the IUCN Red List is a crucial tool for assessing the extinction risk of species, further ranking species within each IUCN category is needed to refine conservation priorities. In practice, managers and policy makers often require to prioritize species according to IUCN categories, and subsequently rank them within these categories. The current IUCN classification system relies on quantitative criteria related to population dynamics such as population size, rate of decline, and geographic range, without considering the functional or evolutionary distinctiveness of species, nor directly accounting for their vulnerability to individual anthropogenic pressures like climate change or fishing. These pressures may instead be considered indirectly through the criteria used, which often reflect the combined effects of multiple, interrelated human-induced threats. Here, we developed an index to quantify the conservation priority of fish species with the same IUCN status by combining five criteria: functional distinctiveness, evolutionary distinctiveness, abundance scarcity, vulnerability to climate change, and vulnerability to fishing. This framework enables managers to customize priorities by assigning varying levels of importance to each criteria, offering a flexible tool for refining conservation plans. To demonstrate its applicability, we tested this framework on the marine fish community of Réunion Island, an area with a significant number of species classified as ‘vulnerable’ on the IUCN Red List. Finally, we discuss how this framework, formalized into an index, could substantially enhance fish species conservation and contribute to the long-term sustainability of ecosystems
Deciphering mixotrophic and cytotoxic activities of the haptophyte Prymnesium parvum
No full textThe study of mixotrophy in harmful microalgae is of increasing interest as it reshapes our understanding of biogeochemical cycles and trophic dynamics. This nutritional strategy affects energy and matter flows, with repercussions on harmful algal blooms, fisheries and climate. The objective of this thesis is to improve our understanding of mixotrophy among harmful microalgae using the haptophyte Prymnesium parvum as a model. P. parvum is a widespread species known for causing fish kills and is a well-known mixotroph, relying on both autotrophy and heterotrophy as a source of energy and nutrients to grow. Results highlighted a maximal growth rate when P. parvum feeds on prey and its ability to grow on prey debris resulting from cell lysis. In addition, this work revealed a positive correlation between the toxins produced and the lytic effect induced on the prey. Finally, in presence of prey, P. parvum would be predominantly phagotrophic. This PhD highlighted the complexity of the mechanisms involved in mixotrophy in the toxic microalga P. parvum, but also provided new tools and opened up new perspectives for more in-depth studies of mixotrophy and prey-predator interactions, in order to assess its impact on marine ecosystems.La mixotrophie chez les microalgues toxiques suscite de plus en plus d'intérêt car elle modifie les cycles biogéochimiques et la dynamique trophique. Cette stratégie nutritionnelle influence les flux d'énergie et de matière, avec des répercussions sur les efflorescences algales nuisibles, les ressources halieutiques et le climat. L'objectif de cette thèse est d'améliorer notre compréhension de la mixotrophie chez les microalgues toxiques et plus particulièrement en utilisant l'haptophyte Prymnesium parvum comme algue modèle. P. parvum est une espèce très répandue, connue pour causer la mort de poissons, et est mixotrophe, dépendant à la fois de l'autotrophie et de l'hétérotrophie comme source d'énergie et de nutriments pour se développer. Les résultats de nos travaux ont montré un taux de croissance maximal lorsque P. parvum se nourrit de proies et ont mis en évidence sa capacité à croître sur des débris de proies résultant de la lyse cellulaire. De plus, une corrélation positive entre les toxines produites et l’effet lytique induit sur la proie a été observée. Enfin, en présence de proies, P. parvum serait majoritairement phagotrophe. Cette thèse a mis en évidence la complexité des mécanismes impliqués dans la mixotrophie chez la microalgue toxique P. parvum, mais a également fourni de nouveaux outils et ouvert de nouvelles perspectives pour l'étude plus approfondie de la mixotrophie et des interactions proie-prédateur, afin d'évaluer leurs impacts sur les écosystème
Building a DNA Reference for Madagascar’s Marine Fishes: Expanding the COI Barcode Library and Establishing the First 12S Dataset for eDNA Monitoring
No full textMadagascar harbors a rich marine biodiversity, yet detailed knowledge of its fish species remains limited. Of the 1689 species listed in 2018, only 22% had accessible cytochrome oxidase I (COI) sequences in public databases. In response to growing pressure on fishery resources, this study aims to strengthen biodiversity monitoring tools. Its objectives were to enrich the COI database for Malagasy marine fishes, create the first 12S reference library, and evaluate the taxonomic resolution of different 12S metabarcodes for eDNA analysis, namely MiFish, Teleo1, AcMDB, Ac12S, and 12SF1/R1. An integrated approach combining morphological, molecular, and phylogenetic analyses was applied for specimen identification of fish captured using various types of fishing gear in Toliara and Ranobe Bays from 2018 to 2023. The Malagasy COI database now includes 2146 sequences grouped into 502 Barcode Index Numbers (BINs) from 82 families, with 14 BINs newly added to BOLD (The Barcode of Life Data Systems), and 133 cryptic species. The 12S library comprises 524 sequences representing 446 species from 78 families. Together, the genetic datasets cover 514 species from 84 families, with the most diverse being Labridae, Apogonidae, Gobiidae, Pomacentridae, and Carangidae. However, the two markers show variable taxonomic resolution: 67 species belonging to 35 families were represented solely in the COI dataset, while 10 species from nine families were identified exclusively in the 12S dataset. For 319 species with complete 12S gene sequences associated with COI BINs (Barcode Index Numbers), 12S primer sets were used to evaluate the taxonomic resolution of five 12S metabarcodes. The MiFish marker proved to be the most effective, with an optimal similarity threshold of 98.5%. This study represents a major step forward in documenting and monitoring Madagascar’s marine biodiversity and provides a valuable genetic reference for future environmental DNA (eDNA) applications
Working Group for the Celtic Seas Ecoregion (WGCSE).
No full textThe Working Group for the Celtic Seas Ecoregion (WGCSE) performs stock assessments on demersal stocks in Rockall, West of Scotland, Irish Sea, West of Ireland, Western English Channel, Bristol Channel, Celtic Sea and Southwest of Ireland. In 2025, the Working Group provided updated fisheries data, reviews and advice for 18 fish stocks. These fish stocks include, three sole, two plaice, three haddock, three whiting, two cod, two megrim, one sea bass, one anglerfish and one pollack stock. For most of the stocks, advice was drafted in May and issued in June. Advice for Rockall megrim will be issued in autumn so that it could take account of the in-year survey information. In 2025, analytical assessments using age-structured models were conducted for 15 fish stocks. For one stock, ple.27.7e, advice is based on an MSE tuned chr rule. A Bayesian state–space biomass dynamic model was used to assess lez.27.4a6a, and the assessment and advice for lez.27.6b will be conducted using SPiCT. In addition, two stocks for which advice is issued on a biennial basis (ple.27.7fg, ple.27.7h-k) was presented and included in the report, although no new advice in issued in 2025. Four stocks have gone through a benchmark procedure in the past year; bss.27.4bc7ad-h, whg.27.7a, pol.27.67 and ple.27.7e. As a result of the benchmark for bss.27.4bc7ad-h, the model was updated to include consideration of migration of seabass from divisions 8.ab into divisions 4.b–c, 7.a, and 7.d–h during quarters 3 and 4, revised approaches to modelling recreational removals, revised discards, additional recruitment surveys and revised fleet structure. Reference points were also revised. Following the benchmark for whg.27.7a, the assessment model was changed to a state-space assessment model (SAM). The stock remains as Category 1. Historical catch data were revised and new spatio-temporal modelled survey indices were included. For the first time, recreational removals were included in the assessment. Reference points were also revised. The pollack assessment was also benchmarked in 2025 and the method for providing advice has changed from Category 2 (SPiCT) to Category 1 (age based analytical assessment (Stock Synthesis – SS3). The new model includes updated life-history parameters, age-structured commercial landings, length-structured recreational removals, commercial LPUE indices and a combined scientific survey index. Reference points were also revised. As part of the ple.27.7e benchmark, various input data were reviewed and updated. Discard survival is now assumed to be 50%. Advice which was previously based on the rfb rule is now based on an MSE tuned chr rule. The 2026 advice that had been issued as part of a biennial cycle for this stock was updated and new biennial advice was given for 2026 and 2027. Of the 18 fish stocks for which stock status was assessed relative to MSY (or MSY proxy) reference points; six were fished below FMSY and were above MSY Btrigger, four were fished above FMSY and were below MSY Btrigger, two stocks were fished at or above FMSY and above MSY Btrigger and four stocks were fished below FMSY and were below MSY Btrigger. For one fish stock for which advice was issued in 2025 reference points were unknown and advice was given to be below FMSY proxy
Plastics: from the rivers to the ocean
No full textThe Indian Ocean is facing serious plastic pollution, which needs to be curbed as a matter of urgency - and research data can hel
Extreme waves and tropical cyclones
No full textTropical cyclones are among the most devastating natural disasters, and the flooding they cause is responsible for over 90% of the human and material losses observed during these events
Particle Flux Attenuation in Northeast Atlantic During Apero Campaign
No full textFlux attenuation controls the magnitude of carbon sequestration in the deep ocean and is therefore key to understanding the efficiency of the biological carbon pump. The APERO cruise (Assessing marine biogenic matter Production, Export, and Remineralization: from the surface to the dark Ocean) aimed to provide new insights on the processes controlling mesopelagic flux attenuation by investigating the dynamic of sinking particles. Here, we present high-resolution vertical profiles (10 depths, from 50 to 1000 m) of downward fluxes of particle organic carbon (POC), nitrogen (PON), total mass, biogenic silica (bSi), transparent exopolymer particles (TEP), and Coomassie-stainable particles (CSP) measured using surface-tethered sediment traps. Surface POC fluxes ranged between 106 and 737 mg m-2 d-1, aligned with previous measurements in the region, whereas POC fluxes at 1000 m (sequestration depth) varied between 11 and 78 mg m-2 d-1. We estimated the POC flux attenuation – according to Martin’s curve equation – giving a coefficients b between 0.33 and 0.60. However, this coefficient did not reflect well the POC transfer efficiency for stations not following a power-law flux attenuation. TEP and CSP content were quantified using a novel approach, combining both spectrophotometry and microscopy analysis. Such method increases the sensitivity and allows morphological analysis of gel-like particles. TEP fluxes were measured between 70 and 288 mg XGeq m-2 d-1 at 50 m (between 20 and 91 mm-2 m-2 day-1), with some stations with similar values until 1000 m depth. CSP fluxes ranged between 3 and 23 mg BSAeq m-2 d-1 at 50 m (between 89 and 695 cm-2 m-2 day-1), with some comparable values until 400 m depth at some stations. This accurate analysis method, combined with a rare sampling resolution in depth, demonstrated that not only biogenic silica but also both TEP and CSP content in particles enhance POC transfer to depth
A baseline for assessing the ecological integrity of Western Amazon rivers
No full textAmazon freshwater systems influence global hydroclimatic patterns, host unparalleled biological diversity, and support unique social-ecological systems. Rivers of the Western Amazon underpin this global importance with an outsized, underrecognized role at the Amazon Basin scale. Here we examined the status of several components—hydrology, sediments, freshwater fish biodiversity, and longitudinal river connectivity—that support the ecological integrity of Western Amazon rivers and their linkage to the greater Amazon Basin. Streamflow is largely driven by precipitation and the region supplies nearly all sediments delivered by the Amazon River to the Atlantic Ocean. The Western Amazon harbors 74% of the ichthyofauna of the entire Amazon Basin. Existing dams and road crossings have disrupted longitudinal river connectivity on several rivers. We estimated that 47.8 million people reside in the Amazon Basin, with more than half (58%) inhabiting the Western Amazon. This study helps establish a baseline for tracking change in Western Amazon river ecosystems