Marine parasite diversity : study of cockle-trematode systems and their phenology using an environmental DNA-type approach
Digenean trematodes are among the most important groups of macroparasites in marine environments and play an important role in ecosystem functioning. Understanding their ecology requires accurate species identification and detection. However, conventional methods based on morphology have limitations, particularly for differentiating morphologically similar or cryptic species, identifying undescribed parasite stages and detecting early-stage or low intensity infections of hosts. As a result, life cycles and infection phenology often remain unresolved. Molecular approaches have the potential to overcome these barriers and help fill these ecological knowledge gaps. This thesis investigated how molecular tools can complement or surpass morphological identification in the diverse trematode community infecting the edible cockle (Cerastoderma edule), a key bivalve species of ecological and economic importance in European intertidal ecosystems, such as Arcachon Bay (France). Field surveys, laboratory experiments as well as morphological and molecular analyses were undertaken to (1) determine the reliability of morphological identification through comparison with molecular phylogenetic analyses of trematodes infecting cockles across Europe; (2) apply a targeted environmental DNA (eDNA) approach to elucidate the life cycle of the himasthlid Curtuteria arguinae by identifying its unknown hosts and assess the environmental drivers of its transmission to cockles; (3) improve detection of Bucephalus minimus sporocyst infections, a highly pathogenic bucephalid trematode, using species-specific molecular assays in order to describe its infection phenology. The European survey revealed 13 trematode species in cockles by morphology, but phylogenetic analyses uncovered 17 distinct genetic lineages. While some species were correctly identified morphologically, many were prone to misidentification or showed unexpected, potentially cryptic diversity, especially within the Himasthlidae family. This work clarified the strengths and limitations of current morphological methods of species identification and revealed that unknown infections might be more common than expected. The DNA dataset generated here also provided a solid foundation for the design of species-specific molecular tools. Building on this, a targeted qPCR-based eDNA approach allowed detection of C. arguinae DNA in water and fecal samples. The needle snail (Bittium reticulatum) and the oystercatcher (Haematopus ostralegus) were thereby identified respectively as the first intermediate host and as the definitive host, elucidating the life cycle for the first time. Experiments showed cercarial emergence was strongly temperature-dependent, driving seasonal transmission to cockles in the field. These results explain the parasite’s southern distribution and suggest potential northward expansion under climate change. Finally, molecular detection of B. minimus in cockles by species-specific qPCR and dPCR assays revealed substantially higher prevalence than microscopy, allowing the first description of infection phenology in Arcachon Bay. Infection dynamics were linked to cockle size and life history, as well as seasonal migration of the definitive host, the European seabass (Dicentrarchus labrax). Altogether, this thesis demonstrates the value of molecular methods for trematode identification and detection. These case studies show how molecular approaches, such as targeted eDNA approaches, can help resolve life cycles, detect inconspicuous infections and improve understanding of parasite phenology. Beyond the cockle-trematode systems studied here, this work highlights the broader value of molecular tools for assessing parasite prevalence, distribution and transmission and better integrating trematodes in our understanding of marine ecosystem functioning.
(05/12/2025)
EPOC, EPHE, PSL, UB, INSU - CNRS, CNRS
From sea to shore: Estimating used, lost and stranded fishing gear in the Southeastern Bay of Biscay through models and a novel gear identification key
Lost large pieces of fishing gear (FG) have well-documented impacts on marine ecosystems, yet the environmental risks of their degradation products remain poorly understood. Assessing these risks requires quantifying the microplastics, nanoplastics, and associated chemicals generated by different FG types. However, regionalscale data on FG used, lost, and beached are scarce. Using the Southeastern Bay of Biscay as a case study, we applied models to estimate the quantities of used and lost plastic FG. Additionally, eight beaches were sampled in four seasons during 2023. Fishing-related items were identified by FG origin using a novel identification key specifically developed for this purpose. Once fishing related items were identified by FG origins, their polymers were determined by ATR-FTIR. In total, we estimated that 211 tons of plastic FG were used and 6 tons were lost in 2023. Gillnets (2.7 tons), and longlines (2.5 tons), were the most frequently lost FG. Altogether, 7.6 % of items collected in the beaches were identified as coming from the fishing sector. Of these, 89.8 % of the items were mending pieces, 2.6 % were lines, and 2.5 % were longlines. In total, we estimated that 3 tons of FG were beached in the coastline during the studied period. Regarding polymer composition, polyethylene and polypropylene accounted for 95.1 % of the FG and polyamide for 3.3 %. This study presents a useful methodology and provides new data for the identification and quantification of used, lost, and beached plastic FG, contributing to future assessments of the environmental risk associated with their degradation products.
(Marine Pollution Bulletin. vol. 224, n° 0025-326X, 04/12/2025)
EPOC, EPHE, PSL, UB, INSU - CNRS, CNRS, UB, OFB - DR NAQ, OFB, CBMN, UB, ENITAB, INC-CNRS, CNRS
Identification and expression of circadian clock genes in the European flat oyster Ostrea edulis
Circadian clocks enable organisms to synchronize their biological processes to environmental daily cycles, thereby increasing species fitness. Components of the molecular clock are conserved across many taxa, though their structure and function can vary. In this study, we aim to investigate the circadian clock of the European flat oyster Ostrea edulis, an endangered species with a pivotal role in biogenic reef ecosystems. Phylogenetic and protein domain analyses were performed to identify orthologues of core clock and clock-associated genes (OeClock, OeBmal1, OePeriod, OeTimeless, OeCryptochrome2, OeRev-erb, OeRor, OeDoubletime, OeClockWorkOrange, OeShaggy), a gene related to melatonin synthesis (OeHiomt) and genes involved in light perception (OeCryptochrome1, OeOpsin4). As a functional output of the clock, we observed daily and circadian rhythms in valve behaviour recorded under light:dark and constant dark conditions. In parallel, gene expression analyses in two tissues under similar light regimes revealed tissue-specific rhythms, suggesting the presence of a functional and plastic endogenous circadian system in O. edulis. These findings offer a first molecular work for deeper exploration of the circadian
(Royal Society Open Science. vol. 12, n° 2054-5703, 01/12/2025)
HIFMB, OFFIS, EPOC, EPHE, PSL, UB, INSU - CNRS, CNRS, GEODE, UT2J, Comue de Toulouse, CNRS, AWI, AWI
Assessing coastal exposure to Sea Level Rise: A coupled approach of qualitative modeling and spatial autocorrelation analysis
Coastal areas are essential for maintaining diverse ecosystems and providing key resources for human populations. However, Climate Change (CC) is a major driver of Sea Level Rise (SLR), manifesting through various impacts such as coastal erosion, flooding, and saline intrusion. This study uses the InVEST model to assess SLR exposure along 25 km of Morocco's Atlantic coastline in the Sale region. The model relies on a qualitative index based on bio-geophysical variables. Four scenarios were analyzed to evaluate the role of natural habitats in coastal protection and how SLR rates influence coastal exposure. The results indicate that with habitat protection, coastal exposure remains between low and moderate (50 %), while without protection, 50 % of the coastline faces high risk. The impact of SLR further amplifies this risk, with habitat loss resulting in 43.8 % of the coastline being classified as "very high risk" and 39.3 % as high risk. The southern coastline (Sidi Moussa) is more exposed than the northern part (Nation Beach), due to geomorphology, altitude, distance from the continental shelf, and habitat distribution. The exposure index showed notable spatial autocorrelation (Moran index ¼ 0.7), indicating clustering of areas with similar exposure. The Moran index remained consistent across all scenarios, highlighting stable spatial dependency patterns. These findings help identify high risk districts along the Sale coastline, providing valuable support for coastal protection and sustainable development.
(Natural Hazards Research. vol. 5, pp. 764 - 777, 01/12/2025)
FSTM, UH2C, UB, EPOC, EPHE, PSL, UB, INSU - CNRS, CNRS, UMI, UCA
Endocrine effects of Imazalil on aromatase expression, vitellogenesis and ovarian histology using cyp19a1a-eGFP-casper transgenic zebrafish
Considering 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.
(Aquatic Toxicology. vol. 289, n° 0166-445X, pp. 107580, 01/12/2025)
INERIS, SEBIO, INERIS, URCA, ULH, NU, URCA, CNRS, LPGP, Biosit : Biologie - Santé - Innovation Technologique, INRAE, LPTC, EPOC, EPHE, PSL, UB, INSU - CNRS, CNRS, UMR MARBEC, IRD, IFREMER, CNRS, UM
Modelling water flow in presence of various obstructions: description and validation of a generic module for 2- and 3-dimensional simulations
In 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.
(Continental Shelf Research. vol. 295, n° 0278-4343, pp. 105580 (20p.), 01/12/2025)
LERAR, COAST, IFREMER, DYNECO, IFREMER, EPOC, EPHE, PSL, UB, INSU - CNRS, CNRS, SHOM, LOPS, IRD, IFREMER, INSU - CNRS, UBO EPE, CNRS
Toward a typology of river functioning: a comprehensive study of the particulate organic matter composition at the multi-river scale
In river systems, particulate organic matter (POM) originates from various sources with distinct dynamics related to production, decomposition, transport, and burial, leading to spatiotemporal heterogeneity in the POM pool. This study uses C and N isotope and element ratios, Bayesian models and multivariate analyses to (1) quantify relationships between POM composition and environmental forcings, and (2) propose a typology of river functioning based on POM composition and their seasonal dynamics. Twenty-three temperate rivers, representing a large diversity of temperate conditions, were sampled fortnightly to monthly over one to seven years at their River-Estuary Interface (REI). Phytoplankton and labile terrestrial material were found in all rivers, while sewage and refractory terrestrial material appeared in a few. Across all rivers, phytoplankton dominance correlated with agricultural surfaces, labile terrestrial material with organic-rich leached soil, and refractory terrestrial matter with steep, soil-poor catchments. Seasonal dynamics mainly depended to phytoplankton growth, river discharge, and sediment resuspension. Statistical regionalisation identified four river-dynamics types: (1) POM is dominated by labile terrestrial material year-round; (2) POM is composed of labile and refractory terrestrial material plus phytoplankton with variable seasonality; (3) POM is composed of phytoplankton and labile terrestrial material without pronounced seasonality; and (4) POM is composed of phytoplankton and labile terrestrial material with pronounced seasonality. This research offers a comprehensive understanding of POM composition, dynamics, and drivers at the REI in temperate climates, complementing similar study in coastal systems. Future similar research on estuaries is called to refine knowledge along the Land-Ocean Aquatic Continuum.
(Biogeosciences. vol. 22, n° 1726-4170, pp. 7363-7401, 27/11/2025)
EPOC, EPHE, PSL, UB, INSU - CNRS, CNRS, LERPC, COAST, IFREMER, IPREM, UPPA, INC-CNRS, CNRS, CRESCO, MNHN, IFREMER, CEFREM, UPVD, INSU - CNRS, CNRS
Study of aerobic and anaerobic cultivable sedimentary microbiota Capability of isolates to produce and degrade extracellular polymeric substances and possible use in biotechnology
(27/11/2025)
CBMN, UB, ENITAB, INC-CNRS, CNRS, EPOC, EPHE, PSL, UB, INSU - CNRS, CNRS, LGL-TPE, ENS de Lyon, UCBL, INSU - CNRS, UJM, UJM EPE, CNRS
ClimLoco1.0: CLimate variable confidence Interval of Multivariate Linear Observational COnstraint
Projections of future climate are key to society's adaptation and mitigation plans in response to climate change. Numerical climate models provide projections, but the large dispersion between them makes future climate very uncertain. To refine them, approaches called observational constraints (OCs) have been developed. They constrain an ensemble of climate projections using some real-world observations. However, there are many difficulties in dealing with the large literature on OC: the methods are diverse, the mathematical formulation and underlying assumptions are not always clear, and the methods are often limited to the use of the observations of only one variable. To address these challenges, this article proposes a new statistical model called ClimLoco1.0, which stands for “CLimate variable confidence Interval of Multivariate Linear Observational COnstraint”. It describes, in a rigorous way, the confidence interval of a projected variable (its best guess associated with an uncertainty at a confidence level) obtained using a multivariate linear OC. The article is built up in increasing complexity by expressing three different cases – the last one being ClimLoco1.0, the confidence interval of a projected variable: unconstrained, constrained by multiple real-world observations assumed to be noiseless, and constrained by multiple real-world observations assumed to be noisy. ClimLoco1.0 thus accounts for observational noise (instrumental error and climate-internal variability), which is sometimes neglected in the literature but is important as it reduces the impact of the OC. Furthermore, ClimLoco1.0 accounts for uncertainty rigorously by taking into account the quality of the estimators, which depends, for example, on the number of climate models considered. In addition to providing an interpretation of the mathematical results, this article proposes graphical interpretations based on synthetic data. ClimLoco1.0 is compared to some methods from the literature at the end of the article and is used in a real case study in the appendix.
(Geoscientific Model Development. vol. 18, n° 1991-9603, pp. 9015-9038, 25/11/2025)
ASTRAL, IMB, UB, Bordeaux INP, CNRS, Inria, UB, Bordeaux INP, EPOC, EPHE, PSL, UB, INSU - CNRS, CNRS
Response of phytoplankton communities to the onset of the 2020 summer marine heatwave in the Drake Passage and Antarctic Peninsula
Abstract. Extreme warming events are increasingly more intense and frequent in the global ocean. These events are predicted to drive profound and widespread effects on marine ecosystems, yet their impact on phytoplankton, the base of the marine food web, is still largely unknown. Our understanding of the impact of these phenomena in marine ecosystems is particularly poor in the remote and logistically challenging Southern Ocean. During summer 2020, the research vessel Hespérides sampled the water column of the Drake Passage and northern Antarctic Peninsula before (early January) and during the early phase (late January-early February) of a Marine Heat Wave (MHW), that resulted in sea surface temperature anomalies of up to +3 °C. Here, we take advantage of this exceptional opportunity to document the effects of an extreme warming event on the nutrient and phytoplankton (diatom and coccolithophores) distributions across the main zonal systems of the Southern Ocean. Overall, our results indicate that biogeographical variability of diatom and coccolithophore assemblages, the two dominant phytoplankton groups in the Southern Ocean, mirrored the physical and chemical properties of the water masses delineated by the Southern Ocean fronts before and during the onset of the marine heat wave. Analysis of a suite of satellite-derived oceanographic parameters revealed that development and persistence of the 2020 marine heat wave were closely tied to mesoscale anticyclonic eddy dynamics. The increase in sea surface temperatures during the onset of the marine heat wave was associated with a remarkable increase in diatom abundance reaching bloom concentrations and a shift in the diatom assemblage towards an increase in the relative abundance of the small diatom Fragilariopsis cylindrus/nana in the southern Drake Passage. Notably, the diatom bloom was not coupled with a statistically significant change in chlorophyll a, as derived from in-situ fluorescence, or modelled Net Primary Production. It is likely that the differing contribution of other phytoplankton groups and/or a shift in the average phytoplankton size before and during the MHW might be responsible for these results. Average coccolithophore abundance was lower than previous studies in the Drake Passage and decreased during the MHW. We speculate that the remarkable nitrate decrease by approximately one order of magnitude lower than average summer concentrations might have been responsible for the reduction in coccolithophore numbers. Low nitrate levels are attributed to either the advection of nitrate poor waters from lower latitudes by an anticyclonic eddy and/or nutrient consumption by substantial development of soft-tissue phytoplankton biomass. Overall, our results reinforce the notion that a warmer Southern Ocean will favour an increase of small phytoplankton cells in the southern Drake Passage and northern Antarctic Peninsula with unpredictable consequences in the marine-food web and biogeochemical cycles that need to be urgently quantified and parametrized.
(Biogeosciences. vol. 22, n° 1726-4170, pp. 7205 - 7232, 25/11/2025)
ICMAN, CSIC, EPHE, PSL, EPOC, EPHE, PSL, UB, INSU - CNRS, CNRS, UB, IACT, CSIC, UGR, IGME, LSCE, UVSQ, INSU - CNRS, CNRS, DRF (CEA), CEA, GEOTRAC, LSCE, UVSQ, INSU - CNRS, CNRS, DRF (CEA), CEA, JAMSTEC